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Nucleic Acids Research Advance Access originally published online on April 24, 2009
Nucleic Acids Research 2009 37(12):3887-3896; doi:10.1093/nar/gkp257
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Nucleic Acids Research, 2009, Vol. 37, No. 12 3887-3896
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA

Suzette A. Pabit, Xiangyun Qiu, Jessica S. Lamb, Li Li, Steve P. Meisburger and Lois Pollack*

School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA

*To whom correspondence should be addressed. Tel: +1 607 255 8695; Fax: +1 607 255 7658; Email: lp26{at}cornell.edu

Received January 27, 2009. Revised April 6, 2009. Accepted April 7, 2009.

The recent discovery of the RNA interference mechanism emphasizes the biological importance of short, isolated, double-stranded (ds) RNA helices and calls for a complete understanding of the biophysical properties of dsRNA. However, most previous studies of the electrostatics of nucleic acid duplexes have focused on DNA. Here, we present 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 (25 bp) dsDNA and RNA molecules of comparable sequence. Consistent with theoretical predictions, we find counterion mediated screening to be more efficient for dsRNA than dsDNA. Furthermore, the topology of the RNA A-form helix alters the spatial distribution of counterions relative to B-form DNA. The experimental results reported here agree well with ion-size-corrected non-linear 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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