SNAP output for PDB entry 3kuy [SNAP web server]

PDB-id

3kuy; SNAP-derived features in text and JSON formats; DNAproDB

Class

structural protein-DNA

Method

X-ray (2.9 Å)

Summary

DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumor agent

Reference

Davey GE, Wu B, Dong Y, Surana U, Davey CA (2010): "DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent." Nucleic Acids Res., 38, 2081-2088. doi: 10.1093/nar/gkp1174.

Abstract

DNA stretching in the nucleosome core can cause dramatic structural distortions, which may influence compaction and factor recognition in chromatin. We find that the base pair unstacking arising from stretching-induced extreme minor groove kinking near the nucleosome centre creates a hot spot for intercalation and alkylation by a novel anticancer compound. This may have far reaching implications for how chromatin structure can influence binding of intercalator species and indicates potential for the development of site selective DNA-binding agents that target unique conformational features of the nucleosome.