CA2486456A1 - Method for sequence determination using nmr - Google Patents

Method for sequence determination using nmr Download PDF

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Publication number
CA2486456A1
CA2486456A1 CA002486456A CA2486456A CA2486456A1 CA 2486456 A1 CA2486456 A1 CA 2486456A1 CA 002486456 A CA002486456 A CA 002486456A CA 2486456 A CA2486456 A CA 2486456A CA 2486456 A1 CA2486456 A1 CA 2486456A1
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CA
Canada
Prior art keywords
oligosaccharide
nmr spectroscopy
measurement
experimental
type
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
Application number
CA002486456A
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French (fr)
Other versions
CA2486456C (en
Inventor
Ram Sasisekharan
Ganesh Venkataraman
Rahul Raman
Benito Casu
Giangiacomo Torri
Marco Guerrini
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Istituto Scientifico di Chimica e Biochimica G Ronzoni
Massachusetts Institute of Technology
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Individual
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Publication of CA2486456A1 publication Critical patent/CA2486456A1/en
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Publication of CA2486456C publication Critical patent/CA2486456C/en
Anticipated expiration legal-status Critical
Expired - Fee Related legal-status Critical Current

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N24/00—Investigating or analyzing materials by the use of nuclear magnetic resonance, electron paramagnetic resonance or other spin effects
    • G01N24/08—Investigating or analyzing materials by the use of nuclear magnetic resonance, electron paramagnetic resonance or other spin effects by using nuclear magnetic resonance
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Abstract

The invention relates to methods for analyzing polysaccharides. In particular, compositional and sequence information about the polysaccharides are derived.
Some methods use NMR in conjunction with another experimental method, such as, capillary electrophoretic techniques for the analysis.

Claims (28)

1. A method of determining the composition of an oligosaccharide, comprising:
obtaining a measurement of a first property of the oligosaccharide using NMR
spectroscopy, and obtaining a measurement of a second property of the oligosaccharide by a second experimental method, wherein the first and second properties determine the composition.
2. The method of claim 1, wherein the second property of the oligosaccharide is measured by capillary electrophoresis.
3. A method of analyzing an oligosaccharide, comprising: obtaining a measurement of a first type of disaccharide linkage of the oligosaccharide by a first experimental method, and obtaining a measurement of a second type of disaccharide linkage of the oligosaccharide by a second experimental method, to analyze the oligosaccharide.
4. The method of claim 3, wherein the first type of disaccharide linkage is measured by NMR spectroscopy.
5. The method of claim 3, wherein the second type of disaccharide linkage is measured by capillary electrophoresis.
6. A method of analyzing an oligosaccharide, comprising: identifying a first property of the oligosaccharide by NMR spectroscopy, and identifying a second property of the oligosaccharide by capillary electrophoresis, to analyze the oligosaccharide.
7. The method of claim 1 or 4, further comprising: determining possible sequences of the oligosaccharide that are consistent with the measurement from the NMR spectroscopy and second experimental method.
8. The method of claim 1 or 4, further comprising: constructing a list of possible sequences based on the measurement from the NMR spectroscopy, and eliminating sequences from the list of possible sequences that are not consistent with the measurement of the second experimental method.
9. The method of claim 1, 3, 4, 7 or 8, wherein the second experimental method distinguishes the reducing and non-reducing ends of the oligosaccharide or fragments thereof.
10. The method of claim 9, wherein the second experimental method includes chemical degradation.
11. The method of claim 9, wherein the second experimental method includes end-labeling.
12. The method of claim 1, 3, 4, 7 or 8, wherein the second experimental method determines the signature of the reducing end of the oligosaccharide or fragments thereof.
13. The method of claim 12, wherein the signature of the reducing end is determined with capillary electrophoresis.
14. The method of claim 1, 2, 4, 6, 7 or 8, wherein the NMR spectroscopy includes the determination of the sulfation pattern of the oligosaccharide or fragments thereof.
15. The method of claim 1, 3, 4, 7 or 8, wherein the second experimental method allows the determination of the sulfation pattern of the second type of disaccharide linkage.
16. The method of any one of claims 1-8, further comprising: obtaining a measure of an additional property of the oligosaccharide by a third experimental method to further eliminate sequences not consistent with measurements obtained from the third experimental method.
17. The method of claim 1, 2, 4, 6, 7 or 8, wherein the NMR spectroscopy is ID
proton or 2D COSY/TOCSY.
18. The method of claim 1, 2, 4, 6, 7 or 8, wherein the NMR spectroscopy is performed on the oligosaccharide in its intact form.
19. The method of claim 1, 3, 4, 7 or 8, wherein the second experimental method includes digesting the oligosaccharide to a fragmented form.
20. The method of claim 19, wherein the fragmented form is produced by enzymatic digestion.
21. The method of claim 20, wherein the enzymatic digestion is complete.
22. The method of claim 1, wherein the NMR is performed to identify and quantify both reducing and non-reducing ends.
23. A method of generating a list of possible sequences of an oligosaccharide, comprising: defining a set of properties of the oligosaccharide by performing NMR
spectroscopy and a second experimental method, wherein the NMR spectroscopy provides a measurement of a first type of disaccharide linkage and the second experimental method provides a measurement of a second type of disaccharide linkage, and constructing a list of possible sequences based on the set of properties of the oligosaccharide.
24. The method of claim 23, wherein the NMR spectroscopy includes a measure of the monosaccharide composition of the oligosaccharide.
25. The method of claim 23, further comprising a data structure which represents the properties as non-character values.
26. The method of claim 25, wherein the data structure includes a value for each type of monosaccharide.
27. The method of claim 25, wherein the data structure encodes a value for each type of disaccharide linkage.
28. The values of claim 25, wherein the values are binary.
CA2486456A 2002-05-20 2003-05-20 Method for sequence determination using nmr Expired - Fee Related CA2486456C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US38194002P 2002-05-20 2002-05-20
US60/381,940 2002-05-20
PCT/US2003/015850 WO2004055491A2 (en) 2002-05-20 2003-05-20 Novel method for sequence determination using nmr

Publications (2)

Publication Number Publication Date
CA2486456A1 true CA2486456A1 (en) 2004-07-01
CA2486456C CA2486456C (en) 2012-07-17

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CA2486456A Expired - Fee Related CA2486456C (en) 2002-05-20 2003-05-20 Method for sequence determination using nmr

Country Status (6)

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US (4) US7508206B2 (en)
EP (1) EP1590648A4 (en)
JP (2) JP4657726B2 (en)
AU (1) AU2003302219B8 (en)
CA (1) CA2486456C (en)
WO (1) WO2004055491A2 (en)

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Publication number Publication date
JP2006505799A (en) 2006-02-16
AU2003302219B2 (en) 2009-02-19
AU2003302219A1 (en) 2004-07-09
US7508206B2 (en) 2009-03-24
AU2003302219B8 (en) 2009-03-26
US8018231B2 (en) 2011-09-13
WO2004055491A2 (en) 2004-07-01
US20040092037A1 (en) 2004-05-13
EP1590648A2 (en) 2005-11-02
JP2009300452A (en) 2009-12-24
WO2004055491A8 (en) 2007-05-18
EP1590648A4 (en) 2007-04-18
US20090045811A1 (en) 2009-02-19
US20080278164A1 (en) 2008-11-13
JP4657726B2 (en) 2011-03-23
CA2486456C (en) 2012-07-17
WO2004055491A3 (en) 2007-04-05
US20100216176A1 (en) 2010-08-26
US7728589B2 (en) 2010-06-01
US7737692B2 (en) 2010-06-15

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