WO1993018175A1

WO1993018175A1 - Udg-facilitated mutagenesis

Info

Publication number: WO1993018175A1
Application number: PCT/US1993/001965
Authority: WO
Inventors: Ayoub Rashtchian
Original assignee: Life Technologies, Inc.
Priority date: 1992-03-10
Filing date: 1993-03-08
Publication date: 1993-09-16

Abstract

The present invention provides improved methods for manipulating recombinant DNA in gene cloning and expression. More specifically, the invention provides methods capable of altering a nucleic acid sequence present at the 5' or 3' end of a target molecule.

Description

TITLE OF THE INVENTION;

UDG-FACILITATED UTAGENESIS

FIELD OF THE INVENTION;

The invention relates to improved methods for manipulating reσombinant DNA in gene cloning and expression. More specifically, the invention provides methods capable of introducing a specific, predefined mutation into a desired site in a nucleic acid molecule.

BACKGROUND OF THE INVENTION;

The ability to clone gene sequences has permitted inquiries into the structure and function of nucleic acids, and has resulted in an ability to express highly desired proteins, such as hormones, enzymes, receptors, antibodies, etc., in diverse hosts. Such inquiries are greatly facilitated by the capacity to produce nucleic acid molecules containing mutations or alterations with respect gene sequence that is encountered in Nature (i.e. the "wild type" sequence) . By comparing the similarities and differences between such wild type and mutant sequences, it is possible to uncover important structure/function relationships. In the case of translated sequences, the formation of mutant proteins can lead to the identification of vaccines, therapeutics, as well as enzymes, and receptors or antibodies having enhanced desired activities.

Increasingly, modern medicine is recognizing the clinical significance of discrete mutations in nucleic acids. A variety of diseases and conditions have been found to be caused by or associated with single nucleotide mutations in a particular gene sequence. The in vivo correction of these mutations ("gene therapy") provides a potential cure for such diseases. The principles of gene therapy are disclosed by Oldham, R.K. (In: Principles of Biotherapy. Raven Press, NY, 1987) , and similar texts. Disclosures of the methods and uses for gene therapy are provided by Boggs, S.S. flnt. J. Cell Clon. 8.:80-96 (1990)); James, . , Antiviral Chem. & Chemother. 2;191-214 (1991)); einberg, K. , Curr. Opin. Pediatr. 2:847-854 (1991)); Karson, E.M. (Biol. Reprod. 42:39-49 (1990)); Ledley, F.D., In: Biotechnology. A Comprehensive Treatise, volume 7B. Gene Technology. VCH Publishers, Inc. NY, pp 399-458 (1989)).

The existence or predisposition of an individual to a disease state can increasingly be diagnosed by virtue of the destruction or creation of a restriction site that is located near to a genetic locus associated with the disease state. Such "polymorphic" analysis is used in genetic counseling, and diagnostics (Puck, J.M. , Curr. Opin. Pediatr. 3:855-862 (1991)).

A number of methods for introducing mutations have been described. In brief, these methods are composed of techniques that result in the alteration of the gene sequence at uncontrolled sites (i.e. "random mutagenesis") (Roth, J.R. , Ann. Rev. Genet. 8:319-346 (1974); Singer, B. et al.. Ann. Rev, biochem. 5_2.:655-693 (1982)), and those in which the alteration is site-specific (Grollman, A.P., Prog. Clin. Biol. Res. 340:61-70 (1989); Kaina, B., Biol. Zentralbl. 9_9_:513-531 (1980); Itakura, K. et al.. Ann. Rev. Biochem. 53:323-356 (1984)).

Similarly, methods capable of amplifying purified nucleic acid fragments have been described. Typically, such methods involve the introduction of the nucleic acid fragment into a DNA or RNA vector, the clonal amplification of the vector, and the recovery of the amplified nucleic acid fragment. Examples of such methodologies are provided by Cohen et al. (U.S. Patent 4,237,224), Maniatis, T. et al. _f Molecular Cloning (A Laboratory Manual) . Cold Spring Harbor Laboratory, 1982, etc.

In some instances, the target nucleic acid molecule can be readily obtained from a source material. The molecule can then be inserted into a suitable vector by either adding "linker molecules" (see Scheller et al. , Science 196:177-180 (1977)) or by treating the target molecule with a restriction endonuclease.

In other instances, however, the target nucleic acid molecule cannot be obtained from a source material at a concentration or in an amount sufficient to permit genetic manipulation. In such a situation, it is necessary to amplify the nucleic acid molecule by, for example, template-directed extension, prior to introducing it into a suitable vector. Primer extension can be mediated by the "polymerase chain reaction" ("PCR") , or other means. In the "polymerase chain reaction" or "PCR" the amplification of a specific nucleic acid sequence is achieved using two oligonucleotide primers complementary to regions of the sequence to be amplified.

The polymerase chain reaction provides a method for selectively increasing the concentration of a nucleic acid molecule having a particular sequence even when that molecule has not been previously purified and is present only in a single copy in a particular sample. The method can be used to amplify either single or double stranded DNA.

Reviews of the polymerase chain reaction are provided by Mullis, K.B. (Cold Spring Harbor Svmp. Quant. Biol. 51:263-273 (1986)); Saiki, R.K., et al. (Bio/Technology 2:1008-1012 (1985)); Mullis, K.B. , et al. (Met. Enzvmol. 155:335-350 (1987); Erlich H. et al.. (EP 50,424; EP 84,796, EP 258,017, EP 237,362); Mullis, K. (EP 201,184); Mullis K. et al.. (US 4,683,202); Erlich, H. (US 4,582,788); and Saiki, R. et al. (US 4,683,194) all of which references are incorporated herein by reference) .

