PERFILS: a program for the quantitative treatment of footprinting data

Area of Science:

• Molecular Biology
• Bioinformatics
• Computational Biology

Background:

• DNA footprinting assays are crucial for studying DNA-protein and DNA-ligand interactions.
• Quantitative analysis of footprinting data can be complex and time-consuming.
• Existing methods may lack the speed and accessibility for widespread use.

Purpose of the Study:

• To develop a user-friendly computer program for quantitative analysis of footprinting experiments.
• To enable rapid generation of differential cleavage plots for visualizing DNA-ligand interactions.
• To provide a tool for analyzing DNA susceptibility to cleavage agents in the presence of ligands.

Main Methods:

• Development of PERFILS software using Borland TurboPascal for IBM PC compatible microcomputers.
• Utilizing densitometric scanning data from footprinting autoradiographs.
• Calculation of fractional cleavage values for DNA fragments.
• Generation of differential cleavage plots displaying DNA susceptibility on a logarithmic scale.

Main Results:

• PERFILS performs quantitative analysis of footprinting experiments efficiently.
• The program calculates fractional cleavage values for control and ligand conditions.
• Differential cleavage plots are generated rapidly, displaying sequence-specific DNA-ligand interactions.
• Provides a table of values for each internucleotidic bond.

Conclusions:

• PERFILS offers a fast and accurate method for quantitative analysis of DNA footprinting data.
• The software facilitates the study of DNA-ligand interactions through accessible differential cleavage plots.
• PERFILS enhances the utility of footprinting experiments in molecular biology research.