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Dynamics of large elongated RNA by NMR carbon relaxation.

Publication ,  Journal Article
Hansen, AL; Al-Hashimi, HM
Published in: J Am Chem Soc
December 26, 2007

We present an NMR strategy for characterizing picosecond-to-nanosecond internal motions in uniformly 13C/15N-labeled RNAs that combines measurements of R1, R1rho, and heteronuclear 13C{1H} NOEs for protonated base (C2, C5, C6, and C8) and sugar (C1') carbons with a domain elongation strategy for decoupling internal from overall motions and residual dipolar coupling (RDC) measurements for determining the average RNA global conformation and orientation of the principal axis of the axially symmetric rotational diffusion. TROSY-detected pulse sequences are presented for the accurate measurement of nucleobase carbon R1 and R1rho rates in large RNAs. The relaxation data is analyzed using a model free formalism which takes into account the very high anisotropy of overall rotational diffusion (Dratio approximately 4.7), asymmetry of the nucleobase CSAs and noncollinearity of C-C, C-H dipolar and CSA interactions under the assumption that all interaction tensors for a given carbon experience identical isotropic internal motions. The approach is demonstrated and validated on an elongated HIV-1 TAR RNA (taum approximately 18 ns) both in free form and bound to the ligand argininamide (ARG). Results show that, while ARG binding reduces the amplitude of collective helix motions and local mobility at the binding pocket, it leads to a drastic increase in the local mobility of "spacer" bulge residues linking the two helices which undergo virtually unrestricted internal motions (S2 approximately 0.2) in the ARG bound state. Our results establish the ability to quantitatively study the dynamics of RNAs which are significantly larger and more anisotropic than customarily studied by NMR carbon relaxation.

Duke Scholars

Published In

J Am Chem Soc

DOI

EISSN

1520-5126

Publication Date

December 26, 2007

Volume

129

Issue

51

Start / End Page

16072 / 16082

Location

United States

Related Subject Headings

  • RNA
  • Nucleic Acid Conformation
  • Nuclear Magnetic Resonance, Biomolecular
  • General Chemistry
  • Carbon
  • 40 Engineering
  • 34 Chemical sciences
  • 03 Chemical Sciences
 

Citation

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Hansen, A. L., & Al-Hashimi, H. M. (2007). Dynamics of large elongated RNA by NMR carbon relaxation. J Am Chem Soc, 129(51), 16072–16082. https://doi.org/10.1021/ja0757982
Hansen, Alexandar L., and Hashim M. Al-Hashimi. “Dynamics of large elongated RNA by NMR carbon relaxation.J Am Chem Soc 129, no. 51 (December 26, 2007): 16072–82. https://doi.org/10.1021/ja0757982.
Hansen AL, Al-Hashimi HM. Dynamics of large elongated RNA by NMR carbon relaxation. J Am Chem Soc. 2007 Dec 26;129(51):16072–82.
Hansen, Alexandar L., and Hashim M. Al-Hashimi. “Dynamics of large elongated RNA by NMR carbon relaxation.J Am Chem Soc, vol. 129, no. 51, Dec. 2007, pp. 16072–82. Pubmed, doi:10.1021/ja0757982.
Hansen AL, Al-Hashimi HM. Dynamics of large elongated RNA by NMR carbon relaxation. J Am Chem Soc. 2007 Dec 26;129(51):16072–16082.
Journal cover image

Published In

J Am Chem Soc

DOI

EISSN

1520-5126

Publication Date

December 26, 2007

Volume

129

Issue

51

Start / End Page

16072 / 16082

Location

United States

Related Subject Headings

  • RNA
  • Nucleic Acid Conformation
  • Nuclear Magnetic Resonance, Biomolecular
  • General Chemistry
  • Carbon
  • 40 Engineering
  • 34 Chemical sciences
  • 03 Chemical Sciences