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Nucleic Acids Research, Vol 26, Issue 16 3626-3633, Copyright © 1998 by Oxford University Press

ARTICLES

Triple helix formation at (AT)n adjacent to an oligopurine tract

DM Gowers and KR Fox
Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.

We have used DNase I footprinting to investigate the recognition of (AT) n tracts in duplex DNA using GT-containing oligonucleotides designed to form alternating G.TA and T.AT triplets. Previous studies have shown that the formation of these complexes is facilitated by anchoring the triplex with a block of adjacent T.AT triplets, i.e. using T11(TG)6to recognize the target A11(AT)6. (AT)6T11. In the present study we have examined how the stability of these complexes is affected by the length of either the T.AT tract or the region of alternating G.TA and T.AT triplets, using oligonucleotides of type T x (TG) y to recognize the sequence A11(AT)11. We find that successful triplex formation at (AT)n (n = 3, 6 or 11) can be achieved with a stabilizing tail of 11xT.AT triplets. The affinity of the third strand increases with the length of the (GT) n tract, suggesting that the alternating G.TA and T.AT triplets are making a positive contribution to stability. These complexes are stabilized by the presence of manganese or a triplex-specific binding ligand. Shorter oligo- nucleotides, such as T7(TG)5, bind less tightly and require the addition of a triplex-binding ligand. T4(GT)5showed no binding under any conditions. Oligo-nucleotides forming a 3'-terminal T.AT are marginally more stable that those with a terminal G.TA. The stability of these complexes was further increased by replacing two of the T.AT triplets in the T n tail region with two C+.GC triplets.
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E. Ayel and C. Escude
In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents
Nucleic Acids Res., December 8, 2009; (2009) gkp1139v1.
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