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

PDB-id

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

Class

DNA-RNA hybrid

Method

X-ray (2.0 Å)

Summary

Crystal structure of an okazaki fragment at 2 angstroms resolution

Reference

Egli M, Usman N, Zhang SG, Rich A (1992): "Crystal structure of an Okazaki fragment at 2-A resolution." Proc.Natl.Acad.Sci.USA, 89, 534-538. doi: 10.1073/pnas.89.2.534.

Abstract

In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template strand. The DNA oligonucleotide d(GGGTATACGC) and the chimeric RNA-DNA oligonucleotide r(GCG)d(TATACCC) were combined to form a synthetic Okazaki fragment and its three-dimensional structure was determined by x-ray crystallography. The fragment adopts an overall A-type conformation with 11 residues per turn. Although the base-pair geometry, particularly in the central TATA part, is distorted, there is no evidence for a transition from the A- to the B-type conformation at the junction between RNA.DNA hybrid and DNA duplex. The RNA trimer may, therefore, lock the complete fragment in an A-type conformation.