Summary information and primary citation
- PDB-id
-
1cw9;
SNAP-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.