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Superhelical duplex destabilization and the recombination position effect.

Sershen CL, Mell JC, Madden SM, Benham CJ - PLoS ONE (2011)

Bottom Line: 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 show that the flanking sequences significantly affect the free energy of denaturation at specific sites interior to the plasmid.

View Article: PubMed Central - PubMed

Affiliation: Baylor College of Medicine, Houston, Texas, United States of America. sershen@bcm.edu

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.

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The correlation between the coefficients of the third principal                            component and the recombination rate.
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pone-0020798-g004: The correlation between the coefficients of the third principal component and the recombination rate.

Mentions: The coefficients associated with the second principal component, described above, were found not to be significantly correlated with the recombination rates. However, the coefficients of the third principal component did correlate with recombination rate, with coefficient  = −0.75. A graph of this data is shown in Figure 4. This is statistically significant at the 2% level, and is at least as strong a correlation as was found above for G+C content. This third principal component appears to capture a contribution of the SIDD properties to the recombination rate that is not due to the average G+C content of the flanks, because the coefficients of this component are not significantly correlated with that parameter. (Data not shown.) Instead, it may depend on higher resolution attributes involving the distribution of the GC base pairs in the flanks.


Superhelical duplex destabilization and the recombination position effect.

Sershen CL, Mell JC, Madden SM, Benham CJ - PLoS ONE (2011)

The correlation between the coefficients of the third principal                            component and the recombination rate.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3111454&req=5

pone-0020798-g004: The correlation between the coefficients of the third principal component and the recombination rate.
Mentions: The coefficients associated with the second principal component, described above, were found not to be significantly correlated with the recombination rates. However, the coefficients of the third principal component did correlate with recombination rate, with coefficient  = −0.75. A graph of this data is shown in Figure 4. This is statistically significant at the 2% level, and is at least as strong a correlation as was found above for G+C content. This third principal component appears to capture a contribution of the SIDD properties to the recombination rate that is not due to the average G+C content of the flanks, because the coefficients of this component are not significantly correlated with that parameter. (Data not shown.) Instead, it may depend on higher resolution attributes involving the distribution of the GC base pairs in the flanks.

Bottom Line: 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 show that the flanking sequences significantly affect the free energy of denaturation at specific sites interior to the plasmid.

View Article: PubMed Central - PubMed

Affiliation: Baylor College of Medicine, Houston, Texas, United States of America. sershen@bcm.edu

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.

Show MeSH
Related in: MedlinePlus