1. Structure determination: Nucleic acids
TIGP Chemical Biology and Molecular Biophysics
Structure determination: Nucleic acids
Lou-Sing Kan, Ph. D.
Institute of Chemistry, Academia Sinica
Department of Bioengineering,
Tatung University
April 30, 2009

2. What is NMR?
Please define
Chemical shift, coupling constant, area under peaks, relaxation times,
and nuclear Overhauser enhancement
Name the five nucleic acids bases
Adenine, cytosine, guanine, thymine, and uracil
Name the five nucleic acids nucleosides
Adenosine, cytidine, guanosine, thymidine, and uridine
The difference between ribonucleic acid and deoxyribonucleic acid ……

3. Structure and nomenclature of nucleic acid bases and sugars

4. Oligonucleotide chain (sugar-phosphate backbone)
Oligonucleotide chain (phosphate-sugar chain)

5. The Watson-Crick base pairs The non Watson-Crick base pairs

6. The structures of DNA
The structures of DNA

7. Supercoil Tetra-stranded Triple-stranded Cruciform
Other structures of nucleic acids
Hairpin loop
Bulge loop
Internal loop
Mismatch
Knots
Supercoil
Tetra-stranded
Triple-stranded
Cruciform

8. Nucleic acids: RNA and DNA
Ribonucleic Acids (RNA) composed by adenosine, guanosine, cytidine, uridine

9. Spectra of nucleosides in DMSO-d6
Adenosine
Cytidine
Guanosine
Uridine

10. Deoxyribonucleic Acids (DNA) composed by deoxyadenosine, deoxyguanosine, deoxycytidine, thymidine

11. Comparison of nucleoside and deoxyribonucleoside in DMSO-d6
Adenosine
Deoxyadenosine
Comparison of nucleoside in DMSO-d6 and D2O
Cytidine in DMSO-d6
Cytidine in D2O

12. Structure and nomenclature of furanose and deoxyfuranose

13. Sugar-phosphate backbone conformation

14. The conformation of glycosidic bond

15. Proton NMR study on two structures of 3'-O-(Acetylimino)3'-de(phosphinico)-thymidylyl-(3’,5')-deoxythymidine in aqueous solution
Tetrahedron 59 (2003)

20. The Application of Chemical Shift
Proton magnetic resonance studies on the nonexchangeable protons of ribosyl ApApGpCpUpU
Biochemistry, 14 (1975) &

23. Biopolymers, 15 (1976)

26. The Application of Coupling Constant

27. The Application of NOE
Detection of a guanine/adenine base pair in a decadeoxyribonucleotide by
proton magnetic resonance spectroscopy
(CCAAGATTGG)2
Proc. Natl. Acad. Sci., 80 (1983)
Science, 238 (1987)

29. The Application of T1 Internal loop vs. hairpin
Biochemistry, 27 (1988)

31. Methods
2D COSY or DQF-COSY
2D TOCSY
2D NOESY
2D E.COSY
2D PE.COSY

32. Assignments based on structure

33. K. C. Wuthrich, NMR of Proteins and Nucleic Acids, John Wiley & Sons (1986)

34. The Study of Triplex Formation of TCTCTCCTCTCTAGAGAG

37. The assignment

38. Biophysical J., (2002) 82,

40. References General Application: small molecules
Edwin D. Becker
High Resolution NMR, Theory and Chemical Applications, 3rd Edition
Academic Press, 2000.
Ray Freeman
Magnetic Resonance in Chemistry And Medicine
Oxford, 2003
Joseph P. Hornak
The Basic of NMR
H. Duddeck, W. Dietrich
Structure Elucidation by Modern NMR, A Workbook
Springer-Verlag, 1989
Application: Peptides and Proteins
Kurt Wuthrich
NMR of Proteins and Nucleic Acids
John Wiley & Sons, 1986
Basic Pulse NMR
Application: Nucleic Acids
T.C. Farrar An Introduction To Pulse NMR Spectroscopy Farragut Press, Chicago, 1987.
H. Gunther "Modern pulse methods in high-resolution NMR spectroscopy." Angew. Chem.. Int. Ed. Engl.22: (1983)
C. A. G. Haasnoot
NMR in Conformation Analysis of Bio-organic Molecules
Application: Others
G. C. K. Roberts
NMR of Macromolecules, A Practical Approach
IRL Press, 1995.
2D NMR
Ad Bax
Two-Dimensional Nuclear Magnetic Resonance in Liquid
Delft University Press, 1982
Richard R. Ernst, Geoffrey Bodenhausen, Alexander Wokaun
Priciples of NMR in One and Two Dimensions
Oxford, 1987
Dictionary
S. Braun, H.-O. Kalinowske, S. Berger
100 and More Basic NMR Experiments
VCH, 1996
S. W. Homans
A Dictionary of Concepts in NMR
Oxford, 1992
Handbook of High Resolution Multinuclear NMR
John Wiley & Sons, 1981
Data Process
Peter Bigler
NMR Spectroscopy Processing Strategies
VCH, 1997