High-resolution structure of a DNA helix forming (C·G)*G base triplets

Abstract

TRIPLE helices result from interaction between single- and double-stranded nucleic acids. Their formation is a possible mechanism for recombination of homologous gene sequences in nature and provides, inter alia, a basis for artificial control of gene activity. Triple-helix motifs have been extensively studied by a variety of techniques, but few high-resolution structural data are available. The only triplet structures characterized so far by X-rav diffraction were in protein–DNA complexes^1,2 studied at about 3 Å resolution. We report here the X-ray analysis of a DNA nonamer, d(GCGAATTCG), to a resolution of 2.05 Å, in which the extended crystal structure contains (C · G)*G triplets as a fragment of triple helix. The guanosine-containing chains are in a parallel orientation. This arrangement is a necessary feature of models for homologous recombination which results ultimately in replacement of one length of DNA by another of similar sequence. The present-structure agrees with many published predictions of triplex organization, and provides an accurate representation of an element that allows sequence-specific association between single- and double-stranded nucleic acids.