The ability to incorporate a gene sequence into a suitable vector is typically performed using restriction endonucleases. Thus, the vector and the target molecules are treated with a restriction nuclease capable of producing compatible termini which can then be ligated together to form a covalently closed vector molecule. Preferably, the restriction enzyme is selected such that its recognition site is not present in the sequence of the target molecule.

In some situations, genetic manipulations have been impeded by the difficulty of introducing a specific, predefined mutation into a desired site in a nucleic acid molecule. It would, therefore, be desirable to be able to introduce such mutations easily in a particular user- defined target molecule. The present invention provides methods suitable for accomplishing these goals.

SUMMARY OF THE INVENTION;

The present invention provides a method for introducing a specific, predefined mutation into a desired site in a nucleic acid target molecule.

In detail, the invention provides a method for introducing a mutation into a predefined site in a target nucleic acid molecule, comprising the steps of:

A) incubating the target molecule in the presence of a first oligonucleotide primer, the first primer: i) being capable of hybridizing to the target molecule at a site on a first strand of the target molecule spanning the predefined site; ii) containing the mutation; and iii) containing a segment whose sequence contains at least one dU residue; B) permitting the oligonucleotide dependent extension of the first primer to thereby obtain a first primer extension product;

C) incubating the first primer extension product with a second oligonucleotide primer, the second primer: i) being capable of hybridizing to the first primer extension product; and ii) containing a segment whose sequence has at least one dU residue, wherein the segment has a sequence complementary to the sequence of the first primer; and

D) permitting the oligonucleotide dependent extension of the second primer to thereby obtain a second primer extension product. The invention further includes the embodiment of the above method which additionally includes the steps:

E) forming a further extension product of the first extension product such that the further extension product additionally contains a segment complementary to the dU- containing segment of the second primer;

F) treating the further extension product and the second extension product under conditions sufficient to remove the dU-containing segments of the molecules;

G) permitting the further extension product and the second extension product to hybridize with one another, to thereby form a target double-stranded DNA molecule having the introduced mutation in the predefined site.

The invention also provides a method for introducing a mutation into a predefined site in a target double- stranded DNA molecule, comprising the steps of:

A) incubating a first strand of the target molecule in the presence of a first oligonucleotide primer, the first primer: i) being capable of hybridizing to the target molecule at a site on the first strand of the target molecule spanning the predefined site; ii) containing the mutation; and iii) containing a segment whose sequence has at least one dU residue;

B) permitting the oligonucleotide dependent extension of the first primer to thereby obtain a first primer extension product;

C) incubating a second strand of the target molecule in the presence of a second oligonucleotide primer, the second primer being capable of hybridizing to the target molecule at a site on the second strand of the target molecule, and containing a segment having at least one dU residue, wherein the segment has a sequence complementary to the sequence of the first primer;

D) permitting the oligonucleotide dependent extension of the second primer to thereby obtain a second primer extension product;

E) incubating the first primer extension product in the presence of a third oligonucleotide primer, the third primer being capable of hybridizing to the first primer extension product, and containing a segment having at least one dU residue; and

F) permitting the oligonucleotide dependent extension of the third primer to thereby form a third primer extension product.

The invention further includes the embodiment of the above method which additionally includes the steps:

G) forming a further extension product of the first extension product such that the further extension product additionally contains a segment complementary to the dU- containing segment of the third primer; H) incubating the second primer extension product in the presence of a fourth oligonucleotide primer, the fourth primer being capable of hybridizing to the second primer extension product, and containing a segment at its 5* terminus whose sequence contains at least one dU residue, wherein the segment has a sequence complementary to the sequence of the second primer; and -1-

I) permitting the oligonucleotide dependent extension of the fourth primer to thereby obtain a fourth primer extension product.

J) forming a further extension product of the second extension product such that the further extension product additionally contains a segment complementary to the dU- containing segment of the fourth primer; K) treating the first and second further extension product and the third and fourth extension product under conditions sufficient to remove the dU-containing segments of the molecules; L) permitting the further extension product and the second extension product to hybridize with one another, to thereby form a target double-stranded DNA molecule having the introduced mutation in the predefined site.

The invention also pertains to the embodiments of the above methods wherein the oligonucleotide dependent extension is performed as a polymerase chain reaction.

The invention also pertains to the embodiments of the above methods wherein the recited further extension products are formed either through the extension of the extension product using a complementary extension product as a template, or using a complementary primer as a template,

The invention also includes the embodiment wherein the dU residues are removed using UDG.

The invention also includes the embodiment wherein the target molecule is a circular molecule, a linear molecule (either formed by the linearization of a vector molecule, or containing part of a vector molecule, or consisting essentially of the target molecule) .

The invention also includes the embodiment wherein the target molecule is single-stranded or double stranded DNA (or cDNA) , single-stranded or double stranded RNA, genomic DNA, viral DNA or a viroid nucleic acid. BR EF DESCRIPTION OF THE FIGURES

Figure 1 shows a depiction of the primer extension reaction using two primers with a circular vector.

Figure 2 shows a depiction of the primer extension reaction using four primers with a circular (Figure 2A) or a linear (Figure 2B) target molecule.

Figure 3 shows cleavage of the vector of Figure 1, or extension of the primers shown in Figure 1 to create a linear molecule. Figure 4 shows the use of the extension products of the first cycle of amplification as substrates for subsequent amplification.

