WO1995022623A1 - Circularizing nucleic acid probe able to interlock with a target sequence through catenation - Google Patents
Circularizing nucleic acid probe able to interlock with a target sequence through catenation Download PDFInfo
- Publication number
- WO1995022623A1 WO1995022623A1 PCT/SE1995/000163 SE9500163W WO9522623A1 WO 1995022623 A1 WO1995022623 A1 WO 1995022623A1 SE 9500163 W SE9500163 W SE 9500163W WO 9522623 A1 WO9522623 A1 WO 9522623A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- probe
- target
- nucleic acid
- sequence
- target sequence
- Prior art date
Links
- 108020004711 Nucleic Acid Probes Proteins 0.000 title description 3
- 239000002853 nucleic acid probe Substances 0.000 title description 3
- 239000000523 sample Substances 0.000 claims abstract description 173
- 150000007523 nucleic acids Chemical group 0.000 claims abstract description 40
- 238000000034 method Methods 0.000 claims abstract description 34
- 239000003153 chemical reaction reagent Substances 0.000 claims abstract description 25
- 108020004707 nucleic acids Proteins 0.000 claims abstract description 23
- 102000039446 nucleic acids Human genes 0.000 claims abstract description 23
- 108091028043 Nucleic acid sequence Proteins 0.000 claims abstract description 20
- 108060002716 Exonuclease Proteins 0.000 claims abstract description 6
- 230000000694 effects Effects 0.000 claims abstract description 6
- 102000013165 exonuclease Human genes 0.000 claims abstract description 6
- 108020004414 DNA Proteins 0.000 claims description 29
- 238000001514 detection method Methods 0.000 claims description 22
- 238000009396 hybridization Methods 0.000 claims description 14
- 238000006243 chemical reaction Methods 0.000 claims description 13
- 230000000295 complement effect Effects 0.000 claims description 12
- 108091034117 Oligonucleotide Proteins 0.000 claims description 9
- 102000004190 Enzymes Human genes 0.000 claims description 6
- 108090000790 Enzymes Proteins 0.000 claims description 6
- 102000053602 DNA Human genes 0.000 claims description 5
- 239000000203 mixture Substances 0.000 claims description 4
- 108090000623 proteins and genes Proteins 0.000 claims description 4
- 239000007790 solid phase Substances 0.000 claims description 4
- 239000000126 substance Substances 0.000 claims description 4
- 241000894006 Bacteria Species 0.000 claims description 3
- 150000001720 carbohydrates Chemical class 0.000 claims description 3
- 230000002255 enzymatic effect Effects 0.000 claims description 3
- 102000004196 processed proteins & peptides Human genes 0.000 claims description 3
- 108090000765 processed proteins & peptides Proteins 0.000 claims description 3
- 102000004169 proteins and genes Human genes 0.000 claims description 3
- 239000003381 stabilizer Substances 0.000 claims description 3
- 229920001059 synthetic polymer Polymers 0.000 claims description 3
- 229920001184 polypeptide Polymers 0.000 claims 2
- 229920001282 polysaccharide Polymers 0.000 claims 2
- 239000007787 solid Substances 0.000 claims 2
- 102000053642 Catalytic RNA Human genes 0.000 claims 1
- 108090000994 Catalytic RNA Proteins 0.000 claims 1
- 230000001404 mediated effect Effects 0.000 claims 1
- 108091092562 ribozyme Proteins 0.000 claims 1
- 230000001131 transforming effect Effects 0.000 claims 1
- 239000012528 membrane Substances 0.000 description 34
- 102000003960 Ligases Human genes 0.000 description 26
- 108090000364 Ligases Proteins 0.000 description 26
- 239000002773 nucleotide Substances 0.000 description 18
- 125000003729 nucleotide group Chemical group 0.000 description 17
- HEMHJVSKTPXQMS-UHFFFAOYSA-M Sodium hydroxide Chemical compound [OH-].[Na+] HEMHJVSKTPXQMS-UHFFFAOYSA-M 0.000 description 15
- 239000002585 base Substances 0.000 description 11
- 239000013612 plasmid Substances 0.000 description 11
- 239000002202 Polyethylene glycol Substances 0.000 description 10
- 229920001223 polyethylene glycol Polymers 0.000 description 10
- 239000000243 solution Substances 0.000 description 10
- 102000012410 DNA Ligases Human genes 0.000 description 7
- 108010061982 DNA Ligases Proteins 0.000 description 7
- 208000037065 Subacute sclerosing leukoencephalitis Diseases 0.000 description 6
- 206010042297 Subacute sclerosing panencephalitis Diseases 0.000 description 6
- 238000005406 washing Methods 0.000 description 6
- 238000003556 assay Methods 0.000 description 5
- FAPWRFPIFSIZLT-UHFFFAOYSA-M Sodium chloride Chemical compound [Na+].[Cl-] FAPWRFPIFSIZLT-UHFFFAOYSA-M 0.000 description 4
- 239000003513 alkali Substances 0.000 description 4
- 230000003321 amplification Effects 0.000 description 4
- 238000009835 boiling Methods 0.000 description 4
- 239000003398 denaturant Substances 0.000 description 4
- 238000003199 nucleic acid amplification method Methods 0.000 description 4
- -1 nucleotide triphosphates Chemical class 0.000 description 4
- 230000015572 biosynthetic process Effects 0.000 description 3
- LOKCTEFSRHRXRJ-UHFFFAOYSA-I dipotassium trisodium dihydrogen phosphate hydrogen phosphate dichloride Chemical compound P(=O)(O)(O)[O-].[K+].P(=O)(O)([O-])[O-].[Na+].[Na+].[Cl-].[K+].[Cl-].[Na+] LOKCTEFSRHRXRJ-UHFFFAOYSA-I 0.000 description 3
- 239000012634 fragment Substances 0.000 description 3
- 230000002068 genetic effect Effects 0.000 description 3
- 239000002953 phosphate buffered saline Substances 0.000 description 3
- YBJHBAHKTGYVGT-ZKWXMUAHSA-N (+)-Biotin Chemical group N1C(=O)N[C@@H]2[C@H](CCCCC(=O)O)SC[C@@H]21 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 0.000 description 2
- OKTJSMMVPCPJKN-UHFFFAOYSA-N Carbon Chemical compound [C] OKTJSMMVPCPJKN-UHFFFAOYSA-N 0.000 description 2
- 108020005187 Oligonucleotide Probes Proteins 0.000 description 2
- 108091093037 Peptide nucleic acid Proteins 0.000 description 2
- 238000010420 art technique Methods 0.000 description 2
- 230000000903 blocking effect Effects 0.000 description 2
- 239000000872 buffer Substances 0.000 description 2
- 229910052799 carbon Inorganic materials 0.000 description 2
- 239000003795 chemical substances by application Substances 0.000 description 2
- 210000000349 chromosome Anatomy 0.000 description 2
- 230000001419 dependent effect Effects 0.000 description 2
- 238000011161 development Methods 0.000 description 2
- NAQMVNRVTILPCV-UHFFFAOYSA-N hexane-1,6-diamine Chemical compound NCCCCCCN NAQMVNRVTILPCV-UHFFFAOYSA-N 0.000 description 2
- 230000035772 mutation Effects 0.000 description 2
- 239000002751 oligonucleotide probe Substances 0.000 description 2
- 108091033319 polynucleotide Proteins 0.000 description 2
- 102000040430 polynucleotide Human genes 0.000 description 2
- 239000002157 polynucleotide Substances 0.000 description 2
- 150000003141 primary amines Chemical group 0.000 description 2
- 238000012216 screening Methods 0.000 description 2
- 239000011780 sodium chloride Substances 0.000 description 2
- 125000006850 spacer group Chemical group 0.000 description 2
- 239000000758 substrate Substances 0.000 description 2
- 239000001226 triphosphate Substances 0.000 description 2
- 235000011178 triphosphate Nutrition 0.000 description 2
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 2
- YMXHPSHLTSZXKH-RVBZMBCESA-N (2,5-dioxopyrrolidin-1-yl) 5-[(3as,4s,6ar)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoate Chemical compound C([C@H]1[C@H]2NC(=O)N[C@H]2CS1)CCCC(=O)ON1C(=O)CCC1=O YMXHPSHLTSZXKH-RVBZMBCESA-N 0.000 description 1
- OCKGFTQIICXDQW-ZEQRLZLVSA-N 5-[(1r)-1-hydroxy-2-[4-[(2r)-2-hydroxy-2-(4-methyl-1-oxo-3h-2-benzofuran-5-yl)ethyl]piperazin-1-yl]ethyl]-4-methyl-3h-2-benzofuran-1-one Chemical compound C1=C2C(=O)OCC2=C(C)C([C@@H](O)CN2CCN(CC2)C[C@H](O)C2=CC=C3C(=O)OCC3=C2C)=C1 OCKGFTQIICXDQW-ZEQRLZLVSA-N 0.000 description 1
- 108700028369 Alleles Proteins 0.000 description 1
- 241000972773 Aulopiformes Species 0.000 description 1
- 108010077544 Chromatin Proteins 0.000 description 1
- 108020004635 Complementary DNA Proteins 0.000 description 1
- 108020003215 DNA Probes Proteins 0.000 description 1
- 239000003298 DNA probe Substances 0.000 description 1
- 102000016928 DNA-directed DNA polymerase Human genes 0.000 description 1
- 108010014303 DNA-directed DNA polymerase Proteins 0.000 description 1
- KCXVZYZYPLLWCC-UHFFFAOYSA-N EDTA Chemical compound OC(=O)CN(CC(O)=O)CCN(CC(O)=O)CC(O)=O KCXVZYZYPLLWCC-UHFFFAOYSA-N 0.000 description 1
- 241000588724 Escherichia coli Species 0.000 description 1
- LYCAIKOWRPUZTN-UHFFFAOYSA-N Ethylene glycol Chemical group OCCO LYCAIKOWRPUZTN-UHFFFAOYSA-N 0.000 description 1
- 206010028980 Neoplasm Diseases 0.000 description 1
- 239000004677 Nylon Substances 0.000 description 1
- 102000003992 Peroxidases Human genes 0.000 description 1
- 241001135910 Phage M13mp18 Species 0.000 description 1
- 108010021757 Polynucleotide 5'-Hydroxyl-Kinase Proteins 0.000 description 1
- 102000008422 Polynucleotide 5'-hydroxyl-kinase Human genes 0.000 description 1
- 108020004511 Recombinant DNA Proteins 0.000 description 1
- 108091081062 Repeated sequence (DNA) Proteins 0.000 description 1
- 108020004682 Single-Stranded DNA Proteins 0.000 description 1
- 101900061264 Thermus thermophilus DNA ligase Proteins 0.000 description 1
- 239000012445 acidic reagent Substances 0.000 description 1
- 125000003277 amino group Chemical group 0.000 description 1
- 238000000137 annealing Methods 0.000 description 1
- 229960002685 biotin Drugs 0.000 description 1
- 235000020958 biotin Nutrition 0.000 description 1
- 239000011616 biotin Substances 0.000 description 1
- 238000010804 cDNA synthesis Methods 0.000 description 1
- 235000014633 carbohydrates Nutrition 0.000 description 1
- 210000003483 chromatin Anatomy 0.000 description 1
- 239000002299 complementary DNA Substances 0.000 description 1
- 125000004122 cyclic group Chemical group 0.000 description 1
- 230000002380 cytological effect Effects 0.000 description 1
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical group NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 1
- 238000004925 denaturation Methods 0.000 description 1
- 230000036425 denaturation Effects 0.000 description 1
- 230000029087 digestion Effects 0.000 description 1
- 239000000975 dye Substances 0.000 description 1
- 238000006872 enzymatic polymerization reaction Methods 0.000 description 1
- 125000003827 glycol group Chemical group 0.000 description 1
- 238000011065 in-situ storage Methods 0.000 description 1
- 238000011534 incubation Methods 0.000 description 1
- 230000016507 interphase Effects 0.000 description 1
- 238000002955 isolation Methods 0.000 description 1
- 230000005923 long-lasting effect Effects 0.000 description 1
- 230000036210 malignancy Effects 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 230000031864 metaphase Effects 0.000 description 1
- 230000011987 methylation Effects 0.000 description 1
- 238000007069 methylation reaction Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 238000010369 molecular cloning Methods 0.000 description 1
- 229920005615 natural polymer Polymers 0.000 description 1
- 238000011330 nucleic acid test Methods 0.000 description 1
- 229920001778 nylon Polymers 0.000 description 1
- 238000002515 oligonucleotide synthesis Methods 0.000 description 1
- 108040007629 peroxidase activity proteins Proteins 0.000 description 1
- 150000008300 phosphoramidites Chemical class 0.000 description 1
- 239000002985 plastic film Substances 0.000 description 1
- 229920006255 plastic film Polymers 0.000 description 1
- 238000002360 preparation method Methods 0.000 description 1
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 1
- 230000002285 radioactive effect Effects 0.000 description 1
- 108091008146 restriction endonucleases Proteins 0.000 description 1
- 235000019515 salmon Nutrition 0.000 description 1
- 238000011896 sensitive detection Methods 0.000 description 1
- 238000000926 separation method Methods 0.000 description 1
- AJPJDKMHJJGVTQ-UHFFFAOYSA-M sodium dihydrogen phosphate Chemical compound [Na+].OP(O)([O-])=O AJPJDKMHJJGVTQ-UHFFFAOYSA-M 0.000 description 1
- 229910000162 sodium phosphate Inorganic materials 0.000 description 1
- 238000012360 testing method Methods 0.000 description 1
- 210000001519 tissue Anatomy 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
Definitions
- the present invention relates to a novel method of detecting specific nucleic acid sequences as well as a detecting reagent and kit therefor.
