Quinoxaline antibiotics enhance peptide nucleic acid binding to double-stranded DNA

TY - JOUR

T1 - Quinoxaline antibiotics enhance peptide nucleic acid binding to double-stranded DNA

AU - Møllegaard, N E

AU - Bailly, C

AU - Waring, M J

AU - Nielsen, Peter E.

PY - 2000/8/8

Y1 - 2000/8/8

N2 - The effects of a wide range of DNA binding drugs on peptide nucleic acid (PNA) binding to double-stranded DNA by strand displacement have been investigated using a gel retardation assay. The bis-PNA [H-(Lys)-TTJTTJTTTT-(eg)(3)-TTTTCTTCTT-Lys-NH(2)] was used together with a 248 bp DNA fragment containing an appropriate target for the PNA. Most of the ligands that were studied, including DNA minor groove binders as well as intercalators and bis-intercalators, either have no effect or strongly inhibit PNA binding to DNA. By contrast, quinoxaline antibiotics facilitate PNA-DNA complex formation. The "PNA-helper" effect of echinomycin was studied in more detail using time and temperature dependence experiments to elucidate the mechanism. PNA binding to DNA follows pseudo-first-order kinetics, but the initial rate of binding is accelerated more than 10-fold in the presence of 10 microM echinomycin. The activation energy for PNA binding to dsDNA is lowered 2-fold by the antibiotic (45 vs 90 kJ/mol in the control). The reasons why quinoxalines promote the binding of PNA to DNA are not entirely clear but may well include distortions (opening) of the double helix that facilitate PNA invasion. This study establishes that the efficacy of DNA-targeted PNA antigene molecules could potentially be enhanced by judiciously adding certain DNA-interactive ligands.

AB - The effects of a wide range of DNA binding drugs on peptide nucleic acid (PNA) binding to double-stranded DNA by strand displacement have been investigated using a gel retardation assay. The bis-PNA [H-(Lys)-TTJTTJTTTT-(eg)(3)-TTTTCTTCTT-Lys-NH(2)] was used together with a 248 bp DNA fragment containing an appropriate target for the PNA. Most of the ligands that were studied, including DNA minor groove binders as well as intercalators and bis-intercalators, either have no effect or strongly inhibit PNA binding to DNA. By contrast, quinoxaline antibiotics facilitate PNA-DNA complex formation. The "PNA-helper" effect of echinomycin was studied in more detail using time and temperature dependence experiments to elucidate the mechanism. PNA binding to DNA follows pseudo-first-order kinetics, but the initial rate of binding is accelerated more than 10-fold in the presence of 10 microM echinomycin. The activation energy for PNA binding to dsDNA is lowered 2-fold by the antibiotic (45 vs 90 kJ/mol in the control). The reasons why quinoxalines promote the binding of PNA to DNA are not entirely clear but may well include distortions (opening) of the double helix that facilitate PNA invasion. This study establishes that the efficacy of DNA-targeted PNA antigene molecules could potentially be enhanced by judiciously adding certain DNA-interactive ligands.

KW - Adjuvants, Pharmaceutic/pharmacology

KW - Anti-Bacterial Agents/pharmacology

KW - Antibiotics, Antineoplastic/pharmacology

KW - Binding Sites/drug effects

KW - DNA/metabolism

KW - Diminazene/analogs & derivatives

KW - Echinomycin/pharmacology

KW - Electrophoresis, Polyacrylamide Gel

KW - Intercalating Agents/pharmacology

KW - Netropsin/pharmacology

KW - Peptide Nucleic Acids/metabolism

KW - Plicamycin/pharmacology

KW - Quinoxalines/pharmacology

M3 - Journal article

C2 - 10924146

SN - 0006-2960

VL - 39

SP - 9502

EP - 9507

JO - Biochemistry

JF - Biochemistry

IS - 31

ER -