DSSR-PyMOL cartoon-block schematics: PDB entry 1cw9

PDB-id

1cw9; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.55 Å)

Summary

DNA decamer with an engineered crosslink in the minor groove

Reference

van Aalten DM, Erlanson DA, Verdine GL, Joshua-Tor L (1999): "A structural snapshot of base-pair opening in DNA." Proc.Natl.Acad.Sci.USA, 96, 11809-11814. doi: 10.1073/pnas.96.21.11809.

Abstract

The response of double-helical DNA to torsional stress may be a driving force for many processes acting on DNA. The 1.55-A crystal structure of a duplex DNA oligonucleotide d(CCAGGCCTGG)(2) with an engineered crosslink in the minor groove between the central guanine bases depicts how the duplex can accommodate such torsional stress. We have captured in the same crystal two rather different conformational states. One duplex contains a strained crosslink that is stabilized by calcium ion binding in the major groove, directly opposite the crosslink. For the other duplex, the strain in the crosslink is relieved through partial rupture of a base pair and partial extrusion of a cytosine accompanied by helix bending. The sequence used is the target sequence for the HaeIII methylase, and this partially flipped cytosine is the same nucleotide targeted for extrusion by the enzyme. Molecular dynamics simulations of these structures show an increased mobility for the partially flipped-out cytosine.