- ligases enzymes that can join separate DNA molecules. Using these enzymes, called ligases, genetic elements derived from different genomes can be brought to be expressed together in an organism. Ligase-assisted reactions have also come to play an increasing role in gene detection. The principle employed in such reactions is that two probe-segments, complementary to target sequences situated in juxtaposition, are joined to a contiguous probe sequence through the agency of a DNA ligase. This is in contrast to more conventional detection schemes where the hybridization of single probes to target sequences is detected after removal of free probe
- ligase-assisted detection method is disclosed in US-A-4,988,617, which relates to an assay for determining the nucleic acid sequence in a region of a nucleic acid test substance which has a known possible mutation in at least one target nucleotide position of the sequence.
- the assay comprises annealing two oligonucleotide probes to immediately adjacent segments of a substantially complementary test DNA or RNA molecule which contains the possible mutation(s) near the segment joint, and adding a linking agent, usually a ligase.
- the conditions are
- the probes are covalently joined, and if not correctly base paired due to a mismatching nucleotide (s) near the the segment joint, the probes are incapable of being covalently joined by the ligase.
- the presence or absence of linking is detected as an indication of the sequence of the target nucleotide.
- reaction is inherently very specific. Ligation reactions are based on the coincidence of two separate probe sequences on a target sequence, and this is unlikely to occur in the absence of the appropriate target molecule even under non-stringent reaction conditions. For this reason the reaction is suitable in standardized, automated schemes.
- the ligation reaction can be employed to assess the accuracy of hybridization at positions immediately surrounding the junction between two probes. Due to the substrate requirements of ligases, terminally mismatched probes are ligated at a substantially reduced rate. In this manner, allelic sequence variants can be distinguished.
- JP-A-4262799 and JP-A-4304900 both disclose the use of ligation reactions combined with amplification reactions for detecting a target nucleic acid sequence in a specimen sample.
- the methodology comprises contacting the sample in the presence of a ligase with a straight chain probe polynucleotide, which has a sequence designed to be
- cyclized, or circularized as the result of the presence of a target nucleic acid sequence.
- the cyclized polynucleotide is then used as a template in an enzymatic polymerization reaction.
- a primer which is at least partially complementary to the cyclized probe together with a nucleic acid polymerase and nucleotide triphosphates, a single stranded chain nucleic acid is formed which has a repeated sequence complementary to the probe and at least partially to the template.
- the amplification product is then detected either via a labelled nucleic acid triphosphate
- the present invention provides a method based upon probe circularization but in which the potential specificity and binding stability of a circularizable DNA probe is fully utilized.
- a probe designed to be circularized in the presence of a target sequence, may be caused to close around the target-containing nucleic acid strand or strands, for example DNA or RNA, such that the cyclic probe will interlock with and thereby be efficiently linked to the target nucleic acid to be detected.
- target-containing nucleic acid strand or strands for example DNA or RNA
- the cyclic probe will interlock with and thereby be efficiently linked to the target nucleic acid to be detected.
- circularized probes will be wound around the target strand,
- probe molecules to target sequences results in the formation of a hybrid that resists extereme washing conditions, serving to reduce non-specific signals in genetic assays, as will be further described below.
- Any probes hybridizing in a non-specific manner may therefore be efficiently removed by subjecting the target to non- hybridizing conditions and/or exonuclease activity.
- the circular probe is properly detectable, such as suitably labelled, it may then be detected to indicate the presence of the target molecule.
- the target is not amplified, highly sensitive detection is possible through efficient reduction of non-specific signals.
- the probe is designed to hybridize to the target sequence with an interspace between the probe ends, and at least one other, or intermediate, probe is provided which is designed to hybridize with the interspatial target sequence.
- the probes are then interconnected to form a cyclized molecule .
- the probe is designed to hybridize to the target sequence with a small gap of from one to a few nucleotides between the probe ends .
- This gap is then filled by an enzyme-assisted extension reaction, such as by DNA polymerase, prior to connecting the probe ends with each other as is per se known in the art. It is readily appreciated that increased specificity may be obtained if such a gap does not contain all four nucleotides.
- One aspect of the present invention therefore relates to an assay method of detecting a target nucleic acid sequence in a sample by contacting the sample with a detectable probe to hybridize the probe to the target sequence, and detecting the hybridized probe, which method comprises the steps of:
- a detectable probe which optionally may be branched and which has two nucleic acid end parts at least partially complementary to and capable of hybridizing to two at least substantially neighbouring regions of the target sequence
- steps b) to d) optionally repeating steps b) to d) one or more times, and
- nucleic acid detecting reagent or probe, comprising a structure having an intermediate part, labelled with at least one detectable tag, and two nucleic acid end parts at least partially complementary to and capable of hybridizing to two at least substantially neighbouring respective regions of a target nucleic acid sequence to form a cyclized structure.
- the probe does preferably not contain more than about 200 bases (i.e. nucleotides), and may, for example, contain from about 10 to about 100 bases, preferably from about 20 to about 100 bases.
- the probe may be completely composed of DNA or RNA or analogous matter, it is, however, sufficient that only the hybridizing ends thereof consist of nucleic acid or analogous matter.
- the rest of the probe molecule, i.e. the intermediate part, may very well have any other desired composition.
- the probe molecule may be free or immobilized to a solid phase. In the latter case, the method of the
- inventions may also be used for selectively isolating a target nucleic acid sequence from a solution. This may be used for preparative purposes, such as for screening DNA or RNA libraries .
- Still another aspect of the invention relates to a kit for detecting a target nucleic acid sequence in a sample, which kit comprises a nucleic acid reagent as described above and ligating means for connecting the reagent ends to each other after hybridization to the target sequence.
- Fig. 1 is a schematic illustration of a probe system hybridized to a target nucleic acid sequence
- Fig. 2 is a schematic representation of a circularized probe catenated to a target sequence
- Fig. 3 is an exemplary representation of a detection cassette comprising two probes
- Fig. 4 is an exemplary representation of a detection cassette comprising a single probe
- Fig. 5 is a photograph of four blotting membranes showing the results of hybridization of a probe to a target molecule in accordance with the method of the invention as well as under other conditions;
- Fig. 6 is a similar photograph as that of Fig. 5 showing eight blotting membranes carrying target molecules hybridized with a probe and treated under various
- Fig. 7 is a photograph of four blotting membranes hybridized with either a circularizable probe or two linear probes corresponding to the respective hybridizing end segments of the circularizable probe; and Fig. 8 is a photograph of blotting membranes where the probe used in Fig. 6 has been circularized to restriction fragments of the target molecule in Fig. 6.
- a detecting reagent according to the invention hybridized to a target nucleic acid sequence, such as a DNA strand, via two end segments of the detecting reagent, designated Probe 1 and Probe 3, the latter being complementary to two respective non-contiguous sequences of the target molecule.
- An additional probe, designated Probe 2 is hybridized to the intermediate segment of the target molecule with the probe ends in juxtaposition to Probe 1 and Probe 3, respectively.
- the detecting reagent is stabilized by an optional stabilizer sequence to prevent the ends of Probe 1 and Probe 3 from directly contacting each other.
- the segment of the detecting reagent between the probes may include at least one detectable element, such as a
- Probes 1, 2 and 3 After Probes 1, 2 and 3 have hybridized to the target molecule, or simultaneously therewith, the probe ends are connected to each other, such as ligated by a ligase, to form a covalently closed circular molecule.
- exemplary ligases are T4 DNA ligase, T7 DNA ligase, E. coli DNA ligase, and Thermus thermophilus DNA ligase.
- Alternative ways of such covalent closure are, for example, ribozome and chemical ligation.
- the circularized molecule will then remain linked to the target molecule also under conditions that would release or degrade any hybridized non-cyclized probe and thereby be selectively detectable, indicating the presence of the target molecule in a sample. Thereby the influence of possible hybridization to irrelevant sequences will be completely eliminated.
- Conditions that will denature or degrade a hybridized but non-cyclized probe include heat, alkali, other denaturants or exonuclease activity, the latter attacking free ends of uncyclized probes .
- intermediate Probe 2 may be advantageous from the viewpoint of specificity, such an intermediate probe is not critical and the method of the invention may readily be performed without it, i.e. that Probes 1 and 3 are designed to hybridize end to end on the target molecule, whereupon these two ends are ligated to circularize the detecting reagent .
- Fig. 2 which shows a linear probe P, the ends of which are
- the hybridizing part of the probe is wound around the target strand and is thereby securely linked to the target strand and cannot be removed even at conditions which interrupt base pairing between complementary DNA strands .
- the designations F indicate labels, such as fluorophores, on the probe P which permit the catenated probe to be detected by suitable detecting means known in the art, e.g. a photodiode or a CCD
- the detection signal may be increased by repeating the cyclizing and dehybridizing steps one or more times.
- the target sequence is at a sufficient distance from the ends of the target molecule, usually at least about 200 base pairs from the nearest end depending on whether and how the target sequence is bound to the support. If the target sequence is free in solution, a longer distance may be required, especially in the case of long-lasting denaturing washes.
- the advantages of detecting a covalently closed circular molecule after subjecting the target to non-hybridizing conditions rather than detecting a conventional labelled straight chain probe under hybridizing conditions are several-fold.
- the ligation reaction provides prominent specificity of detection, using single, synthetic probe molecules in total genomic DNA as terminally
- mismatched probes are poor substrates for ligases.
- the probes circle around or catenate with the target sequences and become covalently linked to the target sequence, thereby becoming substantially insensitive to denaturants. Further, the ends of the detecting reagent become unavailable to exonuclease digestion, aiding in or replacing washes. Thirdly, the simultaneous presence of two terminal probe sequences on one molecule confers kinetic advantages in the hybridization step. Finally, allelic sequence variants can be distinguished by the ligase.
- the detecting reagent may, for example, be a 5'-phosphorylated oligonucleotide.
- the detecting reagent may, for example, be a 5'-phosphorylated oligonucleotide.
- the intermediate segment may wholly or partially have another chemical composition, such as, for example, include residues selected from peptides or proteins, carbohydrates or other natural or synthetic polymers.
- Such an intermediate structure of non-nucleotide nature may even be preferred with regard to stability and ease of introducing labels or tags, and also since a non-nucleotide intermediate structure will not exhibit a secondary structure or cause mishybridization.
- the stabilizer sequence should preferably have the same length as the sum of the probes, such as 40 or 50 nucleotides.
