Quantifying the effects of long-range 13C-13C dipolar coupling on measured relaxation rates in RNA

J Biomol NMR. 2021 May;75(4-5):203-211. doi: 10.1007/s10858-021-00368-8. Epub 2021 Apr 29.

Abstract

Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove 13C-13C dipolar couplings that complicate 13C relaxation analyses. While these phenomena are well documented for sites with adjacent 13C nuclei (e.g. ribose C1'), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) 13C-13C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-13C/15N]-ATP or selectively [2-13C]-ATP labeled RNAs. Our simulations predict non-negligible 13C-13C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R1) relaxation rates in [U-13C/15N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R1 measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-13C/15N]-ATP or [2-13C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range 13C-13C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R1 rates in terms of motional models for large RNAs.

Keywords: Dipolar coupling; Dynamics; NMR spectroscopy; Nucleic acids; Relaxation.

MeSH terms

  • Adenosine / chemistry
  • Carbon Isotopes / chemistry
  • Hepatitis B virus / genetics*
  • Humans
  • Isotope Labeling / methods
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Nucleic Acid Conformation*
  • RNA, Viral / chemistry*

Substances

  • Carbon Isotopes
  • RNA, Viral
  • Adenosine