Nucleic Acids Research Advance Access published online on May 25, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm274
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The electrostatic characteristics of G·U wobble base pairs
1Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA, 2Department of Physics, Florida State University, Tallahassee, FL 32306-4390, USA and 3Institute of Molecular Biophysics Florida State University, Tallahassee, FL 32306-4390, USA
*To whom correspondence should be addressed. Marcia O. Fenley. Tel: +1-850-644-7961; Fax: +1-850-644-7244; Email: mfenley{at}sb.fsu.edu Corrpondence may also be addressed to Nancy L. Greenbaum. Tel: +1-850-644-2005; Fax: +1-850-644-8281; Email: nancy{at}chem.fsu.edu
Received January 13, 2007. Revised April 3, 2007. Accepted April 11, 2007.
G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson–Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G·U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G·U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G·U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G·U sites in RNA are most likely to bind cationic ligands.
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