Figure 5 shows that subsequent amplification yields molecules having exo-sample nucleotide-containing sequences on both ends, but on different strands.

Figure 6 illustrates the structure of the resultant molecule, and its conversion back into a circular vector.

Figure 7, A and B show the extension reaction between the linearized circular molecules of Figure 2A. Figures 8, A and B show the extension products of the respective extension reactions of Figure 7, A and B.

Figure 9 shows a PCR amplification of the relevant extension products of Figure 8, A and B.

Figure 10 shows the removal of the exo-sample nucleotides, and the generation of the circular vector.

Figure 11 shows the use of four primers to amplify the linear target molecule of Figure 2B.

Figure 12 illustrates the use of the present invention to introduce a guanine to adenine substitution into the lacZ alpha complementation gene of pUC19 at position 89.

DESCRIPTION OF THE PREFERRED EMBODIMENTS;

The methods of the present invention allow one to introduce a specific, predefined mutation into a desired site in a nucleic acid "target" molecule. The mutation alters the nucleotide sequence of the "target" molecule, to thereby form a "desired" molecule.

The term "nucleotide" as used herein refers to a base-sugar-phosphate combination. Nucleotides are the monomeric units of nucleic acid polymers, i.e. of DNA and RNA. The term includes ribonucleoside triphosphates, such as rATP, rCTP, rGTP, or rUTP, and deoxyribonucleoside triphosphates, such as dATP, dCTP, dGTP, or dTTP. A "nucleoside" is a base-sugar combination, i.e. a nucleotide lacking phosphate.

In addition to the above-described nucleotides, the present invention, in a preferred embodiment uses "exo- sample nucleotides". An "exo-sample nucleotide", as used herein, is a nucleotide that is generally not found in a sequence of DNA. For most DNA samples, deoxyuridine is an example of an exo-sample nucleotide. Although the triphosphate form of deoxyuridine, dUTP, is present in living organisms as a metabolic intermediate, it is rarely incorporated into DNA. When dUTP is incorporated into DNA, the resulting deoxyuridine is promptly removed in vivo by normal processes, e.g. processes involving the enzyme "Uracil DNA glycosylase" (UDG) .

UDG is an enzymatic activity that cleaves the glycosidic bond between the base uracil and the sugar deoxyribose, only when the monomeric nucleotide dUTP is incorporated into a DNA molecule, resulting in incorporation of a deoxyuridine moiety (Duncan, B. in The Enzymes 14.:565 (1981), ed. : Boyer P) . An enzyme possessing this activity does not act upon free dUTP, free deoxyuridine, or RNA (Duncan, supra) . The action of UDG results in the production of an "abasic" site. The enzyme does not, however, cleave the phophodiester backbone of the nucleic acid molecule. Most preferably, the phophodiester backbone at an abasic site may be claeved through the use of an endonuclease specific for such substrates. A preferred enzyme for this purpose is the J . coli enzyme, Endonuclease IV. Most preferably, Endonuclease IV is used in conjunction with UDG to remove dU residues from a nucleic acid molecule.

As noted, deoxyuridine rarely or never occurs in natural DNA. It is recognized that some organisms may naturally incorporate deoxyuridine into DNA. For nucleic acid samples of those organisms, deoxyuridine would not be considered an exo-sample nucleotide.

Examples of other exo-sample nucleotides include bromodeoxyuridine, 7-methylguanine, 5,6-dihyro-5,6 dihydroxydeoxythymidine, 3-methyldeoxadenosine, etc. (see, Duncan, B.K.. The Enzymes XIV:565-586 (1981)). Other exo- sample nucleotides will be evident to those in the art. For example, RNA nucleotides may be incorporated into the primer(s) and used as an exo-sample nucleotide for the purposes of the present invention. The RNA of such RNA- containing primers (and therefore, the primers themselves) can be readily destroyed by alkali or an appropriate ribonuclease, such as RNase H. RNase H degrades RNA of RNA:DNA hybrids and numerous single-stranded RNases are known which are useful to digest single-stranded RNA after a denaturation step.

The presence of deoxyuridine, or any other exo-sample nucleotide, may be readily determined using methods well known to the art. A nucleic acid molecule containing any such exo-sample nucleotide is functionally equivalent to DNA containing only dA, dC, dG or dT (dT is referred to herein as T) in all respects, except that it is uniquely susceptible to certain treatments, such as glycosylase digestion. Numerous DNA glyσosylases are known to the art. An exo-sample nucleotide which may be chemically or enzy atically incorporated into an oligonucleotide and a DNA glycosylase that acts on it may be used in the preferred embodiment of the present invention. DNA containing bromodeoxyuridine as the exo-sample nucleotide may be degraded by exposure to light under well-known conditions. The use of exo-sample nucleotides to remove potential contaminants from samples being subjected to PCR amplification is disclosed by Longo, M.C. et al. (Gene 12:125-128 (1990), Hartley, U.S. Patent No. 5,035,966), herein incorporated by reference in their entirety. This reference discloses the use of either dU-containing oligonucleotides or dUTP in the PCR-directed amplification of a target molecule. The use of exo-sample nucleotides in gene cloning is disclosed in U.S. patent application serial no. 07/715,623, herein incorporated by reference.

