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 -