257D

ALTERNATING AND NON-ALTERNATING DG-DC HEXANUCLEOTIDES CRYSTALLIZE AS CANONICAL A-DNA

257D の概要

• エントリーDOI: 10.2210/pdb257d/pdb
• 分子名称: DNA (5'-D(*GP*CP*CP*GP*GP*C)-3') (2 entities in total)
• 機能のキーワード: a-dna, double helix, modified, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3620.41

構造登録者

Mooers, B.H.,Schroth, G.P.,Baxter, W.W.,Ho, P.S. (登録日: 1996-03-31, 公開日: 1996-04-15, 最終更新日: 2024-02-14)

主引用文献

Mooers, B.H.,Schroth, G.P.,Baxter, W.W.,Ho, P.S.
Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA.
J.Mol.Biol., 249:772-784, 1995

PubMed Abstract: We have solved the single-crystal X-ray structures of two different hexanucleotides: the alternating sequence d(Gm5CGm5CGC), and the non-alternating sequence d(Gm5CCGGC). Both of these hexamers crystallize readily as A-DNA in the orthorhombic space group C222(1). Although hexanucleotides have been previously crystallized as Z-DNA, and in one case as B-DNA, this is the first time hexanucleotides have been crystallized as A-DNA. Both hexamers adopt a typical A-conformation, which is surprisingly more similar to the structure of A-DNA fibers than to other A-DNA single crystals. The structure of d(Gm5CGm5CGC) was solved to a resolution of 2.1 A (R-factor = 19.6%). This structure has all of the features characteristic of canonical A-DNA, including it's helical repeat (11.2 bp/turn), helical rise (2.6 A/bp), base-pair displacement (-4.7 A), base inclination angle (16.9 degrees), and sugar puckers that are predominantly 3'-endo. The lower resolution, non-alternating structure has similar overall average values for these parameters. We observed several sequence-dependent correlations in these parameters, especially in the d(CG) base step. These steps have lower twist and rise values, coupled with high roll angles as compared to d(GC) steps. The molecular interactions involved in crystal packing and the detailed structure of the bound water in the crystals, however, are similar to those of longer 8 and 10 bp A-DNA crystal structures. Although the structural effect of cytosine methylation on A-DNA appears to be minimal, this modification significantly affects the ability of these sequences to crystallize as A-DNA. In conclusion, we present the A-DNA forming class of hexanucleotides, a new crystallographic system for studying DNA structure at near atomic resolution.

PubMed: 7602589
DOI: 10.1006/jmbi.1995.0336

実験手法

X-RAY DIFFRACTION (2.3 Å)