introduction

Electrostatics play an important role in determining molecular interactions. This is particularly true for RNA as nucleic acids are highly negatively charged. However, electrostatics cannot be trivially predicted, but rather must be calculated. Due to the high charge of nucleic acids, electrostatics must be calculated using the nonlinear Poisson-Boltzmann (NLPB) equation by the program Qnifft, which is available for download.

The electrostatics of RNA can be described in two ways. One way is to describe the potential field surrounding the molecule. Areas of constant potential are shown as isopotential contours around the molecule. It would be expected that these isopotential contours should follow the general shape of the molecule. Although this is mostly true, there appear regions of less negative potential, in essence creating an "isopotential hole," a phenomenon first observed in Sharp et. al., 1990. The second representation is through visualization of surface potentials. These describe areas where electrostatic interactions may occur. For example, areas of large negative charge may signify a metal-binding site.

isopotential contours

When the isopotential contour of yeast tRNA^phe had previously been visualized (Sharp et. al., 1990), there were very few other RNA structures to study. However, in recent years there has been an explosion in the number of RNA structures solved. This, in addition to improved computing power and NLPB solving algorithms, allowed us to undertake a new study on the potentials of RNAs. As a control the yeast tRNA^phe was reanalyzed and the same isopotential holes were seen at the anticodon loop and the amino-acylation end (Fig. 1).

More recent structures were also analyzed for the presence of isopotential holes. Among the most important motifs found in RNA structure is the GNRA tetraloop. Electrostatic analysis of this structure shows a large isopotential hole over the second position of the tetraloop (Fig. 2). It is at this position which both RNAs and proteins interact with the tetraloop.

Other structures were analyzed for isopotential holes. There were potential holes found at the ends of RNA double helices, in the GNRA tetraloop receptor, in the sarcin-ricin loop, and in the MMTV pseudoknots. Each of the positions contains some biological significance, whether it'd be for RNA-RNA interactions or RNA-protein interactions. For further information, see Chin et. al, 1999.

surface potentials

Surface potentials represent a different form of electrostatic analysis. The study of the surface may elucidate areas of unusual negative or positive potential. These in turn may indicate areas where there will be RNA interactions. As a control the basic forms of Watson-Crick base paired nucleic acids were analyzed (Fig. 3) as well as commonly found non-Watson-Crick motifs (Fig. 4).

The most useful aspect of using surface potentials to study RNA structures is the prediction of metal-binding sites. Metals, in particular the divalent cation Mg²⁺, are known to play critical roles in RNA structure and catalysis. Structures with known metal binding sites were analyzed to see if those sites could be predicted. The metal sites for the p456 domains of a group I intron (Fig. 5), the loop E of 5S rRNA, and yeast tRNA^phe were accurately predicted, as well as other possible sites not previously reported in literature (Chin et. al., 1999).