- the illustrated curved segments in Fig. 1 would then require, say, of the order of 3 nucleotides.
- the combined lengths of the probe sequences should preferably be such that the strands will leave the double helix on the same face 10 or a multiple of 10 bases apart, 10 bases representing approximately one turn of the DNA double helix.
- the detecting reagent may be a free molecule or may be immobilized to a support.
- the target nucleic acid molecule which may be DNA or RNA and which contains the specific sequence to be
- the target molecule may be a free molecule, but when the detecting reagent is a free molecule, the target molecule is preferably immobilized to a support. When both the probe and the target molecule are free molecules, probe circularization and catenation with the target molecule may, for example, be detected by electrophoretic separation or by other techniques known per se in the art for
- the target molecule is preferably provided in single-stranded form.
- detection cassettes comprising a detecting reagent of the invention.
- the detecting reagent is a stabilized 92-mer to be cyclized together with an intermediate 17-mer
- the detecting reagent is a 70-mer to be cyclized end to end with itself.
- the labels or tags may, for example, be those
- the detectable groups may advantageously be bound to branches protruding from the cyclized probes.
- such branches will permit template-dependent, highly specific and covalent addition of the detectable groups to the cyclized molecules.
- the invention permits the detection of target sequences in situ in tissue sections or in cytological preparations as well as in metaphase or interphase chromosomes. Due to the high specificity, large numbers of target sequences may be analyzed in parallel, preserving spatial information and with a potential to distinguish among allelic sequence variants.
- the method of the invention will therefore be useful for diagnostic screening at the level of chromosomes or chromatin fibres. Increased signal may be obtained by secondary ligation of detectable molecules to the linker segment of bound probes.
- the inventive concept may also be used for preparative purposes to screen a nucleic acid library in order to isolate clones harbouring a particular target sequence.
- the detecting reagent, or probe is immobilized to a solid phase, such as a membrane.
- the probe may, for example, consist of two target-complementary regions separated by a non-nucleotide segment containing primary amine groups, e.g. of ethylene-glycol residues interrupted by nucleotide carbon (C) residues, modified with primary amines. These amine groups on the probes are reacted with the membrane and covalently coupled at high density.
- the nucleic acid library to be screened for the target complementary region may, for example, be DNA cloned in an Ml3 vector, or in a plasmid or phagemid vector that permits the excision of inserts as circular plasmids.
- the library is incubated with the probe-containing membrane or membranes, and, after washes, the specifically hybridized probe ends are ligated. After highly stringent washes, removing non-specifically bound molecules, one arm of the probe is cut, e.g.
- target sequence-containing molecules are released in a subsequent denaturation step. If the target sequence-containing molecules are single stranded, these are repaired in solution using, e.g., a primer, T7 polymerase and T4 DNA ligase, and then used to transform bacteria. These bacteria will then propagate the specific target sequence.
- unamplified genomic DNA molecules may permit detection of properties, such as methylation, that may be involved in the development of malignancies.
- oligonucleotide were capable of base-pairing adjacent to each other with the polylinker of the single-stranded, circular bacteriophage M13mp18.
- oligonucleotide 0.1 pmol of the above oligonucleotide was allowed to hybridize to the polylinker of M13mp18 added at 0.36 pmol in a solution containing 5 mM ATP, 1 ⁇ l of One-Phor-All Buffer (10 mM tris-Ac, pH 7.5, 10 mM Mg(Ac) 2 , 50 mM KAc; Pharmacia LKB Biotechnology AB, Uppsala, Sweden), 1 ⁇ l of T4 DNA ligase (5 U/ ⁇ l, Pharmacia LKB Biotechnology AB) in 10 ⁇ l.
- One-Phor-All Buffer 10 mM tris-Ac, pH 7.5, 10 mM Mg(Ac) 2 , 50 mM KAc; Pharmacia LKB Biotechnology AB, Uppsala, Sweden
- T4 DNA ligase 5 U/ ⁇ l, Pharmacia LKB Biotechnology AB
- DNA fragments including the CF-mutation delta508 or the normal variant of this sequence were cloned in the pUC19 vector in a conventional manner.
- the two recombinant plasmids obtained were bound to four membrane strips, designated E, F, G and H, by a conventional dot-blot method, 35 ng plasmid (normal or mutant) per dot and two dots per membrane strip, i.e. one with normal DNA and one with mutant DNA.
- the membranes were washed by pouring boiling water over them and adding SDS to a final
- PBS phosphate-buffered saline
- PEG residues were introduced during the oligonucleotide synthesis using a PEG
- the molecule was radioactively labelled by adding a 32p group to the 5 ' -end of the molecule by means of the enzyme T4 polynucleotide kinase .
- the DNA ends of the probe were designed to base-pair end to end with the 100 bp target normal sequence.
- the mutant target is lacking three nucleotides, corresponding to the junction of the probe segments and fails to support the enzymatic joining of these. 15 pmoles of the probe were allowed to hybridize with the target sequence for 30 minutes in a water volume of 500 ⁇ l
- Ligation was performed with membrane strips E and G in 500 ⁇ l of 0.2 M NaCl, 1 mM ATP, 1 ⁇ One-Phor-All Buffer (Pharmacia LKB Biotechnology AB), and 0.15 U/ ⁇ l T4 DNA ligase (Pharmacia LKB Biotechnology AB).
- membrane strips G and H were then washed in 1 ml of 1 ⁇ SSPE, 2% SDS for 30 minutes, whereas membrane strips E and F were treated with 500 ⁇ l of 0.2 M NaOH for 5 minutes to denature the DNA.
- the membranes were
- Denhardt's blocking solution also containing 0.1 ⁇ g/500 ⁇ l of streptavidin-horseradish peroxidase (HRP) conjugate (Sigma) for 5 minutes.
- HRP streptavidin-horseradish peroxidase conjugate
- the membranes were put in a solution of ECL solution A mixed with solution B (Amersham, U.K.) for 1 minute and then left to dry for a few seconds on a 3MM paper.
- the membranes were then placed in a plastic film and put on an X-omat-S film and exposed for 1 second - 1 minute.
- the results are shown in Fig. 5, where dots with the correct target sequence are to the right (designated N) and the dots with the mutant sequence are to the left (designated M) in the figure.
- the detection is ligase-dependent if the membranes are washed with alkali or boiling SDS, whereas a non-stringent wash (membrane 6) did not remove the probe hybridized to the incorrect target sequence.
- Example 2 The target molecule in Example 2 was cleaved by restriction enzymes into fragments having the target sequence located at a distance of about 850, 650, 550 and 200 base pairs, respectively, from the molecule end.
- the plasmids were immobilized on nylon membranes, probed by hybridization with the circularizable oligonucleotide in Example 2, either subjected to a ligation step or not, and
Abstract
Description
Claims
Priority Applications (4)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
EP95910057A EP0745140B1 (en) | 1994-02-16 | 1995-02-16 | Circularizing nucleic acid probe able to interlock with a target sequence through catenation |
US08/693,302 US5871921A (en) | 1994-02-16 | 1995-02-16 | Circularizing nucleic acid probe able to interlock with a target sequence through catenation |
JP52175595A JP3590633B2 (en) | 1994-02-16 | 1995-02-16 | Nucleic acid probe for cyclization capable of linking to a target sequence by strand formation |
DE69519373T DE69519373T2 (en) | 1994-02-16 | 1995-02-16 | CIRCULARIZING NUCLEIC ACID SAMPLE THAT CAN BE FIXED TO THE TARGET SEQUENCE BY TRAINING CATENATES |
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
SE9400522A SE9400522D0 (en) | 1994-02-16 | 1994-02-16 | Method and reagent for detecting specific nucleotide sequences |
SE9400522-0 | 1994-02-16 |
Related Child Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
US09/099,466 Continuation US6235472B1 (en) | 1994-02-16 | 1998-06-18 | Nucleic acid detecting reagent |
Publications (1)
Publication Number | Publication Date |
---|---|
WO1995022623A1 true WO1995022623A1 (en) | 1995-08-24 |
Family
ID=20392954
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/SE1995/000163 WO1995022623A1 (en) | 1994-02-16 | 1995-02-16 | Circularizing nucleic acid probe able to interlock with a target sequence through catenation |
Country Status (6)
Country | Link |
---|---|
US (2) | US5871921A (en) |
EP (1) | EP0745140B1 (en) |
JP (1) | JP3590633B2 (en) |
DE (1) | DE69519373T2 (en) |
SE (1) | SE9400522D0 (en) |
WO (1) | WO1995022623A1 (en) |
Cited By (41)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP0756009A2 (en) * | 1995-07-13 | 1997-01-29 | Laboratory of Molecular Biophotonics | Method for amplification of a base sequence |
WO1997041254A1 (en) * | 1996-04-30 | 1997-11-06 | Ulf Landegren | Improved probing of specific nucleic acids |
WO1998002582A2 (en) * | 1996-07-16 | 1998-01-22 | Gen-Probe Incorporated | Methods for detecting and amplifying nucleic acid sequences using modified oligonucleotides having increased target specific t¿m? |
US5866337A (en) * | 1995-03-24 | 1999-02-02 | The Trustees Of Columbia University In The City Of New York | Method to detect mutations in a nucleic acid using a hybridization-ligation procedure |
US5952201A (en) * | 1994-11-07 | 1999-09-14 | Landegren; Ulf | Method of preparing oligonucleotide probes or primers, vector therefor and use thereof |
EP1007725A1 (en) * | 1996-06-14 | 2000-06-14 | Sarnoff Corporation | Padlock probe detection |
EP1007728A1 (en) * | 1996-07-31 | 2000-06-14 | David Y. Zhang | Nucleic acid amplification method: hybridization signal amplification method (hsam) |
US6143495A (en) * | 1995-11-21 | 2000-11-07 | Yale University | Unimolecular segment amplification and sequencing |
US6183960B1 (en) | 1995-11-21 | 2001-02-06 | Yale University | Rolling circle replication reporter systems |
US6214549B1 (en) * | 1995-10-12 | 2001-04-10 | Roche Diagnostics Gmbh | Method of detecting a substance to be analyzed |
US6225056B1 (en) * | 1996-09-13 | 2001-05-01 | Laboratory Of Molecular Biophotonics | Solid phases for target nucleic acid detection, process for production thereof, and method of target nucleic acid detection |
