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.
Highlights
In macromolecular crystallography the construction of an initial model has been greatly facilitated by programs that automatically build a model into an experimental electrondensity map given a protein sequence (Morris et al, 2002; Terwilliger, 2000; Cowtan, 2006; Emsley & Cowtan, 2004; Emsley et al, 2010)
Our C10-approach results could be regarded as a confirmation of Keating and Pyle’s work, we show here that this approach is advantageous for DNA as well as for RNA structures
Experimental phases for octan were determined by singlewavelength anomalous diffraction (SAD) from the Br atoms in bromouracil that had been substituted for thymine
Summary
In macromolecular crystallography the construction of an initial model has been greatly facilitated by programs that automatically build a model into an experimental electrondensity map given a protein sequence (Morris et al, 2002; Terwilliger, 2000; Cowtan, 2006; Emsley & Cowtan, 2004; Emsley et al, 2010). In this paper a simple but fast procedure to place phosphates and bases in electron density is presented and some geometrical features of nucleic acid structures that might be useful for automated tracing are explored This should enable the development of algorithms for tracing nucleic acids in experimental electron-density maps that are relatively efficient and robust, whilst accommodating most conformations that are found in practice. A67, 1–8 sophisticated use of RNA rotamer libraries but requires the user to provide the phosphate and base coordinates and complements our work Since these authors plan to make their software available as a plug-in to the program COOT (Emsley et al, 2010; Emsley & Cowtan, 2004), we plan to do the same starting with the automated phosphate and base location, even though the optimization of our proposed strategy for building a complete RNA or DNA model is likely to take several years. Our C10-approach results could be regarded as a confirmation of Keating and Pyle’s work, we show here that this approach is advantageous for DNA as well as for RNA structures
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Acta Crystallographica Section A Foundations of Crystallography
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
