MACINETIC RESONANCE ELSEVIER Progress in Nuclear Magnetic Resonance Spectroscopy 32(1998)287-387 The use of nmr methods for conformational studies of nucleic acids Sybren S. Wijmenga*, Bernd N M. van Buuren Umed University, Department of Medical Biochemistry and Biophysics, S 90187 Umed, Sweden Received 10 July 1997 Contents Introduction 2. RNA and DNA synthesis and purification 3. Nomenclature 4. Distances 291 4. 1. Overview of short distances and their general characteristics 4.2. Overview of structurally important intra-nucleotide distances 4.3. Overview of structurally important sequential and cross-strand distances 4.4. Derivation of distances from NOESY spectra and structure characterization using distances 4.5. Conclusion 5. J-couplings 5.1. JHC- and Jcc-couplings 5.2. Overview of J-couplings in the bases 5.3. Ribose sugar 5.4. Determination of the B torsion angle 310 5.5. Determination of the e torsion angle 312 5. 7. x orison angle and JHc sugar to base eo specific assignment 5.6. Torsion angle y and H5 and H5" ste 316 5.8. Measurement of homo- and heteronuclear J-coupling constants 5.8.1. Determination of J-couplings from the shape of the signal 5.8.2. Determination of J-couplings from E COSY patterns 18 5.8. 1. Homonuclear E cosy 318 5.8.2.2. Heteronuclear E cosY 5.8.2.2.1. Determination of JHP- and Jcp-couplings 5.8.2.2.2. Determination of JHc-couplings 5.8.2.2.3. Determination of JHH-couplings via HCC-E. COSY spectra 5.8.3. Determination of J-couplings from signal intensities 321 5.8.3. 1. Determination of JHH-couplings from homonuclear(H, H) TOCSY transfer 5.8.3.2. Determination of J-couplings from heteronuclear experiments Corresponding author. Tel: +469078 6500; fax: +469013 6310, mail: sybren a indigo. chem.umuse 0022-2860798/$19.00@ 1998 Published by Elsevier Science B v. All rights reserved PS0079-6565(97)00023-XThe use of NMR methods for conformational studies of nucleic acids Sybren S. Wijmenga*, Bernd N.M. van Buuren Umea˚ University, Department of Medical Biochemistry and Biophysics, S 901 87 Umea˚, Sweden Received 10 July 1997 Progress in Nuclear Magnetic Resonance Spectroscopy 32 (1998) 287–387 0022-2860/98/$19.00 q 1998 Published by Elsevier Science B.V. All rights reserved PII S0079-6565(97)00023-X * Corresponding author. Tel: +46 9078 6500; fax: +46 9013 6310; e-mail: sybren@indigo.chem.umu.se Contents 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288 2. RNA and DNA synthesis and purification . . . . . . . . . . . . . . . . . . . . . . . . . 290 3. Nomenclature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291 4. Distances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291 4.1. Overview of short distances and their general characteristics . . . . . . . . . . . . . . . . 292 4.2. Overview of structurally important intra-nucleotide distances . . . . . . . . . . . . . . . . 294 4.3. Overview of structurally important sequential and cross-strand distances . . . . . . . . . . . 295 4.4. Derivation of distances from NOESY spectra and structure characterization using distances . . . 295 4.5. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304 5. J-couplings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305 5.1. 1 JHC- and 1 JCC-couplings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307 5.2. Overview of J-couplings in the bases . . . . . . . . . . . . . . . . . . . . . . . . . 307 5.3. Ribose sugar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307 5.4. Determination of the b torsion angle. . . . . . . . . . . . . . . . . . . . . . . . . . 310 5.5. Determination of the e torsion angle . . . . . . . . . . . . . . . . . . . . . . . . . . 312 5.6. Torsion angle g and H59 and H599 stereo specific assignment. . . . . . . . . . . . . . . . 314 5.7. x torison angle and 3 JHC sugar to base . . . . . . . . . . . . . . . . . . . . . . . . . 316 5.8. Measurement of homo- and heteronuclear J-coupling constants . . . . . . . . . . . . . . . 316 5.8.1. Determination of J-couplings from the shape of the signal . . . . . . . . . . . . . . 316 5.8.2. Determination of J-couplings from E.COSY patterns . . . . . . . . . . . . . . . . 318 5.8.2.1. Homonuclear E.COSY . . . . . . . . . . . . . . . . . . . . . . . . 318 5.8.2.2. Heteronuclear E.COSY . . . . . . . . . . . . . . . . . . . . . . . . 319 5.8.2.2.1. Determination of JHP- and JCP-couplings . . . . . . . . . . . . 319 5.8.2.2.2. Determination of JHC-couplings . . . . . . . . . . . . . . . . 320 5.8.2.2.3. Determination of JHH-couplings via HCC-E.COSY spectra . . . . . 320 5.8.3. Determination of J-couplings from signal intensities . . . . . . . . . . . . . . . . 321 5.8.3.1. Determination of JHH-couplings from homonuclear (H,H) TOCSY transfer . . . 321 5.8.3.2. Determination of J-couplings from heteronuclear experiments . . . . . . . . 321