Abstract
Action of short double-stranded RNA (dsRNA) helices is a key component in the RNA interference mechanism. Since past theoretical and experimental work on nucleic acid electrostatics mainly focused on DNA, we conducted a comparative investigation of electrostatic effects in RNA and DNA. Using resonant (anomalous) and non-resonant small-angle x-ray scattering, we characterized the charge screening efficiency and counterion distribution around short (25bp) double-stranded DNA and RNA molecules of comparable sequence. Compared to dsDNA, we find that dsRNA molecules appear charge neutral on shorter length scales under conditions of lower bulk salt concentrations. The experimental results agree well with ion-size-corrected nonlinear Poisson-Boltzmann calculations. We propose that differences in electrostatic properties aid in selective recognition of different types of short nucleic acid helices by target binding partners.
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