PDBsum entry 1n4e

DNA

PDB id: 1n4e

Contents

DNA/RNA

Waters ×56

References listed in PDB file

Key reference

Title

Crystal structure of a DNA decamer containing a cis-Syn thymine dimer.

Authors

H.Park, K.Zhang, Y.Ren, S.Nadji, N.Sinha, J.S.Taylor, C.Kang.

Ref.

Proc Natl Acad Sci U S A, 2002, 99, 15965-15970. [DOI no: 10.1073/pnas.242422699]

PubMed id

12456887

Abstract

It is well known that exposure to UV induces DNA damage, which is the first step in mutagenesis and a major cause of skin cancer. Among a variety of photoproducts, cyclobutane-type pyrimidine photodimers (CPD) are the most abundant primary lesion. Despite its biological importance, the precise relationship between the structure and properties of DNA containing CPD has remained to be elucidated. Here, we report the free (unbound) crystal structure of duplex DNA containing a CPD lesion at a resolution of 2.0 A. Our crystal structure shows that the overall helical axis bends approximately 30 degrees toward the major groove and unwinds approximately 9 degrees, in remarkable agreement with some previous theoretical and experimental studies. There are also significant differences in local structure compared with standard B-DNA, including pinching of the minor groove at the 3' side of the CPD lesion, a severe change of the base pair parameter in the 5' side, and serious widening of both minor and major groves both 3' and 5' of the CPD. Overall, the structure of the damaged DNA differs from undamaged DNA to an extent that DNA repair proteins may recognize this conformation, and the various components of the replicational and transcriptional machinery may be interfered with due to the perturbed local and global structure.

Figure 4.
Fig 4. Schematic diagram illustrating the kink of the helix. Regular B-DNA and CPD-containing DNA are depicted in green and red, respectively. (a) Side view with a helical axis. (b) Top view.

Figure 6.
Fig 6. Electropotential surface models (a); (c) an ideal B-form decamer DNA (b); (d) crystal structure of the CPD containing decamer DNA (same sequence), with probe radii of 1.4 Å. The CPD site and corresponding site of the ideal B-form DNA are indicated by arrows. The duplex DNA molecule containing the CPD has an enlarged minor and major groove. The figure was produced by using VMD (58).