US6255082B1 (en) | 1998-09-15 | 2001-07-03 | Yale University | Artificial long terminal repeat vectors |
US6287824B1 (en) | 1998-09-15 | 2001-09-11 | Yale University | Molecular cloning using rolling circle amplification |
US6316229B1 (en) | 1998-07-20 | 2001-11-13 | Yale University | Single molecule analysis target-mediated ligation of bipartite primers |
US6368801B1 (en) | 2000-04-12 | 2002-04-09 | Molecular Staging, Inc. | Detection and amplification of RNA using target-mediated ligation of DNA by RNA ligase |
EP1299557A1 (en) * | 2000-06-30 | 2003-04-09 | Molecular Staging, Inc. | Signal amplification with lollipop probes |
US6569647B1 (en) | 1994-06-22 | 2003-05-27 | Mount Sinai School Of Medicine Of New York University | Nucleic acid amplification method: ramification-extension amplification method (RAM) |
US6573051B2 (en) | 2001-03-09 | 2003-06-03 | Molecular Staging, Inc. | Open circle probes with intramolecular stem structures |
WO2003052140A2 (en) * | 2001-12-14 | 2003-06-26 | Keygene N.V. | High throughput analysis and detection of multiple target sequences |
US6593086B2 (en) | 1996-05-20 | 2003-07-15 | Mount Sinai School Of Medicine Of New York University | Nucleic acid amplification methods |
EP1444363A1 (en) * | 2001-10-22 | 2004-08-11 | Nucleonics, Inc | Transfection kinetics and structural promoters |
WO2005003386A2 (en) * | 2003-06-30 | 2005-01-13 | Biotage Ab | Oligonucleotide ligation assay by detecting released pyrophosphate |
EP1668148A1 (en) * | 2003-09-04 | 2006-06-14 | Human Genetic Signatures PTY Ltd. | Nucleic acid detection assay |
US7070925B1 (en) | 1996-07-16 | 2006-07-04 | Gen-Probe Incorporated | Method for determining the presence of an RNA analyte in a sample using a modified oligonucleotide probe |
US7527945B2 (en) | 2001-10-22 | 2009-05-05 | Nucleonics, Inc. | Transfection kinetics and structural promoters |
US7799525B2 (en) | 2003-06-17 | 2010-09-21 | Human Genetic Signatures Pty Ltd. | Methods for genome amplification |
US7803580B2 (en) | 2004-09-10 | 2010-09-28 | Human Genetic Signatures Pty. Ltd. | Amplification blocker comprising intercalating nucleic acids (INA) containing intercalating pseudonucleotides (IPN) |
US7833942B2 (en) | 2004-12-03 | 2010-11-16 | Human Genetic Signatures Pty. Ltd. | Methods for simplifying microbial nucleic acids by chemical modification of cytosines |
US7897382B2 (en) | 2001-10-22 | 2011-03-01 | Alnylam Pharmaceuticals, Inc. | Transfection kinetics and structural promoters |
WO2011089393A1 (en) | 2010-01-23 | 2011-07-28 | Trillion Genomics Limited | Detection of target nucleic acids based on oligonucleotide hybridization and chemical ligation |
US8053188B2 (en) | 2001-11-20 | 2011-11-08 | Olink Ab | Nucleic acid enrichment |
US8093030B2 (en) | 2005-10-06 | 2012-01-10 | Lucigen Corporation | Thermostable viral polymerases and methods of use |
US8168777B2 (en) | 2004-04-29 | 2012-05-01 | Human Genetic Signatures Pty. Ltd. | Bisulphite reagent treatment of nucleic acid |
US8343738B2 (en) | 2005-09-14 | 2013-01-01 | Human Genetic Signatures Pty. Ltd. | Assay for screening for potential cervical cancer |
US8431347B2 (en) | 2005-05-26 | 2013-04-30 | Human Genetic Signatures Pty Ltd | Isothermal strand displacement amplification using primers containing a non-regular base |
US8685675B2 (en) | 2007-11-27 | 2014-04-01 | Human Genetic Signatures Pty. Ltd. | Enzymes for amplification and copying bisulphite modified nucleic acids |
US9487823B2 (en) | 2002-12-20 | 2016-11-08 | Qiagen Gmbh | Nucleic acid amplification |
US9683255B2 (en) | 2005-09-09 | 2017-06-20 | Qiagen Gmbh | Method for activating a nucleic acid for a polymerase reaction |
US9732375B2 (en) | 2011-09-07 | 2017-08-15 | Human Genetic Signatures Pty. Ltd. | Molecular detection assay using direct treatment with a bisulphite reagent |
EP3250703B1 (en) * | 2015-01-27 | 2022-06-08 | BioSpyder Technologies, Inc. | Ligation assays in liquid phase |
US11788119B2 (en) | 2016-12-16 | 2023-10-17 | Q-Linea Ab | Padlock probe detection method |
Families Citing this family (244)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US6261808B1 (en) * | 1992-08-04 | 2001-07-17 | Replicon, Inc. | Amplification of nucleic acid molecules via circular replicons |
WO1994003624A1 (en) * | 1992-08-04 | 1994-02-17 | Auerbach Jeffrey I | Methods for the isothermal amplification of nucleic acid molecules |
SE9400522D0 (en) * | 1994-02-16 | 1994-02-16 | Ulf Landegren | Method and reagent for detecting specific nucleotide sequences |
US20070269799A9 (en) * | 1994-06-22 | 2007-11-22 | Zhang David Y | Nucleic acid amplification methods |
SE504798C2 (en) * | 1995-06-16 | 1997-04-28 | Ulf Landegren | Immunoassay and test kits with two reagents that can be cross-linked if adsorbed to the analyte |
US20050026204A1 (en) * | 1995-09-08 | 2005-02-03 | Ulf Landegren | Methods and compositions for nucleic acid targeting |
CA2300938A1 (en) * | 1997-08-20 | 1999-02-25 | Somagenics, Inc. | Antisense and antigene therapeutics with improved binding properties and methods for their use |
MXPA01005267A (en) * | 1998-11-27 | 2002-04-24 | Synaptics Uk Ltd | Position sensor. |
NO986133D0 (en) * | 1998-12-23 | 1998-12-23 | Preben Lexow | Method of DNA Sequencing |
US20060275782A1 (en) * | 1999-04-20 | 2006-12-07 | Illumina, Inc. | Detection of nucleic acid reactions on bead arrays |
US20030207295A1 (en) * | 1999-04-20 | 2003-11-06 | Kevin Gunderson | Detection of nucleic acid reactions on bead arrays |
US6309836B1 (en) | 1999-10-05 | 2001-10-30 | Marek Kwiatkowski | Compounds for protecting hydroxyls and methods for their use |
US6221603B1 (en) | 2000-02-04 | 2001-04-24 | Molecular Dynamics, Inc. | Rolling circle amplification assay for nucleic acid analysis |
US7306904B2 (en) * | 2000-02-18 | 2007-12-11 | Olink Ab | Methods and kits for proximity probing |
US6291187B1 (en) | 2000-05-12 | 2001-09-18 | Molecular Staging, Inc. | Poly-primed amplification of nucleic acid sequences |
EP1313881A2 (en) * | 2000-06-06 | 2003-05-28 | TM Bioscience Corporation | Capture moieties for nucleic acids and uses thereof |
US6323009B1 (en) * | 2000-06-28 | 2001-11-27 | Molecular Staging, Inc. | Multiply-primed amplification of nucleic acid sequences |
ATE380883T1 (en) | 2000-10-24 | 2007-12-15 | Univ Leland Stanford Junior | DIRECT MULTIPLEX CHARACTERIZATION OF GENOMIC DNA |
US7838270B2 (en) * | 2001-05-22 | 2010-11-23 | The University Of Chicago | Target-dependent transcription using deletion mutants of N4 RNA polymerase |
DE10154318A1 (en) * | 2001-10-26 | 2003-05-15 | Epigenomics Ag | Method for analyzing genomic methylation patterns |
US7553619B2 (en) * | 2002-02-08 | 2009-06-30 | Qiagen Gmbh | Detection method using dissociated rolling circle amplification |
US20040029142A1 (en) * | 2002-02-11 | 2004-02-12 | Schon Eric A. | Concatenation-based nucleic acid detection compositions and methods |
US20040058314A1 (en) * | 2002-05-29 | 2004-03-25 | Ming Liang He | Assay for the detection and quantification of HBV cccDNA by real-time PCR |
US20050118616A1 (en) * | 2002-08-16 | 2005-06-02 | Kawashima Tadashi R. | Amplification of target nucleotide sequence without polymerase chain reaction |
US20040086892A1 (en) * | 2002-11-06 | 2004-05-06 | Crothers Donald M. | Universal tag assay |
CA2505687A1 (en) * | 2002-11-19 | 2004-06-03 | Applera Corporation | Polynucleotide sequence detection assays and analysis |
WO2004046344A2 (en) * | 2002-11-19 | 2004-06-03 | Applera Corporation | Polynucleotide sequence detection assays |
US20040101843A1 (en) * | 2002-11-22 | 2004-05-27 | Gerald Zon | Detection of methylated DNA sites |
US20040121338A1 (en) * | 2002-12-19 | 2004-06-24 | Alsmadi Osama A. | Real-time detection of rolling circle amplification products |
CN1791682B (en) * | 2003-02-26 | 2013-05-22 | 凯利达基因组股份有限公司 | Random array DNA analysis by hybridization |
US8043834B2 (en) * | 2003-03-31 | 2011-10-25 | Qiagen Gmbh | Universal reagents for rolling circle amplification and methods of use |
US20040248103A1 (en) * | 2003-06-04 | 2004-12-09 | Feaver William John | Proximity-mediated rolling circle amplification |
EP1682680B2 (en) * | 2003-10-31 | 2018-03-21 | AB Advanced Genetic Analysis Corporation | Methods for producing a paired tag from a nucleic acid sequence and methods of use thereof |
WO2005113804A1 (en) * | 2004-05-20 | 2005-12-01 | Trillion Genomics Limited | Use of mass labelled probes to detect target nucleic acids using mass spectrometry |
CA2587085C (en) | 2004-10-27 | 2017-08-08 | Cepheid | Closed-system multi-stage nucleic acid amplification reactions |
JP2008526224A (en) * | 2005-01-07 | 2008-07-24 | デルイター シーズ アール アンド ディー ビー.ブイ. | Plant virus called tomato trad virus |
US20060160102A1 (en) | 2005-01-18 | 2006-07-20 | Hossein Fakhrai-Rad | Identification of rare alleles by enzymatic enrichment of mismatched heteroduplexes |
US8309303B2 (en) * | 2005-04-01 | 2012-11-13 | Qiagen Gmbh | Reverse transcription and amplification of RNA with simultaneous degradation of DNA |
EP2463386B1 (en) | 2005-06-15 | 2017-04-12 | Complete Genomics Inc. | Nucleic acid analysis by random mixtures of non-overlapping fragments |
US9424392B2 (en) | 2005-11-26 | 2016-08-23 | Natera, Inc. | System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals |
US11111544B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
US11111543B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
CA2624896C (en) | 2005-10-07 | 2017-11-07 | Callida Genomics, Inc. | Self-assembled single molecule arrays and uses thereof |
US7960104B2 (en) | 2005-10-07 | 2011-06-14 | Callida Genomics, Inc. | Self-assembled single molecule arrays and uses thereof |
WO2007133831A2 (en) | 2006-02-24 | 2007-11-22 | Callida Genomics, Inc. | High throughput genome sequencing on dna arrays |
JP2009516525A (en) | 2005-11-22 | 2009-04-23 | プラント リサーチ インターナショナル ベー. フェー. | Complex nucleic acid detection method |
US20070168197A1 (en) * | 2006-01-18 | 2007-07-19 | Nokia Corporation | Audio coding |
WO2007083766A1 (en) | 2006-01-20 | 2007-07-26 | Olympus Corporation | Method for detecting nucleic acid sequence using intramolecular probe |
WO2007092538A2 (en) | 2006-02-07 | 2007-08-16 | President And Fellows Of Harvard College | Methods for making nucleotide probes for sequencing and synthesis |
SG10201405158QA (en) * | 2006-02-24 | 2014-10-30 | Callida Genomics Inc | High throughput genome sequencing on dna arrays |
US8673567B2 (en) * | 2006-03-08 | 2014-03-18 | Atila Biosystems, Inc. | Method and kit for nucleic acid sequence detection |
