A DNA decamer with a sticky end: The crystal structure of d-CGACGATCGT

Hangxia Qiu, John C. Dewan, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

The crystal structure of d-CGACGATCGT has been determined to a resolution of 2.6 Å. The molecule was synthesized by standard phosphoramidite procedures, and purified by anion-exchange HPLC. Crystals are monolclinic, space group P21, with unit cell dimensions, a=26.45 Å, b = 34.66 Å, c = 32.17 Å, β = 113.45°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 > 2σ(F), collected at -120°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.

Original languageEnglish (US)
Pages (from-to)881-898
Number of pages18
JournalJournal of Molecular Biology
Volume267
Issue number4
DOIs
StatePublished - Apr 11 1997

Fingerprint

Cruciform DNA
R388
DNA
B-Form DNA
Bromine
Cytosine
Base Pairing
Anions
Nucleotides
High Pressure Liquid Chromatography

Keywords

  • DNA structure
  • Oligonucleotide
  • Sticky ends
  • X-ray crystallography

ASJC Scopus subject areas

  • Virology

Cite this

A DNA decamer with a sticky end : The crystal structure of d-CGACGATCGT. / Qiu, Hangxia; Dewan, John C.; Seeman, Nadrian.

In: Journal of Molecular Biology, Vol. 267, No. 4, 11.04.1997, p. 881-898.

Research output: Contribution to journalArticle

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