Anion binding to nucleic acids.
Nucleic acids are generally considered as efficient cation binders. Therefore, the likelihood that negatively charged ions might intrude their first hydration shell is rarely considered. Here, we show on the basis of (i) a survey of the Nucleic Acid Database, (ii) several structures extracted from the Cambridge Structural Database, and (iii) molecular dynamics simulations, that the nucleotide electropositive edges involving mainly amino, imino, and hydroxyl groups can cast specific anion binding sites. These binding sites constitute also good locations for the binding of the negatively charged groups of the Asp and Glu residues or the nucleic acid phosphate groups. Furthermore, it is observed in several instances that anions, like water molecules and cations, do mediate protein/nucleic acid interactions. Thus, anions as well as negatively charged groups are directly involved in specific recognition and folding phenomena involving polyanionic nucleic acids.
Auffinger
Pascal
P
Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, UPR 9002, 15, rue René Descartes, 67084 Strasbourg Cedex, France. p.auffinger@ibmc.u-strasbg.fr
Bielecki
Lukasz
L
Westhof
Eric
E
D000838:Anions / Q000737:chemistry / Q000378:metabolism*; D003198:Computer Simulation; D030561:Databases, Nucleic Acid; D008958:Models, Molecular; D009696:Nucleic Acids / Q000737:chemistry / Q000378:metabolism*; D014961:X-Ray Diffraction
D000838:Anions; D009696:Nucleic Acids