Simultaneous binding of a polyamide dimer and an oligonucleotide in the minor and major grooves of DNA

• Published in: Bioorganic & medicinal chemistry Vol. 4; no. 7; pp. 1045 - 1050
• Main Authors: Parks, Michelle E., Dervan, Peter B.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.07.1996
• Subjects: Autoradiography; Base Sequence; Distamycins - metabolism; DNA - metabolism; DNA Footprinting; Electrophoresis, Polyacrylamide Gel; Models, Chemical; Molecular Sequence Data; Netropsin - analogs & derivatives; Netropsin - metabolism; Nucleic Acid Conformation; Nylons - metabolism; Oligonucleotides - metabolism
• ISSN: 0968-0896; 1464-3391
• DOI: 10.1016/0968-0896(96)00089-2

The effect of the polyamide ImPyPy-Dp (Im = N-methylimidazole-2-carboxamide, Py = N-methylpyrrole-2-carboxamide, and Dp = dimethylaminopropylamide), which binds as an antiparallel dimer in the Watson—Crick minor groove, on pyrimidine • purine • pyrimidine triple helix stability was investigated. A DNA restriction fragment was designed which contained two triple helix sites, one which overlapped a minor groove ligand site (proximal), and a control site 13 base pairs away (distal). Using quantitative DNase I footprint titration experiments the equilibrium association constant of oligonucleotide 5′-TTTTTm 5CTTTm 5CTTTm 5CT-3′ ( 1) to each site was measured in the absence and presence of the polyamide dimer. Our data indicate that triple helix formation is compatible with a polyamide dimer binding in the minor groove of DNA at an overlapping site. No cooperative effect of the polyamide dimer on the equilibrium association constant of oligonucleotide 1 was observed. The effect of the polyamide ImPyPy-Dp, (Im- N-methylimidazole-2-carboxamide, Py= N-methylpyrrole-2-carboxamide, and Dp = dimethylaminopropyl-amide), which binds as an antiparallel dimer in the Watson-Crick minor groove, on pyrimidine • purine • pyrimidine triple helix stability was investigated. A DNA restriction fragment was designed which contained two triple helix sites, one which overlapped a minor groove ligand site (proximal), and a control site 13 base pairs away (distal). Using quantitative DNase I footprint titration experiments the equilibrium association constant of oligonucleotide 5′-TTTTTm5CTTTm5TTTm5CT-′ (1) to each site was measured in the absence and presence of the polyamide dimer binding in the minor groove of DNA at an overlapping site. No cooperative effect of the polyamide dimer on the equilibrium association constant of oligonucleotide 1 was observed.