Building of RNA and DNA double helices into electron density.
A method has been developed that automatically fits double-helical regions into the electron density of nucleic acid structures. Rigid fragments consisting of two Watson-Crick base pairs and three pairs of phosphate groups in the A-type or B-type conformation are positioned into the electron density by phased rotation and translation functions. The position and orientation of the localized double-helical fragments are determined by phased refinement. The method has been tested by building double-helical regions of nine RNA structures of variable crystallographic resolution and polynucleotide length and is available for free use.
Pavelcik
Frantisek
F
Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences in Brno, CZ-61242 Brno, Czech Republic. pavelcikf@vfu.cz
Schneider
Bohdan
B
D020029:Base Pairing; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software; D055672:Static Electricity
D012313:RNA; D004247:DNA