Wild-type RNA Microhelix^Ala and 3:70 Variants: Molecular Dynamics Analysis of Tightly Bound Water and Local Helical Structure

Nagan, M. C.; Kerimo, S. S.; Musier-Forsyth, K.; Cramer, C. J.
J. Am. Chem. Soc. 1999, 121, 7310.

Molecular dynamics simulations of RNA microhelix^Ala indicate that G:U and other 3:70 purine:pyrimidine wobble pairs induce local deviations from A-form geometry in their respective microhelices; the helix is underwound at the base-pair step above and overwound at the base-pair step below, in each case by about 7 to 9 degrees compared to canonical A-form RNA. Based on analysis of average water densities and residence lifetimes, the wild-type microhelix strongly binds a water molecule in the minor groove of the 3:70 base pair, consistent with crystallographic analyses of an RNA duplex derived from the acceptor stem of Escherichia coli tRNA^Ala. Other wobble pairs show water binding at this position but to a lesser degree; the strength of water binding correlates directly with the measured aminoacylation activities of the microhelices as substrates for E. coli alanyl-tRNA synthetase (G:U > 2AA:IsoC > G:dU > I:U). Watson-Crick base pairs at the 3:70 position show no tendency towards specific hydration. This tightly bound minor-groove water in the microhelices with 3:70 wobble pairs evidently does not function to stabilize a particular local helical structure, but it may play a role as a specific recognition element or serve as an indicator of interaction specificity between the microhelix and a hydroxylated residue of the aminoacyl-tRNA synthetase.

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