The mutations that can be introduced into the target molecule can be either deletions, substitutions, or insertions relative to the sequence of the target molecule. The present invention may be used to introduce a single mutation or two or multiple mutations into the target sequence. Where the nucleic acid molecule is translated into protein (as opposed to being in an untranslated or non-transcribed locus) , the mutation may alter the sequence of any protein that is expressed from it. Alternatively, the mutation may be "cryptic." A cryptic mutation does not affect either the expression of the mutated gene, or the activity or function of the expressed gene product. Cryptic mutations may be detected through nucleotide sequence analysis. Cryptic mutations include mutations that do not result in a change in the amino acid sequence of the expressed gene product. Most preferably, the mutation will be "non-cryptic" and will therefore introduce a change in the nucleotide sequence of the target molecule that detectably alters either the expression or the activity or function of the gene sequence or regulation of gene expression. A "mutation that detectably alters the expression of a gene sequence," as used herein denotes any change in nucleotide sequence affecting the extent to which the gene sequence is transcribed, processed or translated. Such alterations may be, for example, in an enhancer, promoter, coding or termination region of the sequence, mutations which stabilize the gene product, or its mRNA, etc. A "mutation that detectably alters the activity of a gene sequence," as used herein denotes any change in nucleotide sequence that alters the capacity of the expressed gene product to mediate a function of the gene product. Such mutations include changes that diminish or inactivate one or more functions of the expressed product. Significantly, such mutations also include changes that result in an increase the capacity of the gene product to mediate any function (for example, a catalytic or binding activity) of that gene product.

The present invention is concerned with the mutation of a gene sequence of a target molecule. The sequence of this molecule may be of any size or complexity. In general, some information is known about the desired sequence, such that the sequences of its termini can be ascertained. Any molecule which can be amplified by PCR, or which has restriction sites at its termini that, when cleaved, result in protruding 3' termini, can be used as the desired or target molecules of the present invention.

Most preferably, the present invention achieves its goal through the use of oligonucleotide primers that are capable of hybridizing to the 3• termini of the target molecule. The term "oligonucleotide" as used herein refers collectively and interchangeably to two terms of art, "oligonucleotide" and "polynucleotide". Note that although oligonucleotide and polynucleotide are distinct terms of art, there is no exact dividing line between them and they are used interchangeably herein. An oligonucleotide is said to be "blocked," if its 3• terminus is incapable of serving as a primer.

The term "primer" as used herein refers to a single- stranded oligonucleotide or a single-stranded polynucleotide that is extended by covalent addition of nucleotide monomers during amplification. Nucleic acid amplification often is based on nucleic acid synthesis by a nucleic acid polymerase. Many such polymerases require the presence of a primer that can be extended to initiate such nucleic acid synthesis. A primer is typically 6 bases or longer; most preferably, a primer is 12 bases or longer. A minimum of 3 bases may, however, suffice.

The "terminus" of a nucleic acid molecule denotes a region at the end of the molecule. The term is not used herein as representing the final nucleotide of a linear molecule, but rather a general region which is at or near an end of a linear molecule.

Two termini of two nucleic acid molecules are said to be the "same denominated termini," if the both termini are either the 3^» termini of the respective molecules or both termini are the respective 5' termini of the respective molecules. As used herein, the term "same denominated termini," is not intended to refer to the nucleotide sequence of the termini being compared.

In a preferred embodiment of the invention, two primers are employed, at least one of which has a sequence, that although capable of hybridizing to the target molecule, contains the mutation that is desired to be introduced into the target molecule.

In this embodiment, the primers will contain one or more exo-sample nucleotides. In a preferred embodiment, the primers will contain a segment having about 25% or more exo-sample nucleotides. Preferably, the exo-sample nucleotides will be located 5¹ to the mutation site. The exo-sample nucelotide may also serve as the mutation. The structure of the amplification and mutant primers are selected such that the dU-containing segments of each is complementary to the other. This preferred embodiment is illustrated in Figures 1 and 11, with reference to the sequences disclosed in Example 1.

In the most preferred embodiment, the introduction of the mutation will be accomplished after the target molecule has already been cloned into a vector. In this embodiment, the vector molecule can be used without any cleavage; the circular vector molecule can be used directly in the methods of the invention. This is possible because the extension of any primer will produce a linear molecule that is exactly equal to the size of the circular vector. Hence, after the first primer extension products are obtained, all further molecules are linear. Figures 1 and 2 show a depiction of the primer extension reaction with a circular vector. Where the target molecule is small, the goals of the invention are readily achieved with a single pair of primers (Figure 1) ; where the target molecule is large, it is preferred to perform two separate amplifications, using four total primers (Figure 2) .

Alternatively, the target molecule can be a linear molecule (such as a molecule present in a sample prior to cloning, or may be a linearized vector) . Where the target molecule has been cloned into a vector, the vector may most preferably be linearized via treatment with a restriction endonuclease. Such linearization may be caused by cleavage that is either within or outside of the sequence of the target molecule. In either case, the two strands of the target molecule and the two primers are incubated under conditions suitable for "oligonucleotide- dependent extension," most preferably by PCR. "Oligonucleotide-dependent amplification" as used herein refers to amplification using an oligonucleotide or polynucleotide to amplify a nucleic acid sequence. An oligonucleotide-dependent amplification is any amplification that requires the presence of one or more oligonucleotides or polynucleotides that are two or more mononucleotide subunits in length and that end up as part of the newly-formed, amplified nucleic acid molecule.

