Open AccessGeometric properties of nucleic acids with potential for autobuilding
Author(s) -
Gruene Tim,
Sheldrick George M.
Publication year - 2011
Publication title -
acta crystallographica section a
Language(s) - English
Resource type - Journals
eISSN - 1600-5724
pISSN - 0108-7673
DOI - 10.1107/s0108767310039140
Subject(s) - nucleic acid , electron density , resolution (logic) , asymmetry , dna , polymer , electron , torsion (gastropod) , rna , chemistry , molecule , crystallography , biological system , computational chemistry , chemical physics , physics , computer science , biology , quantum mechanics , biochemistry , organic chemistry , artificial intelligence , zoology , gene
Medium‐ to high‐resolution X‐ray structures of DNA and RNA molecules were investigated to find geometric properties useful for automated model building in crystallographic electron‐density maps. We describe a simple method, starting from a list of electron‐density `blobs', for identifying backbone phosphates and nucleic acid bases based on properties of the local electron‐density distribution. This knowledge should be useful for the automated building of nucleic acid models into electron‐density maps. We show that the distances and angles involving C1′ and the P atoms, using the pseudo‐torsion angles and that describe the …P—C1′—P—C1′… chain, provide a promising basis for building the nucleic acid polymer. These quantities show reasonably narrow distributions with asymmetry that should allow the direction of the phosphate backbone to be established.