335D

THE CRYSTAL STRUCTURE OF THE DNA DECAMER D(GGCAATTGCG) CONTAINS BOTH MAJOR AND MINOR GROOVE BINDING G.(G.C) TRIPLETS

Summary for 335D

• Entry DOI: 10.2210/pdb335d/pdb
• Descriptor: DNA (5'-D(*GP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: a-dna, double helix, flipped-out base, dna
• Total number of polymer chains: 1
• Total formula weight: 3109.33

Authors

Nunn, C.M.,Neidle, S. (deposition date: 1997-06-05, release date: 1998-08-10, Last modification date: 2024-04-03)

Primary citation

Nunn, C.M.,Neidle, S.
Structure of the DNA decamer d(GGCAATTGCG) contains both major- and minor-groove binding G.(G.C) base triplets.
Acta Crystallogr.,Sect.D, 54:577-583, 1998

PubMed Abstract: The crystal structure of the decamer d(GGCAATTGCG) has been determined at 2.4 A resolution. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end-to-end within the unit cell. The terminal 5'-G and G-3' bases of each decamer strand are unpaired, and interact with the neighbouring duplexes via interactions within both the major and minor groove. This results in base triplets of the type G-(G.C) and G*(G.C), with the third guanine base binding to a Watson-Crick G.C base pair from the major groove and the minor groove, respectively. The triplet interaction of the type G-(G.C) involves Hoogsteen hydrogen-bonding interactions between the two guanine bases. The minor- and major-groove base triplet interactions which exist within this structure act to stabilize the d(GCAATTGC)2 B-DNA octamer duplex.

PubMed: 9761852
DOI: 10.1107/S090744499701559X

Experimental method

X-RAY DIFFRACTION (2.4 Å)