Quantitative footprinting analysis of the netropsin-DNA interaction.
The results of a series of quantitative footprinting experiments of the netropsin-DNA interaction as studied using two different DNA cleaving probes, the enzyme DNase I and a cationic manganese porphyrin complex, are described. Plots of the relative change in oligonucleotide concentration as a function of drug concentration, covering approximately 110 base pairs of a DNA restriction fragment, revealed netropsin induced changes in the cleavage rates of both probes. These appeared as inhibitions for the binding sites, enhancements where no binding took place, and enhancement/inhibitions for the weak binding sites. Determination of the concentration of drug necessary to reduce the amount of a particular oligomer to half of its initial value allowed a ranking of the affinities of the various binding sites on the fragment. In addition to uncovering the location of a number of overlapping netropsin binding sites, the data allowed additional insight on the manner in which both probes alter their DNA cleavage rates in the drug-footprinting experiment.
Ward
B
B
Department of Chemistry, Syracuse University, New York 13244-1200.
Rehfuss
R
R
Dabrowiak
J C
JC
D000998:Antiviral Agents / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D015342:DNA Probes; D003850:Deoxyribonuclease I / Q000378:metabolism; D006146:Guanidines / Q000378:metabolism*; D008665:Metalloporphyrins / Q000378:metabolism; D008969:Molecular Sequence Data; D009429:Netropsin / Q000378:metabolism*; D009710:Nucleotide Mapping; D013329:Structure-Activity Relationship
D000998:Antiviral Agents; D015342:DNA Probes; D006146:Guanidines; D008665:Metalloporphyrins; C041471:manganese tetraphenylporphyrin; D009429:Netropsin; D004247:DNA; D003850:Deoxyribonuclease I