DE102006020885A1 (en) * | 2006-05-05 | 2007-11-08 | Qiagen Gmbh | Inserting a tag sequence into a nucleic acid comprises using an anchor oligonucleotide comprising a hybridizing anchor sequence and a nonhybridizing tag-template sequence |
WO2007133682A2 (en) * | 2006-05-11 | 2007-11-22 | Geneohm Sciences, Inc. | 100% sequence identity detection methods for variable genomes |
US7897747B2 (en) * | 2006-05-25 | 2011-03-01 | The Board Of Trustees Of The Leland Stanford Junior University | Method to produce single stranded DNA of defined length and sequence and DNA probes produced thereby |
US8119352B2 (en) * | 2006-06-20 | 2012-02-21 | Cepheld | Multi-stage amplification reactions by control of sequence replication times |
EP1878803A1 (en) * | 2006-07-10 | 2008-01-16 | Wageningen Universiteit | Methods of detecting root knot nematodes |
WO2008070352A2 (en) * | 2006-10-27 | 2008-06-12 | Complete Genomics, Inc. | Efficient arrays of amplified polynucleotides |
US20090111706A1 (en) | 2006-11-09 | 2009-04-30 | Complete Genomics, Inc. | Selection of dna adaptor orientation by amplification |
US20080221832A1 (en) * | 2006-11-09 | 2008-09-11 | Complete Genomics, Inc. | Methods for computing positional base probabilities using experminentals base value distributions |
US20080242560A1 (en) * | 2006-11-21 | 2008-10-02 | Gunderson Kevin L | Methods for generating amplified nucleic acid arrays |
EP1939303A1 (en) * | 2006-12-27 | 2008-07-02 | Wageningen Universiteit | Method for detecting cyst nematodes |
US7862999B2 (en) * | 2007-01-17 | 2011-01-04 | Affymetrix, Inc. | Multiplex targeted amplification using flap nuclease |
NL1033431C2 (en) | 2007-02-20 | 2008-08-21 | Expressive Res Bv | Determination of quality characteristics for agricultural or horticultural products. |
US20080293589A1 (en) * | 2007-05-24 | 2008-11-27 | Affymetrix, Inc. | Multiplex locus specific amplification |
EP2171097A2 (en) | 2007-06-29 | 2010-04-07 | Population Genetics Technologies LTD. | Methods and compositions for isolating nucleic acid sequence variants |
US8951731B2 (en) * | 2007-10-15 | 2015-02-10 | Complete Genomics, Inc. | Sequence analysis using decorated nucleic acids |
US8415099B2 (en) | 2007-11-05 | 2013-04-09 | Complete Genomics, Inc. | Efficient base determination in sequencing reactions |
US7897344B2 (en) * | 2007-11-06 | 2011-03-01 | Complete Genomics, Inc. | Methods and oligonucleotide designs for insertion of multiple adaptors into library constructs |
US20090263872A1 (en) * | 2008-01-23 | 2009-10-22 | Complete Genomics Inc. | Methods and compositions for preventing bias in amplification and sequencing reactions |
US8617811B2 (en) * | 2008-01-28 | 2013-12-31 | Complete Genomics, Inc. | Methods and compositions for efficient base calling in sequencing reactions |
US8518640B2 (en) * | 2007-10-29 | 2013-08-27 | Complete Genomics, Inc. | Nucleic acid sequencing and process |
EP2215209B1 (en) | 2007-10-30 | 2018-05-23 | Complete Genomics, Inc. | Apparatus for high throughput sequencing of nucleic acids |
WO2009061840A1 (en) * | 2007-11-05 | 2009-05-14 | Complete Genomics, Inc. | Methods and oligonucleotide designs for insertion of multiple adaptors employing selective methylation |
WO2009073629A2 (en) * | 2007-11-29 | 2009-06-11 | Complete Genomics, Inc. | Efficient shotgun sequencing methods |
US9551026B2 (en) | 2007-12-03 | 2017-01-24 | Complete Genomincs, Inc. | Method for nucleic acid detection using voltage enhancement |
US8592150B2 (en) | 2007-12-05 | 2013-11-26 | Complete Genomics, Inc. | Methods and compositions for long fragment read sequencing |
DK2565279T3 (en) | 2007-12-05 | 2015-02-16 | Complete Genomics Inc | Efficient base determination in sequencing reactions |
US20090156412A1 (en) * | 2007-12-17 | 2009-06-18 | Helicos Biosciences Corporation | Surface-capture of target nucleic acids |
CN102016068A (en) | 2008-01-09 | 2011-04-13 | 生命科技公司 | Method of making a paired tag library for nucleic acid sequencing |
WO2012044847A1 (en) | 2010-10-01 | 2012-04-05 | Life Technologies Corporation | Nucleic acid adaptors and uses thereof |
US20090233809A1 (en) * | 2008-03-04 | 2009-09-17 | Affymetrix, Inc. | Resequencing methods for identification of sequence variants |
BRPI0908734A2 (en) | 2008-03-17 | 2015-07-28 | Expressive Res Bv | Methods for the identification of genomic DNA in a sample and for the identification of polymorphisms, and kit |
US20090270273A1 (en) * | 2008-04-21 | 2009-10-29 | Complete Genomics, Inc. | Array structures for nucleic acid detection |
JP2009268665A (en) * | 2008-05-07 | 2009-11-19 | Canon Inc | Inhalation device |
WO2010068102A1 (en) | 2008-12-10 | 2010-06-17 | Monsanto Invest N.V. | Novel plant virus |
EP2379739A1 (en) | 2008-12-19 | 2011-10-26 | Monsanto Invest N.V. | Method of breeding cysdv-resistant cucumber plants |
US8790873B2 (en) * | 2009-01-16 | 2014-07-29 | Affymetrix, Inc. | DNA ligation on RNA template |
AU2010242073C1 (en) | 2009-04-30 | 2015-12-24 | Good Start Genetics, Inc. | Methods and compositions for evaluating genetic markers |
WO2010133972A1 (en) | 2009-05-22 | 2010-11-25 | Population Genetics Technologies Ltd | Sorting asymmetrically tagged nucleic acids by selective primer extension |
US9524369B2 (en) | 2009-06-15 | 2016-12-20 | Complete Genomics, Inc. | Processing and analysis of complex nucleic acid sequence data |
CN102459592B (en) | 2009-06-15 | 2017-04-05 | 考利达基因组股份有限公司 | For the method and composition of long fragment read sequencing |
EP2467479B1 (en) | 2009-08-20 | 2016-01-06 | Population Genetics Technologies Ltd | Compositions and methods for intramolecular nucleic acid rearrangement |
EP2294912A1 (en) | 2009-09-04 | 2011-03-16 | Wageningen Universiteit | Method for increasing the level of zeaxanthin in a plant line, method for selecting a plant or part thereof, including a seed and tuber, and use thereof |
WO2011049439A1 (en) | 2009-10-19 | 2011-04-28 | Universiteit Twente | Method for selecting bone forming mesenchymal stem cells |
US20120245041A1 (en) | 2009-11-04 | 2012-09-27 | Sydney Brenner | Base-by-base mutation screening |
EP2504448B1 (en) * | 2009-11-25 | 2016-10-19 | Bio-Rad Laboratories, Inc. | Methods and compositions for detecting genetic material |
CA2787385C (en) | 2010-01-18 | 2018-12-11 | Universiteit Utrecht Holding B.V. | Means and methods for distinguishing fecv and fipv |
US20130053253A1 (en) | 2010-02-22 | 2013-02-28 | Population Genetics Technologies Ltd | Region of Interest Extraction and Normalization Methods |
WO2011107887A2 (en) | 2010-03-02 | 2011-09-09 | Population Genetic Technologies Ltd. | Methods for replicating polynucleotides with secondary structure |
US20190300945A1 (en) | 2010-04-05 | 2019-10-03 | Prognosys Biosciences, Inc. | Spatially Encoded Biological Assays |
ES2555106T3 (en) | 2010-04-05 | 2015-12-29 | Prognosys Biosciences, Inc. | Spatially coded biological assays |
US10787701B2 (en) | 2010-04-05 | 2020-09-29 | Prognosys Biosciences, Inc. | Spatially encoded biological assays |
US11332785B2 (en) | 2010-05-18 | 2022-05-17 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
US11322224B2 (en) | 2010-05-18 | 2022-05-03 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
CA2798758C (en) | 2010-05-18 | 2019-05-07 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
US11939634B2 (en) | 2010-05-18 | 2024-03-26 | Natera, Inc. | Methods for simultaneous amplification of target loci |
US10316362B2 (en) | 2010-05-18 | 2019-06-11 | Natera, Inc. | Methods for simultaneous amplification of target loci |
US9677118B2 (en) | 2014-04-21 | 2017-06-13 | Natera, Inc. | Methods for simultaneous amplification of target loci |
US11332793B2 (en) | 2010-05-18 | 2022-05-17 | Natera, Inc. | Methods for simultaneous amplification of target loci |
US20190010543A1 (en) | 2010-05-18 | 2019-01-10 | Natera, Inc. | Methods for simultaneous amplification of target loci |
US11339429B2 (en) | 2010-05-18 | 2022-05-24 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
US11408031B2 (en) | 2010-05-18 | 2022-08-09 | Natera, Inc. | Methods for non-invasive prenatal paternity testing |
US11326208B2 (en) | 2010-05-18 | 2022-05-10 | Natera, Inc. | Methods for nested PCR amplification of cell-free DNA |
US8828688B2 (en) | 2010-05-27 | 2014-09-09 | Affymetrix, Inc. | Multiplex amplification methods |
US9096952B2 (en) | 2010-06-24 | 2015-08-04 | Population Genetics Technologies Ltd. | Methods and compositions for polynucleotide library production, immortalization and region of interest extraction |
WO2011162612A1 (en) | 2010-06-25 | 2011-12-29 | Wageningen Universiteit | Method for modulating the level of phosphorylation of starch in a plant line, method for selecting a plant or part thereof, including a seed and tuber, and use thereof |
SG187101A1 (en) | 2010-07-16 | 2013-02-28 | Stichting Vu Vumc | A method of analysing a blood sample of a subject for the presence of a disease marker |
CN103228796B (en) | 2010-08-11 | 2016-06-01 | 赛路拉公司 | Gene typing DNA |
ES2523140T3 (en) | 2010-09-21 | 2014-11-21 | Population Genetics Technologies Ltd. | Increased confidence in allele identifications with molecular count |
US8725422B2 (en) | 2010-10-13 | 2014-05-13 | Complete Genomics, Inc. | Methods for estimating genome-wide copy number variations |
WO2012049279A1 (en) | 2010-10-14 | 2012-04-19 | Universitaet Des Saarlandes | MEANS AND METHODS APPLYING SINGLE NUCLEOTIDE PRIMER EXTENSION WITH ION PAIR-, REVERSED-PHASE HPLC (SIRPH) FOR THE DIAGNOSIS OF SNPs |
EP2652148B1 (en) | 2010-12-17 | 2016-11-30 | Life Technologies Corporation | Methods, compositions, systems, apparatuses and kits for nucleic acid amplification |
WO2013082164A1 (en) | 2011-11-28 | 2013-06-06 | Life Technologies Corporation | Enhanced ligation reactions |
CN103608466B (en) | 2010-12-22 | 2020-09-18 | 纳特拉公司 | Non-invasive prenatal paternity testing method |
US9163281B2 (en) | 2010-12-23 | 2015-10-20 | Good Start Genetics, Inc. | Methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction |
DK2665833T3 (en) | 2011-01-17 | 2017-07-24 | Life Technologies Corp | WORKING PROCEDURE FOR DETECTING LIGANDS USING NUCLEIC ACIDS |
EP3733867A1 (en) | 2011-01-17 | 2020-11-04 | Life Technologies Corporation | Enzymatic ligation of nucleic acids |
US9365897B2 (en) | 2011-02-08 | 2016-06-14 | Illumina, Inc. | Selective enrichment of nucleic acids |
EP2673380B1 (en) | 2011-02-09 | 2018-12-12 | Bio-Rad Laboratories, Inc. | Analysis of nucleic acids |
CA2827497C (en) | 2011-02-15 | 2014-12-02 | Leica Biosystems Newcastle Ltd. | Method for localized in situ detection of mrna |
US9556473B2 (en) | 2011-02-15 | 2017-01-31 | Leica Biosystems Newcastle Ltd | Methods for identifying nucleic acid sequences |