The use of PCR in conjunction with site-specific mutagenesis is discussed by Jones, D.H. , Technioue 2:273- 278 (1990); Jones, D.H. et al.. Biotechnique 10:62-66 (1991) ; Medin, J.A. et al.. FASEB J. 5_:A826 (1991) ; Shyamala, V. et al. , Gene 97:1-6 (1991); Perrin, S. et al.. Nucl. Acids Res. 18:7433-7438 (1990); Jones, D.H. et al.. J. Cell. Biol. 109:308A (1989); Nelson, R.M. et al.. Anal. Biochem. .180-147-151 (1989); and Uhlen, M. et al.. J. Cell Biochem. Suppl 0 (13 Part E) page 310 (1989) , all of which references are herein incorporated by reference. As stated above, in order to use the methods of the present invention, it is not necessary that the target molecule has been previously cloned. Thus, the present invention can, in one process, achieve the amplification and mutagenesis of the target molecule. This capacity may be exploited to create "restriction fragment polymorphism" of a target molecule, for diagnostic purposes. For example, where a chromosomal locus associated with a normal gene contains or is closely linked to the sequence such as GACGTC, and the corresponding sequence that is contained within or closely linked to a mutant variant of this gene has the sequence GACTTC, then the present invention provides the means to create a detectable restriction fragment polymorphism through the use of a primer that mutates the sequence to GAATTC, a restriction site for the EcoRl enzyme. Although the primer will amplify both the normal and the mutant locus, a restriction site is created only when the mutant locus is amplified. The capacity, however, to additionally effect the cloning of the mutated sequence is highly desirable. Many important human proteins (such as hormones, antibodies, enzymes, receptors, etc.) differ only slightly in amino acid composition from the sequences of the analogous proteins of other animals. The present invention permits one to readily convert a gene for an animal protein into a gene that encodes a human protein (and vice versa) provided that the amino acid sequences of both molecules has been determined. Similarly, it greatly simplifies the process of cloning mutant variants of cloned target molecules, particularly, when such target molecules are large, such as would be encountered in studies of the DNA of the human genome.

A. THE FIRST PREFERRED METHOD

Where the target molecule can be directly amplified in its entirety, the desired mutation can be introduced into the target molecule with a single pair of primer molecules. As indicated above, the target molecule can be either a circular or linear molecule, with or without any vector sequences. Most preferably, the molecule is denatured, or partially denatured, and then permitted to anneal with the "amplification primer" (i.e. any primer whose sequence does not introduce the mutation into the target molecule) and the "mutant primer" (i.e. any primer whose sequence is selected such that the desired mutation will be introduced into the target molecule) . As will be appreciated, the mutation can be in both of these primers.

The target molecule strand that is hybridized to the amplification primer serves as the template for the extension of the amplification primer. This extension results in the production of an extension product that, because it contains the protruding sequence of the primer, is larger than the initial target molecule strand. The additional sequences are present at the 5• end of the strand. The 3' end of this extension product is capable of hybridizing to the mutant primer, and of serving as a template for the oligonucleotide-depeneent extension of the mutant primer.

As will be appreciated, the extension of the mutant primer results in the formation of an extension product that contains additional sequences at its 5¹ end (these sequences correspond to the 5' protrusion of the primer) .

Significantly, the extension product also contains the complement of the additional sequences that were on the 5* end of the template. As in any PCR, the extension product of a first cycle round of replication is a substrate of all subsequent cycles. Thus, the result of the PCR is the formation of a double-stranded molecule whose termini have overlapping sequences. In particular, the resultant products will be found to contain terminal regions of overlapping sequence in which the exo-sample nucleotides are present in the 5' ends of the two strands. Treatment that results in the loss of the exo-sample nucleotides thus produces complementary termini, such that a circular molecule is formed that contains a complete, now-mutated gene sequence. Since the circular molecule is a vector, it may be directly transformed into a host either as a hydrogen-bonded circle, or as a covalently closed circle after the addition of "ligase." A ligase is an activity that is capable of joining the 3¹ hydroxyl terminus of one nucleic acid molecule to a 5• phosphate terminus of a second nucleic acid molecule to form a single molecule. Ligase enzymes are discussed in Watson, J.D. , In: Molecular Biology of the Gene. 3rd Ed., W.A. Benjamin, Inc., Menlo Park, CA (1977), and similar texts. This embodiment of the invention is illustrated in Figures 1 and 3-6. Figure 1 depicts a circular vector in which the target molecule (depicted at the top of the vector) has a site (x) that is to be mutated to Z. Cleavage of the vector, or extension of the primers, creates a linear molecule as shown in Figure 3 (the exo- sample nucleotide-containing sequences are shown as ddddd; it is complementary to the corresponding sequence of the target) . The extension products of the first cycle of amplification are substrates for subsequent amplification as shown in Figure 4. As will be appreciated, such subsequent amplification yields molecules having exo- sample nucleotide-containing sequences on both ends, but on different strands (Figure 5) . Figure 6 illustrates the structure of the resultant molecule, and its conversion back into a circular vector. In addition to the vector illustrated in Figure 6, the sum of the PCR reactions will also recreate a mismatch vector at approximately equal frequency. Thus, it is desirable to screen the cloned vectors in order to identify those vectors containing the desired sequence.

B. THE SECOND PREFERRED METHOD

Where the target molecule is too large to conveniently be amplified in its entirety, the desired mutation can be introduced into the target molecule two or more pairs of primer molecules. As indicated above, the target molecule can be either a circular or linear molecule, with or without any vector sequences.

