Formation of DNA triple helices incorporating blocks of G·GC and T·AT triplets using short acridine-linked oligonucleotides

Fox, Keith R. (1994) Formation of DNA triple helices incorporating blocks of G·GC and T·AT triplets using short acridine-linked oligonucleotides. Nucleic Acids Research, 22 (11), 2016-2021. (doi:10.1093/nar/22.11.2016).

Record type: Article

Abstract

We have used DNase I footprinting to assess triple helix formation at target sites containing the sequences A₆G₆·C₆T₆ and G₆A₆·T₆C₆. These sequences can be recognized by the acridine-linked oligopyrimidines Acr-T₅C₅ and Acr-C₅T₅ respectively at low pH, using well-characterised T·AT and C⁺·GC triplets. At pH 7.5 A₆G₆·C₆T₆ is specifically bound by Acr-G₅T₅, utilising G·GC and T·AT triplets in which the third strand runs antiparallel to the purine strand of the duplex. This interaction requires the presence of magnesium ions. No interaction was detected with Acr-T₅G₅, an oligonucleotide designed to form parallel G·GC and T·AT triplets. In contrast neither Acr-T₅G₅ nor Acr-G₅T₅ produced DNase I footprints with the target sequence G₆A₆·T₆C₆. These results suggest that, in an antiparallel R·RY triple helix, the T·AT triplet is weaker than the G·GC triplet. We find no evidence for the formation of structures containing parallel G·GC triplets.

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Published date: 11 June 1994

Additional Information: Funding Information: This work was supported by grants from the Cancer Research Campaign and The Royal Society. KRF is a Lister Institute Research Fellow.