title: Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, Box 36, New York, New York 10032, USA.
authors.forename: K
authors.initials: K
authors.lastname: Chin
authors.forename: K A
authors.initials: KA
authors.lastname: Sharp
authors.forename: B
authors.initials: B
authors.lastname: Honig
authors.forename: A M
authors.initials: AM
authors.lastname: Pyle
mesh_terms: 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
chemical_list: D000926:Anticodon; D012313:RNA; D004247:DNA