In this embodiment the target molecule is fully or partially denatured, and preferably divided into two reaction tubes and permitted to separately anneal with two sets of two primers (i.e. four primers are used) . If the portions that are to be amplified by the primers are still too large to be conveniently amplified, it is possible to employ additional reaction tubes and aditional pairs of primers in order to decrease the amplification portions to a convenient size. Each pair of primers contains a segment having at least one (and preferably a plurality of) exo-sample nucleotide(s) at its 5' terminus. Where the primer pair are intended to amplify a sequence that is to be mutated, either or both of the primers may cause such mutation(s) . The primers are extended, as by PCR, in the same manner as described above. The resultant products of PCR with each primer pair will be a linear double-stranded DNA molecule having at one terminus the exo-sample nucleotides which are overlapping, and having at the other terminus information that is desirable for subsequent cloning into an appropriate vector. This cloning information may be blunt ends, restriction sites, etc. In a preferred embodiment, the information may employ the exo-sample cloning method disclosed in U.S. Patent Application Serial No. 715,623 (filed June 14, 1991), herein incorporated by reference. Moreover, the exo-sample nucleotides of the resultant product from PCR with one primer pair will be on the opposite strand from the exo-sample nucleotides of the resultant product from PCR with the other primer pair. As in the above method, the exo-sample segments of the primer pairs are selected such that they are complementary to one another. Again, because of the complementary nature of the sequences, the removal of the exo-sample nucleotides will create overhanging ends that are complementary to one another. In sum, each of the two PCR reactions yields a double-stranded molecule that comprises a portion of the target molecule. Moreover, each such double-stranded molecule can be ligated back together (or merely hydrogen bonded together) to form a linear DNA fragment. This linear fragment can be readily cloned.

This embodiment of the invention is illustrated in Figures 2 and 7-10. Figure 2 shows the target molecule and the use of the two primer pairs in a PCR. Figure 2A depicts the use of two primer pairs with a circular target molecule. Figure 2B depicts the use of two primer pairs with a linear target molecule (the site to be mutated is designated x; the desired mutation is designated Z; the ends of the portion of interest of the target molecule are indicated by "|"). In Figure 2, the target molecule may include an entire vector, or a fragment of a vector; the target molecule may alternatively be free of any vector sequences) . In Figures 2 and 7, the exo-sample nucleotide-containing sequence is shown as ddddd; it is complementary to (and hybridized to) the corresponding sequence of the target molecule) .

Figures 7A and 7B show the extension reaction between the linearized circular target molecule of Figure 2A (the linearized molecule may be produced either by restriction cleavage of the circular target molecule, or more preferably, by a prior primer extension reaction) . Figures 8A and 8B show the extension products of the respective extension reactions of Figures 7A and 7B. The result of the two extension reactions is the production of four extension products (see. Figures 8A and 8B) . The extension products contain partial sequences such that when combined, they lead to the formation of the desired mutated sequence. To simplify the exposition of the method, only the fate of the two most relevant extension products will be followed. Figure 9 shows a PCR amplification of the relevant extension products of Figure 8A and 8B. Figure 10 shows the removal of the exo-sample nucleotides, and the generation of the circular target molecule.

As shown in Figure 11A, the four primers are selected such that they can hybridize to the target molecule and be extended, as by a polymerase. Although it is possible for the primers to be extended to the end of the template, in practice, and especially if the concentration of primer exceeds that of the target molecule, a PCR amplification will be achieved, leading to the formation of the amplified double-stranded molecules shown in Figure 11B. After treatment to remove the exo-sample-containing segments of the molecule, the molecules having the structures shown in Figure 11C are obtained. These molecules can hybridize to one another (Figure 11D) to form a mutated target molecule. In Figure 11D, the termini of the mutated target molecule are shown as protruding 3' ends. such a structure is not a requirement of the invention, since the amplified region can be altered to contain restriction sites (thus permitting the formation of 3* or 5¹ protruding ends, or blunt ends). Similarly, the exo-sample-containing primer can be replaced with a primer that lacks exo-sample nucleotides (for example in the last step of the amplification) in order to produce other types of termini, when such are desired. The present invention includes articles of manufacture, such as "kits." Such kits will, typically, be specially adapted to contain in close compartmentalization a first container which contains an exo-sample nucleotide or an exo-sample nucleotide- containing oligonucleotide (such as dUTP or dU) ; a second container which contains an enzyme capable of degrading an oligonucleotide which contains the exo-sample nucleotide. The kit may additionally contain buffers, RNAse enzymes, instructional brochures, and the like.

Having now generally described the invention, the same will be more readily understood through reference to the following examples which are provided by way of illustration, and are not intended to be limiting of the present invention, unless specified.

EXAMPLE 1 UDG MUTAGENESIS

To demonstrate the application of the UDG mutagenesis method the plasmid pUC19 which contains the lac Z alpha complementation gene was used. Normally E. coli strains harboring this plasmid grow as blue colonies on agar plates containing the chromogenic dye, X-gal and IPTG (an inducer of the lac Z gene. However, inactivation of the alpha complementation gene results in production of white colonies (Miller, J.H. , In: Experiments in Molecular Genetics, Cold Spring Harbor Press, Cold Spring Harbor, NY (1972)). Kunkel, et al. (Proc. Natl. Acad. Sci. (U.S.A.) 84.∑4865-4869 (1987)) have shown that a single base substitution (guanine to adenine) at position 89 of this gene results in generation white colonies. To illustrate the invention, an amplification primer and a mutant primer, both containing dU residues, were synthesized and used in the manner described above to introduce the guanine to adenine substitution to the alpha complementation gene of pUC19 at position 89. As a control, a separate experiment was performed using the amplification primer and a wild type primer (differeing from the mutant primer in having the wild type sequence at position 89) . The experiment is illustrated by reference to Figure 12. The sequence of the oligonucleotides are as follows:

Mutant primer (<SEQ ID N0:1>): 5' AAC GUC GUG ACU GAG AAA ACC CTG G 3'

Wild type primer (<SEQ ID NO:2>):

