DSSR-PyMOL cartoon-block schematics: PDB entry 1b4y

PDB-id

1b4y; DSSR-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

Structure and mechanism of formation of the h-y5 isomer of an intramolecular DNA triple helix.

Reference

van Dongen MJ, Doreleijers JF, van der Marel GA, van Boom JH, Hilbers CW, Wijmenga SS (1999): "Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix." Nat.Struct.Biol., 6, 854-859. doi: 10.1038/12313.

Abstract

H-DNA, thought to play a regulatory role in transcription, exists in two isomeric forms, H-y3 and H-y5. We present the first solution structure of a DNA fragment representing the H-y5 fold. The structure shows the H-y5 triple helix, and for the first time how in an H-DNA isomer the purine strand extension interacts with the triplex loop. It gives direct insight into the mechanism of H-DNA formation, and explains a host of biochemical and biophysical data on the relative stability of the H-DNA isomers. In addition, the observed interaction of the purine strand extension and the triplex loop provides new clues to the design of clamp-type triple helix-forming oligonucleotides.