DNA base order parameter determination without influence of chemical exchange

Binhan Yu, Xi Wang, Tianzhi Wang, Junji Iwahara

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool used to investigate the dynamic properties of biological macromolecules and their complexes. NMR relaxation data can provide order parameters S2, which represent the mobility of bond vectors reorienting within a molecular frame. Determination of S2 parameters typically involves the use of transverse NMR relaxation rates. However, the accuracy in S2 determination can be diminished by elevation of the transverse relaxation rates through conformational or chemical exchange involving protonation/deprotonation or non-Watson-Crick base-pair states of nucleic acids. Here, we propose an approach for determination of S2 parameters without the influence of exchange processes. This approach utilizes transverse and longitudinal 13C chemical shift anisotropy (CSA) – dipole–dipole (DD) cross-correlation rates instead of 13C transverse relaxation rates. Anisotropy in rotational diffusion is taken into consideration. An application of this approach to nucleotide base CH groups of a uniformly 13C/15N-labeled DNA duplex is demonstrated.

Original languageEnglish (US)
Pages (from-to)1-9
Number of pages9
JournalMethods
Volume210
DOIs
StatePublished - Feb 2023
Externally publishedYes

Keywords

  • Chemical exchange
  • Cross-correlation
  • NMR relaxation
  • Nucleic acids
  • Structural dynamics

ASJC Scopus subject areas

  • Molecular Biology
  • General Biochemistry, Genetics and Molecular Biology

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