5• AAC GUC GUG ACU GGG AAA ACC CTG G 3^■

Amplification primer (<SEQ ID N0:3>):

5' AGU CAC GAC GUU GUA AAA CGA CGG C 3¹

PCR amplifications were performed using circular pUC19 DNA as amplification target with a mixture of mutant primer and amplification primer or the wild type primer and amplification primers. The concentration of each primer was 1 micro M in the PCR. All amplifications were performed in Ix PCR buffer in a thermocylcler for 30 cycles as follows: 94 C, 30 sec; 55 C, 1 min; 72 C, 3 min. The amplification resulted in generation of a linear double stranded plasmid for each set of amplifications (Figures 3 and 11) . Four microliter of the PCR products were treated with 1 unit of UDG for 30 min at 37 C in a final volume of 20 microliters. Treatment of the PCR products with UDG resulted in removal of the dU residues and genration of 3* overhangs at the 3• ends of the PCR products. The complementary nature of the 3* ends resulted in circularization of the PCR products. Two microliters of the circularized PCR products were then used to transfom competent E. coli cells. An identical sample of the PCR product which had not been treated with UDG was used as control. The transformants were plated on agar plates contaning 50 microgram/ml ampicillin and X-gal and IPTG. After overnight growth the colonies were scored for blue or white phenotype. The results are summarized in Table 1.

EXAMPLE 2 UDG MUTAGENESIS

A plasmid containing the human C-RAF gene was used to generate a single amino acid change in the ATP binding site of this protein. It has previously shown that substitution of the lysine with tryptophan at the ATP binding site inactivates the transforming activity of this protein. For mutagenesis of this site two overlapping primers were synthesized in which the codon for lysine had been changed to tryptophan. The gene was amplified in two segments using one of the mutant primers with an appropriate vector primer containing the UDG cloning sequence. The two PCR products were mixed with plasmid pAMPl (Life Technologies, Inc.) and treated with UDG for 30 min at 37 C. A portion of this annealing mix was used to transform competent E. coli cells. The transformants were selected on ampicilin plates. An identical preparation which had not been treated with UDG was used as control. Transformation mix with UDG treated PCR products resulted in 155 colonies while the untreated products resulted only in 7 colonies. The plasmid DNA in the transformants were with UDG treated PCR products showed all tested clones to contain a 2.2 kb insert in plasmid pAMPl. The clones from untreated mixture were found to be the original wild type plasmid used as the PCR target for amplification (pUC19 containing the wild type C-RAF gene) .

While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims.

SEQUENCE LISTING

(1) GENERAL INFORMATION:

(i) APPLICANT: LIFE TECHNOLOGIES, INC. (ii) TITLE OF INVENTION: UDG-FACILITATED MUTAGENESIS (iii) NUMBER OF SEQUENCES: 3

(iv) CORRESPONDENCE ADDRESS:

(A) ADDRESSEE: WEIL, GOTSHAL & MANGES

(B) STREET: 1615 L STREET, N.W. , SUITE 700

(C) CITY: WASHINGTON

(D) STATE: D.C.

(E) COUNTRY: U.S.A.

(F) ZIP: 20036

(V) COMPUTER READABLE FORM:

(A) MEDIUM TYPE: Floppy disk

(B) COMPUTER: IBM PC compatible

(C) OPERATING SYSTEM: PC-DOS/MS-DOS

(D) SOFTWARE: Patentln Release #1.0, Version #1.25

(Vi) CURRENT APPLICATION DATA:

(A) APPLICATION NUMBER: US TO BE ACCORDED

(B) FILING DATE:

(C) CLASSIFICATION:

(viii) ATTORNEY/AGENT INFORMATION:

(A) NAME: AUERBACH, JEFFREY I

(B) REGISTRATION NUMBER: 32,680

(C) REFERENCE/DOCKET NUMBER: 59452-0006-B

(ix) TELECOMMUNICATION INFORMATION:

(A) TELEPHONE: (202) 682-7033

(B) TELEFAX: (202) 857-0939

(2) INFORMATION FOR SEQ ID NO:l:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 25 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: YES (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:

(A) ORGANISM: Escherichia coli

(B) STRAIN: K-12

(vii) IMMEDIATE SOURCE: (B) CLONE: PUC-19

(Xi) SEQUENCE DESCRIPTION: SEQ ID NO:l:

AACGUCGUGA CUGAGAAAAC CCTGG 25

(2) INFORMATION FOR SEQ ID NO:2:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 25 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: YES (iv) ANTI-SENSE: NO

(vi) ORIGINAL SOURCE:

(A) ORGANISM: Escherichia coli

(B) STRAIN: K-12

(Vii) IMMEDIATE SOURCE: (B) CLONE: PUC-19

(Xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:

AACGUCGUGA CUGGGAAAAC CCTGG 25

(2) INFORMATION FOR SEQ ID NO:3:

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 25 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(A) ORGANISM: Escherichia coli

(B) STRAIN: K-12

(vii) IMMEDIATE SOURCE: (B) CLONE: PUC-19

(Xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:

AGUCACGACG UUGUAAAACG ACGGC 25

Claims

WHAT IS CLAIMED IS:

1. A method for introducing a mutation into a predefined site in a target nucleic acid molecule, comprising the steps of: A) incubating said target molecule in the presence of a first oligonucleotide primer, said first primer: i) being capable of hybridizing to said target molecule at a site on a first strand of said target molecule spanning said predefined site; ii) containing said mutation; and iii) containing a segment whose sequence contains at least one dU residue;

B) permitting the oligonucleotide dependent extension of said first primer to thereby obtain a first primer extension product;

C) incubating said first primer extension product with a second oligonucleotide primer, said second primer: i) being capable of hybridizing to said first primer extension product; and ii) containing a segment whose sequence has at least one dU residue, wherein said segment has a sequence complementary to the sequence of said first primer; and

D) permitting the oligonucleotide dependent extension of said second primer to thereby obtain a second primer extension product.