NL2006378C2 (en) | 2011-03-11 | 2012-09-12 | Univ Wageningen | Tyclv resistance. |
EP2686677B1 (en) | 2011-03-18 | 2018-10-03 | Stichting VUmc | A method of analysing a blood sample of a subject for the presence of a disease marker |
US8759036B2 (en) | 2011-03-21 | 2014-06-24 | Affymetrix, Inc. | Methods for synthesizing pools of probes |
GB201106254D0 (en) | 2011-04-13 | 2011-05-25 | Frisen Jonas | Method and product |
WO2012165943A1 (en) | 2011-05-27 | 2012-12-06 | Vereniging Voor Christelijk Hoger Onderwijs, Wetenschappelijk Onderzoek En Patiëntenzorg | A method of analysing a blood sample of a subject for the presence of an infectious disease marker |
US8778848B2 (en) | 2011-06-09 | 2014-07-15 | Illumina, Inc. | Patterned flow-cells useful for nucleic acid analysis |
EP2980226A1 (en) | 2011-07-08 | 2016-02-03 | Keygene N.V. | Sequence based genotyping based on oligonucleotide ligation assays |
EP2742150A1 (en) | 2011-08-09 | 2014-06-18 | Vereniging voor Christelijk Hoger Onderwijs, Wetenschappelijk Onderzoek en Patiëntenzorg | A method of analysing a blood sample of a subject for the presence of a foetal disease or condition marker |
AU2012299323B2 (en) * | 2011-08-24 | 2016-02-25 | Grifols Therapeutics Inc. | Compositions, methods, and kits for nucleic acid hybridization |
EP4219740A3 (en) | 2011-09-06 | 2023-08-16 | Gen-Probe Incorporated | Closed nucleic acid structures |
GB201116131D0 (en) * | 2011-09-19 | 2011-11-02 | Epistem Ltd | Probe |
EP3604555A1 (en) | 2011-10-14 | 2020-02-05 | President and Fellows of Harvard College | Sequencing by structure assembly |
CA2852665A1 (en) | 2011-10-17 | 2013-04-25 | Good Start Genetics, Inc. | Analysis methods |
WO2013063382A2 (en) | 2011-10-28 | 2013-05-02 | Illumina, Inc. | Microarray fabrication system and method |
US10837879B2 (en) | 2011-11-02 | 2020-11-17 | Complete Genomics, Inc. | Treatment for stabilizing nucleic acid arrays |
WO2014163886A1 (en) | 2013-03-12 | 2014-10-09 | President And Fellows Of Harvard College | Method of generating a three-dimensional nucleic acid containing matrix |
US11021737B2 (en) | 2011-12-22 | 2021-06-01 | President And Fellows Of Harvard College | Compositions and methods for analyte detection |
CA2859761C (en) | 2011-12-22 | 2023-06-20 | President And Fellows Of Harvard College | Compositions and methods for analyte detection |
US10202628B2 (en) | 2012-02-17 | 2019-02-12 | President And Fellows Of Harvard College | Assembly of nucleic acid sequences in emulsions |
WO2013124743A1 (en) | 2012-02-22 | 2013-08-29 | Population Genetics Technologies Ltd. | Compositions and methods for intramolecular nucleic acid rearrangement ii |
ES2741099T3 (en) | 2012-02-28 | 2020-02-10 | Agilent Technologies Inc | Method of fixing a counting sequence for a nucleic acid sample |
US8209130B1 (en) | 2012-04-04 | 2012-06-26 | Good Start Genetics, Inc. | Sequence assembly |
US8812422B2 (en) | 2012-04-09 | 2014-08-19 | Good Start Genetics, Inc. | Variant database |
US10227635B2 (en) | 2012-04-16 | 2019-03-12 | Molecular Loop Biosolutions, Llc | Capture reactions |
WO2013184754A2 (en) | 2012-06-05 | 2013-12-12 | President And Fellows Of Harvard College | Spatial sequencing of nucleic acids using dna origami probes |
US9488823B2 (en) | 2012-06-07 | 2016-11-08 | Complete Genomics, Inc. | Techniques for scanned illumination |
US9628676B2 (en) | 2012-06-07 | 2017-04-18 | Complete Genomics, Inc. | Imaging systems with movable scan mirrors |
WO2014045254A2 (en) | 2012-09-23 | 2014-03-27 | Erasmus University Medical Center Rotterdam | Human betacoronavirus lineage c and identification of n-terminal dipeptidyl peptidase as its virus receptor |
WO2014165061A1 (en) | 2013-03-13 | 2014-10-09 | Meso Scale Technologies, Llc. | Improved assay methods |
US10114015B2 (en) | 2013-03-13 | 2018-10-30 | Meso Scale Technologies, Llc. | Assay methods |
WO2014152421A1 (en) | 2013-03-14 | 2014-09-25 | Good Start Genetics, Inc. | Methods for analyzing nucleic acids |
EP3312295A1 (en) | 2013-03-19 | 2018-04-25 | Directed Genomics, LLC | Enrichment of target sequences |
US8847799B1 (en) | 2013-06-03 | 2014-09-30 | Good Start Genetics, Inc. | Methods and systems for storing sequence read data |
WO2014210225A1 (en) | 2013-06-25 | 2014-12-31 | Prognosys Biosciences, Inc. | Methods and systems for determining spatial patterns of biological targets in a sample |
US20150037787A1 (en) * | 2013-07-31 | 2015-02-05 | International Business Machines Corporation | Polynucleotide configuration for reliable electrical and optical sensing |
US10851414B2 (en) | 2013-10-18 | 2020-12-01 | Good Start Genetics, Inc. | Methods for determining carrier status |
WO2015057565A1 (en) | 2013-10-18 | 2015-04-23 | Good Start Genetics, Inc. | Methods for assessing a genomic region of a subject |
GB2520765A (en) | 2013-12-02 | 2015-06-03 | Vanadis Diagnostics Ab | Multiplex detection of nucleic acids |
US10112194B2 (en) | 2014-04-14 | 2018-10-30 | Q-Linea Ab | Detection of microscopic objects |
RU2717641C2 (en) | 2014-04-21 | 2020-03-24 | Натера, Инк. | Detection of mutations and ploidy in chromosomal segments |
WO2015175530A1 (en) | 2014-05-12 | 2015-11-19 | Gore Athurva | Methods for detecting aneuploidy |
CN112239774A (en) | 2014-05-15 | 2021-01-19 | 中尺度技术有限责任公司 | Improved assay method |
SG11201610168YA (en) | 2014-05-16 | 2017-01-27 | Illumina Inc | Nucleic acid synthesis techniques |
US10655188B2 (en) | 2014-06-13 | 2020-05-19 | Q-Linea Ab | Method for determining the identity and antimicrobial susceptibility of a microorganism |
AU2015294354B2 (en) | 2014-07-21 | 2021-10-28 | Illumina, Inc. | Polynucleotide enrichment using CRISPR-Cas systems |
US11091810B2 (en) * | 2015-01-27 | 2021-08-17 | BioSpyder Technologies, Inc. | Focal gene expression profiling of stained FFPE tissues with spatial correlation to morphology |
US10683534B2 (en) * | 2015-01-27 | 2020-06-16 | BioSpyder Technologies, Inc. | Ligation assays in liquid phase |
WO2016040446A1 (en) | 2014-09-10 | 2016-03-17 | Good Start Genetics, Inc. | Methods for selectively suppressing non-target sequences |
EP3224595A4 (en) | 2014-09-24 | 2018-06-13 | Good Start Genetics, Inc. | Process control for increased robustness of genetic assays |
CA2965661C (en) * | 2014-10-23 | 2023-09-26 | Ricardo Mancebo | Reagents and methods for isothermal chain reaction |
CN114438174A (en) | 2014-11-11 | 2022-05-06 | 伊鲁米那股份有限公司 | Polynucleotide amplification using CRISPR-CAS system |
WO2016093838A1 (en) | 2014-12-11 | 2016-06-16 | New England Biolabs, Inc. | Enrichment of target sequences |
US10066259B2 (en) | 2015-01-06 | 2018-09-04 | Good Start Genetics, Inc. | Screening for structural variants |
EP3901281B1 (en) | 2015-04-10 | 2022-11-23 | Spatial Transcriptomics AB | Spatially distinguished, multiplex nucleic acid analysis of biological specimens |
GB201507026D0 (en) | 2015-04-24 | 2015-06-10 | Linea Ab Q | Medical sample transportation container |
US11479812B2 (en) | 2015-05-11 | 2022-10-25 | Natera, Inc. | Methods and compositions for determining ploidy |
MX2018005611A (en) | 2015-11-03 | 2018-11-09 | Harvard College | Method and apparatus for volumetric imaging of a three-dimensional nucleic acid containing matrix. |
AU2016352829B2 (en) | 2015-11-10 | 2022-11-10 | Vilmorin & Cie | Resistance to ToLCNDV in squash |
WO2017173279A1 (en) * | 2016-03-31 | 2017-10-05 | Arizona Board Of Regents On Behalf Of Arizona State University | Probes and methods for measuring tandem repeats |
GB2554767A (en) | 2016-04-21 | 2018-04-11 | Q Linea Ab | Detecting and characterising a microorganism |
CA3210120C (en) | 2016-04-25 | 2024-04-09 | President And Fellows Of Harvard College | Hybridization chain reaction methods for in situ molecular detection |
EP3656873A3 (en) | 2016-05-11 | 2020-07-29 | Illumina, Inc. | Polynucleotide enrichment and amplification using argonaute systems |
JP7239465B2 (en) | 2016-08-31 | 2023-03-14 | プレジデント アンド フェローズ オブ ハーバード カレッジ | Methods for preparing nucleic acid sequence libraries for detection by fluorescence in situ sequencing |
CN109923216A (en) | 2016-08-31 | 2019-06-21 | 哈佛学院董事及会员团体 | By the detection combination of biomolecule to the method for the single test using fluorescent in situ sequencing |
US11485996B2 (en) | 2016-10-04 | 2022-11-01 | Natera, Inc. | Methods for characterizing copy number variation using proximity-litigation sequencing |
US10011870B2 (en) | 2016-12-07 | 2018-07-03 | Natera, Inc. | Compositions and methods for identifying nucleic acid molecules |
WO2018136856A1 (en) | 2017-01-23 | 2018-07-26 | Massachusetts Institute Of Technology | Multiplexed signal amplified fish via splinted ligation amplification and sequencing |
CA3056650A1 (en) | 2017-03-30 | 2018-10-04 | Pioneer Hi-Bred International, Inc. | Methods of identifying and characterizing gene editing variations in nucleic acids |
EP3639022A4 (en) * | 2017-06-15 | 2021-03-10 | Technion - Research & Development Foundation Ltd | Compositions and methods for detection of genomic variations |
US11180804B2 (en) | 2017-07-25 | 2021-11-23 | Massachusetts Institute Of Technology | In situ ATAC sequencing |
CN111263819A (en) * | 2017-10-06 | 2020-06-09 | 卡特阿纳公司 | RNA templated ligation |
US11485966B2 (en) | 2017-10-11 | 2022-11-01 | Mgi Tech Co., Ltd. | Method for improving loading and stability of nucleic acid |
JP7208911B2 (en) * | 2017-10-11 | 2023-01-19 | 日東電工株式会社 | Regulation of nucleic acid molecule expression |
CN112292460A (en) | 2018-06-12 | 2021-01-29 | 主基因有限公司 | Nucleic acid amplification method |
US11525159B2 (en) | 2018-07-03 | 2022-12-13 | Natera, Inc. | Methods for detection of donor-derived cell-free DNA |
WO2020028194A1 (en) | 2018-07-30 | 2020-02-06 | Readcoor, Inc. | Methods and systems for sample processing or analysis |
US11519033B2 (en) | 2018-08-28 | 2022-12-06 | 10X Genomics, Inc. | Method for transposase-mediated spatial tagging and analyzing genomic DNA in a biological sample |
US11926867B2 (en) | 2019-01-06 | 2024-03-12 | 10X Genomics, Inc. | Generating capture probes for spatial analysis |
US11649485B2 (en) | 2019-01-06 | 2023-05-16 | 10X Genomics, Inc. | Generating capture probes for spatial analysis |
CA3127572A1 (en) | 2019-02-21 | 2020-08-27 | Keygene N.V. | Genotyping of polyploids |
KR20220088632A (en) | 2019-10-25 | 2022-06-28 | 일루미나 케임브리지 리미티드 | Method of generating and sequencing an asymmetric adapter at the end of a polynucleotide template comprising a hairpin loop |
EP4025711A2 (en) | 2019-11-08 | 2022-07-13 | 10X Genomics, Inc. | Enhancing specificity of analyte binding |
