309D

A DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGT

「273D」から置き換えられました

309D の概要

• エントリーDOI: 10.2210/pdb309d/pdb
• 分子名称: DNA (5'-D(*CP*GP*AP*CP*GP*AP*TP*CP*GP*T)-3') (2 entities in total)
• 機能のキーワード: b-dna, double helix, overhanging bases, continuous helix, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 6090.01

構造登録者

Qiu, H.X.,Dewan, J.C.,Seeman, N.C. (登録日: 1997-01-07, 公開日: 1997-01-22, 最終更新日: 2024-02-21)

主引用文献

Qiu, H.,Dewan, J.C.,Seeman, N.C.
A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT.
J.Mol.Biol., 267:881-898, 1997

PubMed Abstract: The crystal structure of d-CGACGATCGT has been determined to a resolution of 2.6 A. The molecule was synthesized by standard phosphoramidite procedures, and purified by anion-exchange HPLC. Crystals are monolclinic, space group P2(1), with unit cell dimensions, a = 26.45 A, b = 34.66 A, c = 32.17 A, beta = 113.45 degrees and Z = 4, containing a B-DNA double helix in each crystallographic asymmetric unit. The structure was solved using molecular replacement, aided by an isomorphous derivative, in which a bromine atom was attached to the 5 position of cytosine 8. Problems of fit between the search model and the structure ultimately obtained necessitated the use of Patterson correlation procedures between the determination of the orientation and the translation of the molecule. In all, 69 solvent molecules have been identified, and the structure has been refined to an R-factor of 0.214, using the 1421 reflections with F > 2sigma(F), collected at -120 degrees C. The sequence produces a molecule containing eight Watson-Crick base-pairs and a two-nucleotide 5'-sticky end at each end of the duplex. The sticky ends cohere with one another, so the molecules form continuous 10-fold double helices throughout the crystal, with each strand being interrupted by inherent staggered nicks. The relative angular relationships between helices in the structure differ from each other; most of the arrangements differ from Holliday junctions, whose rotational orientations are phased by a crossover and which are modeled to contain double helices that are exactly parallel or antiparallel. However, one helical juxtaposition in this crystal is similar to the alignment of double helices in parallel Holliday junctions. A survey of DNA decamers that also form infinite helices in crystals reveals relationships that approximate both parallel and antiparallel Holliday junction alignments.

PubMed: 9135119
DOI: 10.1006/jmbi.1997.0918

実験手法

X-RAY DIFFRACTION (2.6 Å)