title: Superhelical duplex destabilization and the recombination position effect.
abstract: The susceptibility to recombination of a plasmid inserted into a chromosome varies with its genomic position. This recombination position effect is known to correlate with the average G+C content of the flanking sequences. Here we propose that this effect could be mediated by changes in the susceptibility to superhelical duplex destabilization that would occur. We use standard nonparametric statistical tests, regression analysis and principal component analysis to identify statistically significant differences in the destabilization profiles calculated for the plasmid in different contexts, and correlate the results with their measured recombination rates. We show that the flanking sequences significantly affect the free energy of denaturation at specific sites interior to the plasmid. These changes correlate well with experimentally measured variations of the recombination rates within the plasmid. This correlation of recombination rate with superhelical destabilization properties of the inserted plasmid DNA is stronger than that with average G+C content of the flanking sequences. This model suggests a possible mechanism by which flanking sequence base composition, which is not itself a context-dependent attribute, can affect recombination rates at positions within the plasmid.
authors.affiliation: Baylor College of Medicine, Houston, Texas, United States of America. sershen@bcm.edu
authors.forename: Cheryl L
authors.initials: CL
authors.lastname: Sershen
authors.forename: Joshua C
authors.initials: JC
authors.lastname: Mell
authors.forename: Sally M
authors.initials: SM
authors.lastname: Madden
authors.forename: Craig J
authors.initials: CJ
authors.lastname: Benham
mesh_terms: D001482:Base Composition / Q000235:genetics; D055012:Chromosomal Position Effects / Q000235:genetics*; D016000:Cluster Analysis; D004271:DNA, Fungal / Q000235:genetics; D004278:DNA, Superhelical / Q000235:genetics*; D016681:Genome, Fungal / Q000235:genetics; D016254:Mutagenesis, Insertional / Q000235:genetics; D009692:Nucleic Acid Heteroduplexes / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D025341:Principal Component Analysis; D011995:Recombination, Genetic / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D004271:DNA, Fungal; D004278:DNA, Superhelical; D009692:Nucleic Acid Heteroduplexes