WO2021091611A1 (en) | 2019-11-08 | 2021-05-14 | 10X Genomics, Inc. | Spatially-tagged analyte capture agents for analyte multiplexing |
SG11202106899SA (en) | 2019-12-23 | 2021-09-29 | 10X Genomics Inc | Methods for spatial analysis using rna-templated ligation |
US11702693B2 (en) | 2020-01-21 | 2023-07-18 | 10X Genomics, Inc. | Methods for printing cells and generating arrays of barcoded cells |
US11732299B2 (en) | 2020-01-21 | 2023-08-22 | 10X Genomics, Inc. | Spatial assays with perturbed cells |
US11821035B1 (en) | 2020-01-29 | 2023-11-21 | 10X Genomics, Inc. | Compositions and methods of making gene expression libraries |
US11898205B2 (en) | 2020-02-03 | 2024-02-13 | 10X Genomics, Inc. | Increasing capture efficiency of spatial assays |
US11732300B2 (en) | 2020-02-05 | 2023-08-22 | 10X Genomics, Inc. | Increasing efficiency of spatial analysis in a biological sample |
US11835462B2 (en) | 2020-02-11 | 2023-12-05 | 10X Genomics, Inc. | Methods and compositions for partitioning a biological sample |
KR20220142501A (en) * | 2020-02-18 | 2022-10-21 | 에이전시 포 사이언스, 테크놀로지 앤드 리서치 | Nucleic Acid Probe |
US11891654B2 (en) | 2020-02-24 | 2024-02-06 | 10X Genomics, Inc. | Methods of making gene expression libraries |
US11926863B1 (en) | 2020-02-27 | 2024-03-12 | 10X Genomics, Inc. | Solid state single cell method for analyzing fixed biological cells |
US11768175B1 (en) | 2020-03-04 | 2023-09-26 | 10X Genomics, Inc. | Electrophoretic methods for spatial analysis |
WO2021216708A1 (en) | 2020-04-22 | 2021-10-28 | 10X Genomics, Inc. | Methods for spatial analysis using targeted rna depletion |
EP4153775A1 (en) | 2020-05-22 | 2023-03-29 | 10X Genomics, Inc. | Simultaneous spatio-temporal measurement of gene expression and cellular activity |
WO2021237087A1 (en) | 2020-05-22 | 2021-11-25 | 10X Genomics, Inc. | Spatial analysis to detect sequence variants |
WO2021242834A1 (en) | 2020-05-26 | 2021-12-02 | 10X Genomics, Inc. | Method for resetting an array |
WO2021247568A1 (en) | 2020-06-02 | 2021-12-09 | 10X Genomics, Inc. | Spatial trancriptomics for antigen-receptors |
EP4025692A2 (en) | 2020-06-02 | 2022-07-13 | 10X Genomics, Inc. | Nucleic acid library methods |
EP4162074B1 (en) | 2020-06-08 | 2024-04-24 | 10X Genomics, Inc. | Methods of determining a surgical margin and methods of use thereof |
EP4165207A1 (en) | 2020-06-10 | 2023-04-19 | 10X Genomics, Inc. | Methods for determining a location of an analyte in a biological sample |
CN116034166A (en) | 2020-06-25 | 2023-04-28 | 10X基因组学有限公司 | Spatial analysis of DNA methylation |
US11761038B1 (en) | 2020-07-06 | 2023-09-19 | 10X Genomics, Inc. | Methods for identifying a location of an RNA in a biological sample |
US11926822B1 (en) | 2020-09-23 | 2024-03-12 | 10X Genomics, Inc. | Three-dimensional spatial analysis |
US11827935B1 (en) | 2020-11-19 | 2023-11-28 | 10X Genomics, Inc. | Methods for spatial analysis using rolling circle amplification and detection probes |
AU2021409136A1 (en) | 2020-12-21 | 2023-06-29 | 10X Genomics, Inc. | Methods, compositions, and systems for capturing probes and/or barcodes |
KR20230134617A (en) | 2021-03-09 | 2023-09-21 | 일루미나, 인코포레이티드 | Expression analysis of protein-coding variants in cells |
KR20230154078A (en) | 2021-03-09 | 2023-11-07 | 일루미나, 인코포레이티드 | Genomic library construction and targeted epigenetic assay using CAS-gRNA ribonucleoprotein |
WO2022197589A1 (en) | 2021-03-15 | 2022-09-22 | President And Fellows Of Harvard College | Methods for in situ sequencing |
WO2022198068A1 (en) | 2021-03-18 | 2022-09-22 | 10X Genomics, Inc. | Multiplex capture of gene and protein expression from a biological sample |
WO2023034489A1 (en) | 2021-09-01 | 2023-03-09 | 10X Genomics, Inc. | Methods, compositions, and kits for blocking a capture probe on a spatial array |
WO2024015766A1 (en) | 2022-07-12 | 2024-01-18 | Topogene Inc. | Scalable, submicron-resolution replication of dna arrays |
Citations (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US4988617A (en) * | 1988-03-25 | 1991-01-29 | California Institute Of Technology | Method of detecting a nucleotide change in nucleic acids |
Family Cites Families (15)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
JPS61501747A (en) * | 1984-04-06 | 1986-08-21 | ライフ テクノロジ−ズ インコ−ポレ−テツド | Method for detecting nucleic acid sequences |
US4883750A (en) * | 1984-12-13 | 1989-11-28 | Applied Biosystems, Inc. | Detection of specific sequences in nucleic acids |
US5242794A (en) * | 1984-12-13 | 1993-09-07 | Applied Biosystems, Inc. | Detection of specific sequences in nucleic acids |
DE3732130A1 (en) | 1987-09-24 | 1989-04-06 | Gutehoffnungshuette Man | RAMP SECTION FOR FOLDABLE FLOATING BRIDGE OR FERRY |
CA1323293C (en) * | 1987-12-11 | 1993-10-19 | Keith C. Backman | Assay using template-dependent nucleic acid probe reorganization |
US5449602A (en) * | 1988-01-13 | 1995-09-12 | Amoco Corporation | Template-directed photoligation |
CA1341584C (en) * | 1988-04-06 | 2008-11-18 | Bruce Wallace | Method of amplifying and detecting nucleic acid sequences |
GB8818150D0 (en) * | 1988-07-29 | 1988-09-01 | Crc Technology | Gene modification |
US5516663A (en) * | 1990-01-26 | 1996-05-14 | Abbott Laboratories | Ligase chain reaction with endonuclease IV correction and contamination control |
CA2049879A1 (en) * | 1990-08-30 | 1992-03-01 | Keith C. Backman | Controlled initial target-dependent production of templates for ligase chain reaction |
JP3080178B2 (en) * | 1991-02-18 | 2000-08-21 | 東洋紡績株式会社 | Method for amplifying nucleic acid sequence and reagent kit therefor |
US5426180A (en) * | 1991-03-27 | 1995-06-20 | Research Corporation Technologies, Inc. | Methods of making single-stranded circular oligonucleotides |
JP3085409B2 (en) * | 1991-03-29 | 2000-09-11 | 東洋紡績株式会社 | Method for detecting target nucleic acid sequence and reagent kit therefor |
SE9400522D0 (en) * | 1994-02-16 | 1994-02-16 | Ulf Landegren | Method and reagent for detecting specific nucleotide sequences |
SE9403805D0 (en) * | 1994-11-07 | 1994-11-07 | Ulf Landegren | Method of preparing oligonucleotide probes or primers, vector therefor and use thereof |
-
1994
- 1994-02-16 SE SE9400522A patent/SE9400522D0/en unknown
-
1995
- 1995-02-16 WO PCT/SE1995/000163 patent/WO1995022623A1/en active IP Right Grant
- 1995-02-16 US US08/693,302 patent/US5871921A/en not_active Expired - Lifetime
- 1995-02-16 JP JP52175595A patent/JP3590633B2/en not_active Expired - Lifetime
- 1995-02-16 DE DE69519373T patent/DE69519373T2/en not_active Expired - Lifetime
- 1995-02-16 EP EP95910057A patent/EP0745140B1/en not_active Expired - Lifetime
-
1998
- 1998-06-18 US US09/099,466 patent/US6235472B1/en not_active Expired - Lifetime
Patent Citations (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US4988617A (en) * | 1988-03-25 | 1991-01-29 | California Institute Of Technology | Method of detecting a nucleotide change in nucleic acids |
Non-Patent Citations (2)
Title |
---|
DIALOG INFORMATION SERVICES, File 351, Derwent WPI, Dialog Accession No. 009233973, WPI Accession No. 92-361394/44, (TOYM), TOYOBOKK: "Method and Reagent Kit for Amplification of Nucleic Acid (I) Sequence - in which a Straight Chain Probe Nucleotide is Hybridised with a Target, and can Easily Diagnose Hereditary Diseases, Cancer and Infective Diseases Easily"; & JP,A,4 262 799, 18-09-1992, 9244, (Basic). * |
DIALOG INFORMATION SERVICES, File 351, Derwent WPI, Dialog Accession No. 009282380, WPI Accession No. 92-409791/50, (TOYM), TOYOBO KK: "Target Nucleic Acid Sequence Detection Method, Useful in Diagnosis of Genetic Diseases - by Hybridising Strainght Chain Probe Nucleotide with Target Nucleic Acid Sequence"; & JP,A,4 304 900, 28-10-1992, 9250, (Basic). * |
Cited By (74)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US6855523B2 (en) | 1994-06-22 | 2005-02-15 | Mount Sinai School Of Medicine Of New York University | Nucleic acid amplification method: ramification-extension amplification method (RAM) |
US8632999B1 (en) | 1994-06-22 | 2014-01-21 | David Y. Zhang | Nucleic acid amplification methods |
US6569647B1 (en) | 1994-06-22 | 2003-05-27 | Mount Sinai School Of Medicine Of New York University | Nucleic acid amplification method: ramification-extension amplification method (RAM) |
US5952201A (en) * | 1994-11-07 | 1999-09-14 | Landegren; Ulf | Method of preparing oligonucleotide probes or primers, vector therefor and use thereof |
US5866337A (en) * | 1995-03-24 | 1999-02-02 | The Trustees Of Columbia University In The City Of New York | Method to detect mutations in a nucleic acid using a hybridization-ligation procedure |
EP0756009A2 (en) * | 1995-07-13 | 1997-01-29 | Laboratory of Molecular Biophotonics | Method for amplification of a base sequence |
EP0756009A3 (en) * | 1995-07-13 | 1998-07-22 | Laboratory of Molecular Biophotonics | Method for amplification of a base sequence |
US6503714B1 (en) | 1995-10-12 | 2003-01-07 | Roche Diagnostics Gmbh | Method of detecting a substance to be analyzed |
US6214549B1 (en) * | 1995-10-12 | 2001-04-10 | Roche Diagnostics Gmbh | Method of detecting a substance to be analyzed |
US6143495A (en) * | 1995-11-21 | 2000-11-07 | Yale University | Unimolecular segment amplification and sequencing |
US6183960B1 (en) | 1995-11-21 | 2001-02-06 | Yale University | Rolling circle replication reporter systems |
US6210884B1 (en) | 1995-11-21 | 2001-04-03 | Yale University | Rolling circle replication reporter systems |
US6797474B2 (en) | 1995-11-21 | 2004-09-28 | Yale University | Rolling circle replication reporter systems |
US6632609B2 (en) | 1995-11-21 | 2003-10-14 | Yale University | Unimolecular segment amplification and sequencing |
US6329150B1 (en) | 1995-11-21 | 2001-12-11 | Yale University | Unimolecular segment amplification and sequencing |
US6344329B1 (en) | 1995-11-21 | 2002-02-05 | Yale University | Rolling circle replication reporter systems |
US7351528B2 (en) * | 1996-04-30 | 2008-04-01 | Olink Ab | Probing of specific nucleic acids |
WO1997041254A1 (en) * | 1996-04-30 | 1997-11-06 | Ulf Landegren | Improved probing of specific nucleic acids |
US6593086B2 (en) | 1996-05-20 | 2003-07-15 | Mount Sinai School Of Medicine Of New York University | Nucleic acid amplification methods |
EP1007725A4 (en) * | 1996-06-14 | 2003-01-02 | Sarnoff Corp | Padlock probe detection |
EP1007725A1 (en) * | 1996-06-14 | 2000-06-14 | Sarnoff Corporation | Padlock probe detection |
US7572588B2 (en) | 1996-07-16 | 2009-08-11 | Gen-Probe Incorporated | Modified probe molecules having self-complementary regions |
