Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.

ABSTRACT: Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural data sets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work, we used a combination of theoretical approaches, i.e., classical molecular dynamics simulations, multiscale quantum mechanical/molecular mechanical calculations, and enhanced sampling techniques in order to compute and interpret the differential reactivity of individual residues in several RNA motifs, including members of the mos

SUBMITTER: Mlynsky V 

PROVIDER: S-EPMC5393180 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature