Folding Topology of a Bimolecular DNA Quadruplex Containing a Stable Mini-hairpin Motif within the Diagonal Loop

Graham D. Balkwill, Thomas P. Garner, H. E L Williams, Mark S. Searle

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

We describe the NMR structural characterisation of a bimolecular anti-parallel DNA quadruplex d(G3ACGTAGTG3)2 containing an autonomously stable mini-hairpin motif inserted within the diagonal loop. A folding topology is identified that is different from that observed for the analogous d(G3T4G3)2 dimer with the two structures differing in the relative orientation of the diagonal loops. This appears to reflect specific base stacking interactions at the quadruplex-duplex interface that are not present in the structure with the T4-loop sequence. A truncated version of the bimolecular quadruplex d(G2ACGTAGTG2)2, with only two core G-tetrads, is less stable and forms a heterogeneous mixture of three 2-fold symmetric quadruplexes with different loop arrangements. We demonstrate that the nature of the loop sequence, its ability to form autonomously stable structure, the relative stabilities of the hairpin loop and core quadruplex, and the ability to form favourable stacking interactions between these two motifs are important factors in controlling DNA G-quadruplex topology.

Original languageEnglish (US)
Pages (from-to)1600-1615
Number of pages16
JournalJournal of Molecular Biology
Volume385
Issue number5
DOIs
StatePublished - Feb 6 2009
Externally publishedYes

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G-Quadruplexes

Keywords

  • bimolecular DNA quadruplex
  • DNA hairpins
  • NMR spectroscopy
  • structural topology

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Folding Topology of a Bimolecular DNA Quadruplex Containing a Stable Mini-hairpin Motif within the Diagonal Loop. / Balkwill, Graham D.; Garner, Thomas P.; Williams, H. E L; Searle, Mark S.

In: Journal of Molecular Biology, Vol. 385, No. 5, 06.02.2009, p. 1600-1615.

Research output: Contribution to journalArticle

Balkwill, Graham D. ; Garner, Thomas P. ; Williams, H. E L ; Searle, Mark S. / Folding Topology of a Bimolecular DNA Quadruplex Containing a Stable Mini-hairpin Motif within the Diagonal Loop. In: Journal of Molecular Biology. 2009 ; Vol. 385, No. 5. pp. 1600-1615.
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