2. The method of claim 1, wherein said oligonucleotide dependent extension is performed as a polymerase chain reaction.

3. The method of claim 1, wherein said target molecule is a circular molecule.

4. The method of claim 1, wherein said target molecule is a linear molecule.

5. The method of claim 5, wherein said linear molecule was formed by the linearization of a vector molecule.

6. The method of claim 5, wherein said linear molecule contains a part of a vector molecule.

7. The method of claim 1, wherein said target molecule is double-stranded DNA.

8. The method of claim 1, wherein said target molecule is single-stranded DNA.

9. The method of claim 1, wherein said target molecule is cDNA.

10. The method of claim 1, wherein said target molecule is double-stranded RNA.

11. The method of claim 1 , wherein said target molecule is single-stranded RNA.

12. The method of claim 1, wherein said target molecule is cDNA.

13. The method of claim 1, which additionally includes the steps:

E) forming a further extension product of said first extension product such that said further extension product additionally contains a segment complementary to said dU- containing segment of said second primer; F) treating said further extension product and said second extension product under conditions sufficient to remove the dU-containing segments of said molecules; and G) permitting said further extension product and said second extension product to hybridize with one another, to thereby form a target double-stranded DNA molecule having said introduced mutation in said predefined site.

14. The method of claim 13, wherein said at least one dU residue is removed using UDG.

15. The method of claim 13, wherein, in step E, said further extension product is formed through the extension of said first extension product using said second extension product as a template.

16. The method of claim 13, wherein, in step E, said further extension product is formed through the oligonucleotide dependent extension of said first primer using said second extension product as a template.

17. A method for introducing a mutation into a predefined site in a target double-stranded DNA molecule, comprising the steps of:

A) incubating a first strand of said target molecule in the presence of a first oligonucleotide primer, said first primer: i) being capable of hybridizing to said target molecule at a site on said first strand of said target molecule spanning said predefined site; ii) containing said mutation; and iii) containing a segment whose sequence has at least one dU residue;

B) permitting the oligonucleotide dependent extension of said first primer to thereby obtain a first primer extension product; C) incubating a second strand of said target molecule in the presence of a second oligonucleotide primer, said second primer being capable of hybridizing to said target molecule at a site on said second strand of said target molecule, and containing a segment having at least one dU residue, wherein said segment has a sequence complementary to the sequence of said first primer;

D) permitting the oligonucleotide dependent extension of said second primer to thereby obtain a second primer extension product;

E) incubating said first primer extension product in the presence of a third oligonucleotide primer, said third primer being capable of hybridizing to said first primer extension product, and containing a segment having at least one dU residue; and

F) permitting the oligonucleotide dependent extension of said third primer to thereby form a third primer extension product.

18. The method of claim 17, which additionally includes the steps:

G) forming a further extension product of said first extension product such that said further extension product additionally contains a segment complementary to said dU- containing segment of said third primer;

H) incubating said second primer extension product in the presence of a fourth oligonucleotide primer, said fourth primer being capable of hybridizing to said second primer extension product, and containing a segment at its 5¹ terminus whose sequence contains at least one dU residue, wherein said segment has a sequence complementary to the sequence of said second primer; and

I) permitting the oligonucleotide dependent extension of said fourth primer to thereby obtain a fourth primer extension product.

19. The method of claim 18, which additionally includes the steps:

J) forming a further extension product of said second extension product such that said further extension product additionally contains a segment complementary to said dU- containing segment of said fourth primer; K) treating said first and second further extension product and said third and fourth extension product under conditions sufficient to remove the dU-containing segments of said molecules; and

L) permitting said further extension product and said second extension product to hybridize with one another, to thereby form a target double-stranded DNA molecule having said introduced mutation in said predefined site.

20. The method of claim 17, wherein said oligonucleotide dependent extension is performed as a polymerase chain reaction.

21. The method of claim 18, wherein in step G said further extension product is formed through the extension of said first extension product using said third extension product as a template.

22. The method of claim 18, wherein in step G said further extension product is formed through the oligonucleotide dependent extension of said first primer using said third extension product as a template.

23. The method of claim 19, wherein in step J said further extension product is formed through the extension of said second extension product using said fourth extension product as a template.

24. The method of claim 19, wherein in step J said further extension product is formed through the oligonucleotide dependent extension of said second primer using said fourth extension product as a template.

25. The method of claim 19, wherein said at least one dU residue is removed using UDG.

26. The method of claim 17, wherein said target molecule is a circular molecule.

27. The method of claim 17, wherein said target molecule is a linear molecule.

28. The method of claim 27, wherein said linear molecule was formed by the linearization of a vector molecule.

29. The method of claim 27, wherein said linear molecule contains a part of a vector molecule.

30. The method of claim 27, wherein said linear molecule consists essentially of said target molecule.

31. The method of claim 17, wherein said target molecule is double-stranded DNA.

32. The method of claim 17, wherein said target molecule is single-stranded DNA.

33. The method of claim 17, wherein said target molecule is cDNA.

34. The method of claim 17, wherein said target molecule is double-stranded RNA.

35. The method of claim 17, wherein said target molecule is single-stranded RNA.