Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.
Solutions to the nonlinear Poisson-Boltzmann equation were used to obtain the electrostatic potentials of RNA molecules that have known three-dimensional structures. The results are described in terms of isopotential contours and surface electrostatic potential maps. Both representations have unexpected features: 'cavities' within isopotential contours and areas of enhanced negative potential on molecular surfaces. Intriguingly, the sites of unusual electrostatic features correspond to functionally important regions, suggesting that electrostatic properties play a key role in RNA recognition and stabilization. These calculations reveal that the electrostatic potentials generated by RNA molecules have a variety of functionally important characteristics that cannot be discerned by simple visual inspection of the molecular structure.
Chin
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Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, Box 36, New York, New York 10032, USA.
Sharp
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Honig
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Pyle
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D000926:Anticodon / Q000737:chemistry; D020029:Base Pairing; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D030541:Databases, Genetic; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D055672:Static Electricity; D013329:Structure-Activity Relationship
D000926:Anticodon; D012313:RNA; D004247:DNA