Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function

Nat Struct Biol. 1999 Nov;6(11):1055-61. doi: 10.1038/14940.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Anticodon / chemistry
  • Base Pairing
  • Computer Simulation*
  • DNA / chemistry
  • DNA / metabolism
  • Databases, Genetic
  • Hydrogen Bonding
  • Models, Molecular
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA / metabolism*
  • Software
  • Static Electricity
  • Structure-Activity Relationship


  • Anticodon
  • RNA
  • DNA