Modeling the Dynamics of a Mutated Stem-loop in the SL1 Domain of HIV-1Lai Genomic RNA by 1H-NOESY Spectra

Overview

Journal J Biomol NMR

Publisher Springer

Specialties Molecular Biology
Nuclear Medicine

Date 2001 Sep 21

PMID 11563557

Authors

S Fausti

G La Penna

J Paoletti

D Genest

G Lancelot

A Perico

Affiliations

Soon will be listed here.

Abstract

The cross-peaks of 1H-NOESY spectra at different time delays are compared to a mode-coupling diffusion (MCD) calculation, including the evaluation of the full 1H relaxation matrix, in the case of a 23 nucleotide fragment of the stem-loop SL1 domain of HIV-1Lai genomic RNA mutated in a single position. The MCD theory gives significant agreement with 1H relaxation experiments enabling a thorough understanding of the differential local dynamics along the sequence and particularly of the dynamics of nucleotides in the stem and in the loop. The differential dynamics of this hairpin structure is important in directing the dimerization of the retroviral genome, a fundamental step in the infectious process. The demonstration of a reliable use of time dependent NOE cross-peaks, largely available from NMR solution structure determination, coupled to MCD analysis, to probe the local dynamics of biological macromolecules, is a result of general interest of this paper.

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