Quantitative Gamma-HCNCH: Determination of the Glycosidic Torsion Angle Chi in RNA Oligonucleotides from the Analysis of CH Dipolar Cross-correlated Relaxation by Solution NMR Spectroscopy

Overview

Journal J Biomol NMR

Publisher Springer

Specialties Molecular Biology
Nuclear Medicine

Date 2007 Jul 21

PMID 17641824

Citations 10

Authors

Jorg Rinnenthal

Christian Richter

Jan Ferner

Elke Duchardt

Harald Schwalbe

Affiliations

Soon will be listed here.

Abstract

A novel NMR pulse sequence is introduced to determine the glycosidic torsion angle chi in (13)C,(15)N-labeled oligonucleotides. The quantitative Gamma-HCNCH measures the dipolar cross-correlated relaxation rates Gamma(DD,DD)(C8H8,C1'H1') (pyrimidines) and Gamma(DD,DD)(C6H6,C1'H1') (purines). Cross-correlated relaxation rates of a (13)C,(15)N-labeled RNA 14mer containing a cUUCGg tetraloop were determined and yielded chi-angles that agreed remarkably well with data derived from the X-ray structure of the tetraloop. In addition, the method was applied to the larger stemloop D (SLD) subdomain of the Coxsackievirus B3 cloverleaf 30mer RNA and the effect of anisotropic rotational motion was examined for this molecule. It could be shown that the chi-angle determination especially for nucleotides in the anti conformation was very accurate and the method was ideally suited to distinguish between the syn and the anti-conformation of all four types of nucleotides.

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