Structure determination: Nucleic acid

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TIGP Chemical Biology and Molecular Biophysics
Structure determination Nucleic acid
Lou-Sing Kan, Ph. D. Institute of Chemistry
May 13, 2004
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Structure and nomenclature of nucleic acid bases
and sugars
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Oligonucleotide chain (sugar-phosphate backbone)
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The Watson-Crick base pairs
The non Watson-Crick base pairs
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The structures of DNA
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Other structures of nucleic acids
Hairpin loop Bulge loop Internal
loop Mismatch Knots
Supercoil
Tetra-stranded
Triple-stranded
Cruciform
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Nucleic acids RNA and DNA Ribonucleic Acids
(RNA) composed by adenosine, guanosine, cytidine,
uridine
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Spectra of nucleosides in DMSO-d6
www.aist.go.jp/RIODB/SDBS/menu-e.html
Adenosine
Cytidine
Guanosine
Uridine
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Deoxyribonucleic Acids (DNA) composed by
deoxyadenosine, deoxyguanosine, deoxycytidine,
thymidine
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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
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Structure and nomenclature of furanose and
deoxyfuranose
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Sugar-phosphate backbone conformation
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The conformation of glycosidic bond
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Proton NMR study on two structures of
3'-O-(Acetylimino)3'-de(phosphinico)-thymidylyl-(3
,5')-deoxythymidine in aqueous solution
Tetrahedron 59 (2003) 1981-1988
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The Application of Chemical Shift
Proton magnetic resonance studies on the
nonexchangeable protons of ribosyl ApApGpCpUpU
Biochemistry, 14 (1975) 4847-4863 4864-4869.
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Biopolymers, 15 (1976) 2277-2286.
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The Application of Coupling Constant
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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)
4263-4265. Science, 238 (1987) 498-504.
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The Application of T1
Internal loop vs. hairpin
Biochemistry, 27 (1988) 3024-3031.
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Methods
2D COSY or DQF-COSY 2D TOCSY 2D NOESY 2D
E.COSY 2D PE.COSY
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Assignments based on structure
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K. C. Wuthrich, NMR of Proteins and Nucleic
Acids, John Wiley Sons (1986)
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The Study of Triplex Formation of
TCTCTCCTCTCTAGAGAG
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The assignment
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Biophysical J., (2002) 82, 3170-3180.
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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 http//www.cis.rit.edu/htb
ooks/nmr/bnmr.htm
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. FarrarAn Introduction To Pulse NMR
SpectroscopyFarragut Press, Chicago, 1987. H.
Gunther"Modern pulse methods in high-resolution
NMR spectroscopy."Angew. Chem.. Int. Ed.
Engl.22350-380 (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