Method for sequence determination using NMR
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.
1. 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 oligosaccharide sequences based on the set of properties of the oligosaccharide,
wherein the oligosaccharide is a heparin/heparan sulfate (HSGAG) oligosaccharide.
2. The method of claim 1 , wherein the NMR spectroscopy includes a measure of the monosaccharide composition of the oligosaccharide.
3. The method of claim 1 , further comprising a data structure which represents the properties as non-character values.
4. The method of claim 3 , wherein the data structure includes a value for each type of monosaccharide.
5. The method of claim 3 , wherein the data structure encodes a value for each type of disaccharide linkage.
6. The method of claim 3 , wherein the values are binary.
7. The method of claim 1 , wherein the NMR spectroscopy includes the determination of the sulfation pattern of the oligosaccharide or fragments thereof.
8. The method of claim 1 , wherein the NMR spectroscopy is COSY, TOCSY, HSQC, DQF-COSY, NOESY, ROESY or a combination thereof.
9. The method of claim 1 , wherein the NMR spectroscopy is 1D proton or 2D COSY/TOCSY.
10. The method of claim 1 , wherein the NMR spectroscopy is performed on the oligosaccharide in a fragmented form.
11. The method of claim 10 , wherein the fragmented form is produced by enzymatic digestion.
12. The method of claim 11 , wherein the enzymatic digestion is with a heparinase, glucuronidase, iduronidase or sulfatase.
13. The method of claim 11 , wherein the enzymatic digestion is complete.
14. The method of claim 1 , wherein the NMR spectroscopy is performed on the oligosaccharide in its intact form.
15. The method of claim 1 , wherein the second type of disaccharide linkage is measured by capillary electrophoresis.
16. The method of claim 1 , wherein the second experimental method includes chemical degradation.
17. The method of claim 1 , wherein the second experimental method includes end-labeling.
18. The method of claim 1 , wherein the second experimental method distinguishes the reducing and non-reducing ends of the oligosaccharide or fragments thereof.
19. The method of claim 1 , 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 with a heparinase, glucuronidase, iduronidase or sulfatase.
22. The method of claim 20 , wherein the enzymatic digestion is complete.