Structure determination: Nucleic acid May 13, 2004 TIGP Chemical Biology and Molecular Biophysics Lou-Sing Kan, Ph. D. Institute of Chemistry

Structure and nomenclature of nucleic acid bases and sugars

Oligonucleotide chain (sugar-phosphate backbone)

The Watson-Crick base pairs The non Watson-Crick base pairs

The structures of DNA

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

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

Spectra of nucleosides in DMSO-d6 Adenosine Cytidine Guanosine Uridine

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

Comparison of nucleoside and deoxyribonucleoside in DMSO-d6 Comparison of nucleoside in DMSO-d6 and D2O Adenosine Deoxyadenosine 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)

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

Biopolymers, 15 (1976)

The Application of Coupling Constant

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

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

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

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,

References Edwin D. Becker High Resolution NMR, Theory and Chemical Applications, 3rd Edition Academic Press, Ray Freeman Magnetic Resonance in Chemistry And Medicine Oxford, 2003 Joseph P. Hornak The Basic of NMR General T.C. Farrar An Introduction To Pulse NMR Spectroscopy Farragut Press, Chicago, H. Gunther "Modern pulse methods in high-resolution NMR spectroscopy." Angew. Chem.. Int. Ed. Engl.22: (1983) Basic Pulse 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, D NMR Peter Bigler NMR Spectroscopy Processing Strategies VCH, 1997 Data Process H. Duddeck, W. Dietrich Structure Elucidation by Modern NMR, A Workbook Springer-Verlag, 1989 Application: small molecules Kurt Wuthrich NMR of Proteins and Nucleic Acids John Wiley & Sons, 1986 C. A. G. Haasnoot NMR in Conformation Analysis of Bio-organic Molecules Application: Peptides and Proteins Application: Nucleic Acids G. C. K. Roberts NMR of Macromolecules, A Practical Approach IRL Press, Application: Others 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 Dictionary