Study of nucleic acid structure by novel NMR methods

Bax, Ad -

Abstract

Upon alignment of oligonucleotides in a magnetic field, the downfield, TROSY-component of the 13C-1H doublet changes its resonance frequency as a result of residual dipolar 13C-1H dipolar coupling (RDC) and residual 13C chemical shift anisotropy (RCSA), and the sum of these two second rank tensors is referred to as the pseudo-CSA. The experimentally measured difference in the resonance frequency of the 13C TROSY component in the aligned and isotropic samples is referred to as residual pseudo-CSA (RPCSA), and it can be used directly as a restraint during structure calculation. Because measurement of the RPCSA involves detection of the narrow TROSY 13C doublet component, it is applicable to systems with larger rotational correlation times than RDC measurement. The method is demonstrated for structure refinement of the helical region of a 24-nt stem-loop segment or ribosomal helix 35, uniformly enriched in 13C and 15N, with RPCSA values measured at 5 and 25 C. Substantial cross-validated improvements in structural accuracy are obtained upon incorporation of RPCSA restraints.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
• Type: Intramural Research (Z01)
• Project #: 1Z01DK029051-01
• Application #: 7593499
• Support Year: 1
• Fiscal Year: 2007
• Total Cost: $325,243

Institution

• Name: National Institute of Diabetes and Digestive and Kidney Diseases
• Country: United States

Publications

Tolbert, Blanton S; Miyazaki, Yasuyuki; Barton, Shawn et al. (2010) Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement. J Biomol NMR 47:205-19

Ying, Jinfa; Chill, Jordan H; Louis, John M et al. (2007) Mixed-time parallel evolution in multiple quantum NMR experiments: sensitivity and resolution enhancement in heteronuclear NMR. J Biomol NMR 37:195-204

Ying, Jinfa; Grishaev, Alexander; Latham, Michael P et al. (2007) Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field. J Biomol NMR 39:91-6

Grishaev, Alexander; Ying, Jinfa; Bax, Ad (2006) Pseudo-CSA restraints for NMR refinement of nucleic acid structure. J Am Chem Soc 128:10010-1

Ying, Jinfa; Grishaev, Alexander; Bryce, David L et al. (2006) Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements. J Am Chem Soc 128:11443-54

Ying, Jinfa; Bax, Ad (2006) 2'-hydroxyl proton positions in helical RNA from simultaneously measured heteronuclear scalar couplings and NOEs. J Am Chem Soc 128:8372-3

Ying, Jinfa; Grishaev, Alexander; Bax, Ad (2006) Carbon-13 chemical shift anisotropy in DNA bases from field dependence of solution NMR relaxation rates. Magn Reson Chem 44:302-10