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
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 ……
Structure and nomenclature of nucleic acid bases and sugars
Oligonucleotide chain (sugar-phosphate backbone) Oligonucleotide chain (phosphate-sugar chain)
The Watson-Crick base pairs The non Watson-Crick base pairs
The structures of DNA The structures of DNA
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
Nucleic acids: RNA and DNA Ribonucleic Acids (RNA) composed by adenosine, guanosine, cytidine, uridine
Spectra of nucleosides in DMSO-d6 www.aist.go.jp/RIODB/SDBS/menu-e.html Adenosine Cytidine Guanosine Uridine
Deoxyribonucleic Acids (DNA) composed by deoxyadenosine, deoxyguanosine, deoxycytidine, thymidine
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
Structure and nomenclature of furanose and deoxyfuranose
Sugar-phosphate backbone conformation
The conformation of glycosidic bond
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
The Application of Chemical Shift Proton magnetic resonance studies on the nonexchangeable protons of ribosyl ApApGpCpUpU Biochemistry, 14 (1975) 4847-4863 & 4864-4869.
Biopolymers, 15 (1976) 2277-2286.
The Application of Coupling Constant
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.
The Application of T1 Internal loop vs. hairpin Biochemistry, 27 (1988) 3024-3031.
Methods 2D COSY or DQF-COSY 2D TOCSY 2D NOESY 2D E.COSY 2D PE.COSY
Assignments based on structure
K. C. Wuthrich, NMR of Proteins and Nucleic Acids, John Wiley & Sons (1986)
The Study of Triplex Formation of TCTCTCCTCTCTAGAGAG
The assignment
Biophysical J., (2002) 82, 3170-3180.
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/htbooks/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. 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.22:350-380 (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