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

1994; Elsevier BV; Volume: 1218; Issue: 3 Linguagem: Inglês

10.1016/0167-4781(94)90184-8

1879-2634

Timothy J. Stonehouse, Keith R. Fox,

Advanced biosensing and bioanalysis techniques

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-5BrU5Me5C5. 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-5BrU5Me5C5. 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 AnG4A and TAC3Tn, 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.