Dataset Information

Slow conformational dynamics at C2'-endo nucleotides in RNA.

ABSTRACT: RNA molecules undergo local conformational dynamics on timescales spanning picoseconds to minutes. Slower local motions have the greater potential to govern RNA folding, ligand recognition, and ribonucleoprotein assembly reactions but are difficult to detect in large RNAs with complex structures. RNA SHAPE chemistry employs acylation of the ribose 2'-hydroxyl position to measure local nucleotide flexibility in RNA and is well-characterized by a mechanism in which each nucleotide samples unreactive (closed) and reactive (open) states. We monitor RNA conformational dynamics over distinct time domains by varying the electrophilicity of the acylating reagent. Select C2'-endo nucleotides are nonreactive toward fast reagents but reactive toward slower SHAPE reagents in both model RNAs and in a large RNA with a tertiary fold. We conclude, first, that the C2'-endo conformation by itself does not govern SHAPE reactivity. However, some C2'-endo nucleotides undergo extraordinarily slow conformational changes, on the order of 10(-4) s(-1). Due to their distinctive local dynamics, C2'-endo nucleotides have the potential to function as rate-determining molecular switches and are likely to play central, currently unexplored, roles in RNA folding and function.

SUBMITTER: Gherghe CM

PROVIDER: S-EPMC4501255 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature

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Publications

Slow conformational dynamics at C2'-endo nucleotides in RNA.

Gherghe Costin M CM Mortimer Stefanie A SA Krahn Joseph M JM Thompson Nancy L NL Weeks Kevin M KM

Journal of the American Chemical Society 20080618 28

RNA molecules undergo local conformational dynamics on timescales spanning picoseconds to minutes. Slower local motions have the greater potential to govern RNA folding, ligand recognition, and ribonucleoprotein assembly reactions but are difficult to detect in large RNAs with complex structures. RNA SHAPE chemistry employs acylation of the ribose 2'-hydroxyl position to measure local nucleotide flexibility in RNA and is well-characterized by a mechanism in which each nucleotide samples unreacti ...[more]

PMID: 18558680

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Dataset Information

Slow conformational dynamics at C2'-endo nucleotides in RNA.

Publications

Slow conformational dynamics at C2'-endo nucleotides in RNA.

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