title: DNase I footprinting of triple helix formation at polypurine tracts by acridine-linked oligopyrimidines: stringency, structural changes and interaction with minor groove binding ligands.
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-5BrU5(5Me)C5. 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-5BrU5(5Me)C5. 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.
authors.affiliation: Department of Physiology and Pharmacology, University of Southampton, UK.
authors.forename: T J
authors.initials: TJ
authors.lastname: Stonehouse
authors.forename: K R
authors.initials: KR
authors.lastname: Fox
mesh_terms: D000166:Acridines; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D003850:Deoxyribonuclease I / Q000378:metabolism*; D004214:Distamycins; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D008926:Plicamycin; D011687:Purines; D011743:Pyrimidines
chemical_list: D000166:Acridines; D004214:Distamycins; D008024:Ligands; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D011687:Purines; D011743:Pyrimidines; D004247:DNA; D003850:Deoxyribonuclease I; D008926:Plicamycin