Biomathematics Emphasis Program at San Diego State University


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Matthew Corby

A Three Pool Model of Bacterial DNA Fragmentation in Response to Antibiotics

Matthew Corby¤, Julien Laurent¤, Ilham Naili§, Anca Segall §, and Peter Salamon %.

Department of Chemistry¤, Department of Biology§, and Department of Mathematics and Statistics%, San Diego State University

The purpose of the project is to determine the effectiveness and to clarify the mechanism of action of potential antibiotic compounds to interfere with the mechanisms of DNA repair in bacteria. After treating the bacteria with the compounds of interest (norfloxacin, novobiocin, and a novel antibiotic, peptide wrwycr), the DNA, now broken into many fragments, was separated based on size using pulse field gel electrophoresis. Preliminary analysis of the gels reveals three pools of DNA fragments: (1) unbroken, (2) broken at a few random spots into fragments larger than about 30 kb and described by a Poisson distribution, and (3) digested into fragments smaller than 30 kb, probably with help of the exonuclease RecBCD. Fits to these three pools are presented and the implications for antibiotic activity are discussed.