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WIREs Comput Mol Sci
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The atomistic simulation of DNA

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Abstract We review the current state of the art relating to the atomistic simulation of the structure and dynamics of DNA. We begin with a brief historical overview to set the scene and introduce some of the key issues that had to be addressed to progress the field and then we divide our discussion of the current situation into two sections. First, we overview the role that simulation has played, closely intertwined with experimental studies, in increasing our understanding of the biomechanical properties of DNA, for example, the way in which its structure responds to perturbations such as stretching and over‐ and under‐twisting. Second, we discuss how atomistic simulations are contributing to our deeper understanding of nucleic acid recognition—both by proteins and by small‐molecule ligands. In both areas, we emphasize not only where simulation has been particularly successful but also where thorny problems remain to tax the ingenuity of computational scientists in close collaboration with their experimental colleagues. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 590–600 DOI: 10.1002/wcms.46 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics

Comparison of (left) the crystal structure of the DNA dodecamer d(CGCGAATTCGCG)2 [PDB code 1BNA, (2)] and (center) a canonical B‐form model of the same sequence. A variety of deviations from a fully regular structure are evident in the crystal structure, particularly if the two are overlaid (right; crystal structure in blue and regular B‐form model in green).

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Examples of ‘direct’ and ‘indirect’ sequence recognition in DNA–protein complexes. (Left) The complex of C2 repressor protein with DNA (PDB code 3JXB60) shows little deformation of the double helix. (Right) In contrast, the TATA‐binding protein (PDB code 1CDW61) causes gross distortion of the DNA structure.

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Types of DNA–ligand interactions. (Left) Intercalation, exemplified here by daunomycin (PDB code 1DA0; Ref 51). (Center) Minor groove binding, exemplified here by netropsin (PDB code 261D; Ref 52). (Right) Covalent attachment, exemplified here by cisplatin (PDB code 1A84; Ref 53).

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DNA under mechanical stress. The S‐DNA structure from molecular dynamics (top left) showing the unusual inclination of the DNA bases; an over‐wound P‐DNA structure44 (top middle) showing a flipped out base at the top of the structure; a relaxed 90 bp DNA circle (top right); and an under‐wound and writhed 178 bp circle (bottom), where the DNA has relieved torsional stress by adopting a ‘figure of 8’ type structure. This image was produced using QuteMol.31

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A schematic representation of DNA stretching (left), unzipping (middle), and twisting (right) using atomic force microscopy (left and middle) and magnetic tweezers (right).

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