Folding of single-stranded DNA quadruplexes containing an autonomously stable mini-hairpin loop

Graham D. Balkwill, Thomas P. Garner, Mark S. Searle

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


The single-stranded DNA quadruplex motif TG3-L 1-G3-L2-G3-L3-G 3T (where L1, L2 and L3 are the three loop sequences) was used as a template for probing the effects of the loop sequences on stability and folding topology. An autonomously stable mini-hairpin sequence (ACGTAGT) was inserted into the central loop (L 2) of different sequences with intrinsic propensities to form either parallel or anti-parallel structures. Single nucleotides (T) at positions L 1 and L3 strongly favour the formation of a parallel structure with the L2 hairpin insert affecting stability in the same way as a T7 loop. However, in the context of an anti-parallel quadruplex with T3 loops in positions L1 and L 3, the mini-hairpin in the central loop forms a stable structure which enhances the Tm of the quadruplex by ∼10 °C when compared with the T7 insert. The CD and UV melting data show that base pairing interactions within the ACGTAGT hairpin loop sequence, when accommodated as a diagonal loop in an anti-parallel structure, can enhance stability and lead to novel quadruplex structures, adding complexity to the folding landscape and expanding the potential repertoire of sequences that are able to regulate gene expression in vivo.

Original languageEnglish (US)
Pages (from-to)542-547
Number of pages6
JournalMolecular BioSystems
Issue number5
StatePublished - 2009
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology


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