1S9B

Crystal Structure Analysis of the B-DNA GAATTCG

Summary for 1S9B

• Entry DOI: 10.2210/pdb1s9b/pdb
• Descriptor: 5'-D(*GP*AP*AP*TP*TP*CP*G)-3', NICKEL (II) ION (3 entities in total)
• Functional Keywords: double helix, cubic dna, nickel, dna
• Total number of polymer chains: 2
• Total formula weight: 4509.64

Authors

Valls, N.,Uson, I.,Gouyette, C.,Subirana, J.A. (deposition date: 2004-02-04, release date: 2004-09-07, Last modification date: 2024-04-03)

Primary citation

Valls, N.,Uson, I.,Gouyette, C.,Subirana, J.A.
A cubic arrangement of DNA double helices based on nickel-guanine interactions
J.Am.Chem.Soc., 126:7812-7816, 2004

PubMed 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.

PubMed: 15212528
DOI: 10.1021/ja049393i

Experimental method

X-RAY DIFFRACTION (2.81 Å)