DSSR-PyMOL cartoon-block schematics: PDB entry 5t4w

PDB-id

5t4w; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (2.3 Å)

Summary

Crystal structure of a DNA sequence d (cgtgaattcacg) with dapi

Reference

Sbirkova-Dimitrova HI, Shivachev B (2017): "Crystal structure of the DNA sequence d(CGTGAATTCACG)2 with DAPI." Acta Crystallogr F Struct Biol Commun, 73, 500-504. doi: 10.1107/S2053230X17011384.

Abstract

The structure of 4',6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space group P212121 by single-crystal X-ray diffraction at a resolution of 2.2 Å. The structure is nearly isomorphous to that of the previously reported crystal structure of the oligonucleotide d(CGTGAATTCACG) alone. The adjustments in crystal packing between the native DNA molecule and the DNA-DAPI complex are described. DAPI lies in the narrow minor groove near the centre of the B-DNA fragment, positioned over the A-T base pairs. It is bound to the DNA by hydrogen-bonding and van der Waals interactions. Comparison of the two structures (with and without ligand) shows that DAPI inserts into the minor groove, displacing the ordered spine waters. Indeed, as DAPI is hydrophobic it confers this behaviour on the DNA and thus restricts the presence of water molecules.