US7495093B2 (en) | 1996-07-16 | 2009-02-24 | Gen-Probe Incorporated | Amplification and detection method |
US6130038A (en) * | 1996-07-16 | 2000-10-10 | Gen-Probe Incorporated | Method for amplifying target nucleic acids using modified primers |
US7070925B1 (en) | 1996-07-16 | 2006-07-04 | Gen-Probe Incorporated | Method for determining the presence of an RNA analyte in a sample using a modified oligonucleotide probe |
US6903206B1 (en) | 1996-07-16 | 2005-06-07 | Gen-Probe Incorporated | Kits for amplifying target nucleic acid sequences using modified oligonucleotides |
WO1998002582A2 (en) * | 1996-07-16 | 1998-01-22 | Gen-Probe Incorporated | Methods for detecting and amplifying nucleic acid sequences using modified oligonucleotides having increased target specific t¿m? |
WO1998002582A3 (en) * | 1996-07-16 | 1998-07-02 | Gen Probe Inc | Methods for detecting and amplifying nucleic acid sequences using modified oligonucleotides having increased target specific t¿m? |
US7563579B2 (en) | 1996-07-16 | 2009-07-21 | Gen-Probe Incorporated | Method for detecting a structured target |
US7399852B2 (en) | 1996-07-16 | 2008-07-15 | Gen-Probe Incorporated | Kits and reaction mixtures containing modified probe molecules |
EP1007728A1 (en) * | 1996-07-31 | 2000-06-14 | David Y. Zhang | Nucleic acid amplification method: hybridization signal amplification method (hsam) |
EP1007728A4 (en) * | 1996-07-31 | 2004-04-07 | David Y Zhang | Nucleic acid amplification method: hybridization signal amplification method (hsam) |
US6225056B1 (en) * | 1996-09-13 | 2001-05-01 | Laboratory Of Molecular Biophotonics | Solid phases for target nucleic acid detection, process for production thereof, and method of target nucleic acid detection |
US6316229B1 (en) | 1998-07-20 | 2001-11-13 | Yale University | Single molecule analysis target-mediated ligation of bipartite primers |
US6255082B1 (en) | 1998-09-15 | 2001-07-03 | Yale University | Artificial long terminal repeat vectors |
US6287824B1 (en) | 1998-09-15 | 2001-09-11 | Yale University | Molecular cloning using rolling circle amplification |
US6368801B1 (en) | 2000-04-12 | 2002-04-09 | Molecular Staging, Inc. | Detection and amplification of RNA using target-mediated ligation of DNA by RNA ligase |
US6686157B2 (en) | 2000-06-30 | 2004-02-03 | Molecular Staging Inc. | Signal amplification with lollipop probes |
EP1299557B1 (en) * | 2000-06-30 | 2007-10-03 | Qiagen GmbH | Signal amplification with lollipop probes |
EP1299557A1 (en) * | 2000-06-30 | 2003-04-09 | Molecular Staging, Inc. | Signal amplification with lollipop probes |
US6573051B2 (en) | 2001-03-09 | 2003-06-03 | Molecular Staging, Inc. | Open circle probes with intramolecular stem structures |
EP1444363A1 (en) * | 2001-10-22 | 2004-08-11 | Nucleonics, Inc | Transfection kinetics and structural promoters |
AU2002348372B2 (en) * | 2001-10-22 | 2008-08-28 | Alnylam Pharmaceuticals, Inc. | Transfection kinetics and structural promoters |
US7897382B2 (en) | 2001-10-22 | 2011-03-01 | Alnylam Pharmaceuticals, Inc. | Transfection kinetics and structural promoters |
EP1444363A4 (en) * | 2001-10-22 | 2004-12-15 | Nucleonics Inc | Transfection kinetics and structural promoters |
US7527945B2 (en) | 2001-10-22 | 2009-05-05 | Nucleonics, Inc. | Transfection kinetics and structural promoters |
US8053188B2 (en) | 2001-11-20 | 2011-11-08 | Olink Ab | Nucleic acid enrichment |
WO2003052142A3 (en) * | 2001-12-14 | 2003-10-30 | Keygene Nv | Analysis and detection of multiple target sequences using circular probes |
WO2003052140A3 (en) * | 2001-12-14 | 2003-11-13 | Keygene Nv | High throughput analysis and detection of multiple target sequences |
WO2003052141A3 (en) * | 2001-12-14 | 2004-02-26 | Keygene Nv | High troughput analysis and detection of multiple target sequences using circular probes |
US7498131B2 (en) | 2001-12-14 | 2009-03-03 | Keygene, Nv | Analysis and detection of multiple target sequences using circular probes |
WO2003052140A2 (en) * | 2001-12-14 | 2003-06-26 | Keygene N.V. | High throughput analysis and detection of multiple target sequences |
WO2003052142A2 (en) * | 2001-12-14 | 2003-06-26 | Keygene N.V. | Analysis and detection of multiple target sequences using circular probes |
WO2003052141A2 (en) * | 2001-12-14 | 2003-06-26 | Keygene N.V. | High troughput analysis and detection of multiple target sequences using circular probes |
US9487823B2 (en) | 2002-12-20 | 2016-11-08 | Qiagen Gmbh | Nucleic acid amplification |
US7799525B2 (en) | 2003-06-17 | 2010-09-21 | Human Genetic Signatures Pty Ltd. | Methods for genome amplification |
WO2005003386A3 (en) * | 2003-06-30 | 2005-04-14 | Biotage Ab | Oligonucleotide ligation assay by detecting released pyrophosphate |
WO2005003386A2 (en) * | 2003-06-30 | 2005-01-13 | Biotage Ab | Oligonucleotide ligation assay by detecting released pyrophosphate |
US7846693B2 (en) | 2003-09-04 | 2010-12-07 | Human Genetic Signatures Pty. Ltd. | Nucleic acid detection assay |
EP1668148A1 (en) * | 2003-09-04 | 2006-06-14 | Human Genetic Signatures PTY Ltd. | Nucleic acid detection assay |
EP1668148A4 (en) * | 2003-09-04 | 2007-11-14 | Human Genetic Signatures Pty | Nucleic acid detection assay |
US8168777B2 (en) | 2004-04-29 | 2012-05-01 | Human Genetic Signatures Pty. Ltd. | Bisulphite reagent treatment of nucleic acid |
US7803580B2 (en) | 2004-09-10 | 2010-09-28 | Human Genetic Signatures Pty. Ltd. | Amplification blocker comprising intercalating nucleic acids (INA) containing intercalating pseudonucleotides (IPN) |
US7833942B2 (en) | 2004-12-03 | 2010-11-16 | Human Genetic Signatures Pty. Ltd. | Methods for simplifying microbial nucleic acids by chemical modification of cytosines |
US8598088B2 (en) | 2004-12-03 | 2013-12-03 | Human Genetic Signatures Pty. Ltd. | Methods for simplifying microbial nucleic acids by chemical modification of cytosines |
US8431347B2 (en) | 2005-05-26 | 2013-04-30 | Human Genetic Signatures Pty Ltd | Isothermal strand displacement amplification using primers containing a non-regular base |
US9683255B2 (en) | 2005-09-09 | 2017-06-20 | Qiagen Gmbh | Method for activating a nucleic acid for a polymerase reaction |
US8343738B2 (en) | 2005-09-14 | 2013-01-01 | Human Genetic Signatures Pty. Ltd. | Assay for screening for potential cervical cancer |
US8093030B2 (en) | 2005-10-06 | 2012-01-10 | Lucigen Corporation | Thermostable viral polymerases and methods of use |
US8685675B2 (en) | 2007-11-27 | 2014-04-01 | Human Genetic Signatures Pty. Ltd. | Enzymes for amplification and copying bisulphite modified nucleic acids |
WO2011089393A1 (en) | 2010-01-23 | 2011-07-28 | Trillion Genomics Limited | Detection of target nucleic acids based on oligonucleotide hybridization and chemical ligation |
US9732375B2 (en) | 2011-09-07 | 2017-08-15 | Human Genetic Signatures Pty. Ltd. | Molecular detection assay using direct treatment with a bisulphite reagent |
EP3250703B1 (en) * | 2015-01-27 | 2022-06-08 | BioSpyder Technologies, Inc. | Ligation assays in liquid phase |
US11788119B2 (en) | 2016-12-16 | 2023-10-17 | Q-Linea Ab | Padlock probe detection method |
Also Published As
Publication number | Publication date |
---|---|
JP3590633B2 (en) | 2004-11-17 |
DE69519373D1 (en) | 2000-12-14 |
SE9400522D0 (en) | 1994-02-16 |
DE69519373T2 (en) | 2001-06-13 |
EP0745140A1 (en) | 1996-12-04 |
US5871921A (en) | 1999-02-16 |
US6235472B1 (en) | 2001-05-22 |
EP0745140B1 (en) | 2000-11-08 |
JPH09509063A (en) | 1997-09-16 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
EP0745140B1 (en) | Circularizing nucleic acid probe able to interlock with a target sequence through catenation | |
AU2008204338B2 (en) | Circular chromosome conformation capture (4C) | |
EP0870842B1 (en) | Adaptor-tagged competitive PCR | |
US4988617A (en) | Method of detecting a nucleotide change in nucleic acids | |
ES2256920T3 (en) | AMPLIFICATION AND DETECTION OF HIV-1 AND / OR HIV-2. | |
JP2622255B2 (en) | Alternative nucleotide sequence identification method | |
US6830884B1 (en) | Method of amplification | |
JP3535159B2 (en) | Selective approach to DNA analysis | |
JPH07509371A (en) | Methods, reagents and kits for detection and amplification of nucleic acid sequences | |
CN110079592B (en) | High throughput sequencing-targeted capture of target regions for detection of genetic mutations and known, unknown gene fusion types | |
JP2004301849A (en) | Liquid phase nucleic acid sandwich assay accompanied by reduction of background noise | |
JP2002209594A (en) | Method for identifying nucleotide base | |
JP2002505117A (en) | Methods for detecting zymogenic nucleic acids, and related molecules and kits | |
EP0849363B1 (en) | Method of identifying a nucleic acid using triple helix formation of adjacently annealed probes | |
JP2004523201A5 (en) | ||
US6461871B1 (en) | Method for the preparation of a probe for nucleic acid hybridization | |
EP0387452B1 (en) | Method of preparing nucleotide probes using a hybridizable complementary element | |
JP4163386B2 (en) | Amplification method for circular nucleic acid probe | |
EP0857791B1 (en) | Method of analysis using signal amplification | |
US6020132A (en) | Method of analysis using signal amplification | |
EP1300473B1 (en) | Method of detecting nucleotide polymorphism | |
JP2003510011A (en) | Coupled polymerase chain reaction-restriction endonuclease digestion-ligase detection reaction | |
US5098824A (en) | Polynucleotide probes for horses | |
Babcock | Mutation Analysis of Fibrillin-2 (FBN2) and Microfibril Associated Protein-3 (MFAP-3): Two Genes Associated with Congenital Contractural Arachnodactyly (CCA), also known as Beal's Syndrome | |
CA2324787A1 (en) | Personal gene library |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
AK | Designated states |
Kind code of ref document: A1 Designated state(s): JP US |
|
AL | Designated countries for regional patents |
Kind code of ref document: A1 Designated state(s): AT BE CH DE DK ES FR GB GR IE IT LU MC NL PT SE |
|
121 | Ep: the epo has been informed by wipo that ep was designated in this application | ||
DFPE | Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101) | ||
WWE | Wipo information: entry into national phase |
Ref document number: 1995910057 Country of ref document: EP |
|
WWE | Wipo information: entry into national phase |
Ref document number: 08693302 Country of ref document: US |
|
WWP | Wipo information: published in national office |
Ref document number: 1995910057 Country of ref document: EP |
|
WWG | Wipo information: grant in national office |
Ref document number: 1995910057 Country of ref document: EP |