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Geometric properties of nucleic acids with potential for autobuilding.

ABSTRACT: 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 \eta' and \theta\,' 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.

SUBMITTER: Gruene T

PROVIDER: S-EPMC3006036 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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Geometric properties of nucleic acids with potential for autobuilding.

Gruene Tim T Sheldrick George M GM

Acta crystallographica. Section A, Foundations of crystallography 20101111 Pt 1

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 ...[more]

PMID: 21173468

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