DSSR-PyMOL cartoon-block schematics: PDB entry 1s9b

PDB-id

1s9b; SNAP-derived features in text and JSON formats

Class

DNA

Method

X-ray (2.81 Å)

Summary

Crystal structure analysis of the b-DNA gaattcg

Reference

Valls N, Uson I, Gouyette C, Subirana JA (2004): "A cubic arrangement of DNA double helices based on nickel-guanine interactions." J.Am.Chem.Soc., 126, 7812-7816. doi: 10.1021/ja049393i.

Abstract

DNA oligonucleotides can be used in order to assemble highly structured materials. Oligonucleotides with sticky ends can form long linear structures, whereas branching is required to form two- and three-dimensional nanostructures. In this paper, we show that when Ni(2+) is attached to the N7 atom of guanine, it can also act as a branching point. Thus, we have found that the heptanucleotide d(GAATTCG) can assemble into long linear duplex structures, which cross in space to generate a cubic structure. The three-dimensional arrays are stabilized by phosphate-Ni(2+)-guanine interactions. For the first time, the crystallization of a B form DNA oligonucleotide in a cubic system is reported, space group I23. Large solvent cavities are found among the DNA duplexes.