DNase I footprinting of triple helix formation at polypurine tracts by acridine-linked oligopyrimidines: Stringency, structural changes and interaction with minor groove binding ligands

Stonehouse, Timothy J. and Fox, Keith R. (1994) DNase I footprinting of triple helix formation at polypurine tracts by acridine-linked oligopyrimidines: Stringency, structural changes and interaction with minor groove binding ligands. BBA - Gene Structure and Expression, 1218 (3), 322-330. (doi:10.1016/0167-4781(94)90184-8).

Abstract

We have investigated the binding of short (10 base) acridine-linked triplex-forming oligonucleotides to the target sequence A₆G₆·C₆T₆ by DNase I footprinting. Specific binding is detected at low pH (<6.0) for 5′-Acr-T₅C₅ and 5′-Acr-^5BrU^5Me₅C₅. The sequence T₅C₅, lacking the acridine modification, binds less strongly, though specific binding is still evident. 5′-Acr-T₅C₅ produces footprints at slightly lower concentrations than 5′-Acr-^5BrU^5Me₅C₅. All three oligonucleotides produce enhanced DNase I digestion at the 3′-end of the target purine strand, suggesting that there is a DNA structural change at the triplex-duplex boundary. Target sequences A_nG₄A and TAC₃T_n, containing one and two triplex mismatches, show no interaction with the acridine-free oligonucleotide, but bind the acridine-linked oligonucleotides. In these secondary binding modes the third strand is positioned so that the mismatches are located at the 3′-end of the oligonucleotide. Mithramycin and distamycin, binding in the minor groove to GC- and AT-rich sequences respectively, abolish triple helix formation.

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Contributors

Author: Keith R. Fox

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