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Biophys J, November 2000, p. 2692-2704, Vol. 79, No. 5
Department of Chemistry, New York University, New York, NY 10003 USA
Ligation of short DNA fragments results in the formation
of linear and circular multimers of various lengths. The distribution of products in such a reaction is often used to evaluate fragment bending caused by specific chemical modification, by bound ligands or
by the presence of irregular structural elements. We have developed a
more rigorous quantitative approach to the analysis of such experimental data based on determination of j-factors for
different multimers from the distribution of the reaction products.
j-Factors define the effective concentration of one end of a
linear chain in the vicinity of the other end. To extract
j-factors we assumed that kinetics of the reaction is
described by a system of differential equations where
j-factors appear as coefficients. The assumption was
confirmed by comparison with experimental data obtained here for DNA
fragments containing A-tracts. At the second step of the analysis
j-factors are used to determine conformational parameters of
DNA fragments: the equilibrium bend angle, the bending rigidity of the
fragment axis, and the total twist of the fragments. This procedure is
based on empirical equations that connect the conformational parameters
with the set of j-factors. To obtain the equations, we
computed j-factors for a large array of conformational
parameters that describe model fragments. The approach was tested on
both simulated and actual experimental data for DNA fragments
containing A-tracts. A-tract DNA bend angle determined here is in good
agreement with previously published data. We have established a set of
experimental conditions necessary for the data analysis to be successful.
Biophys J, November 2000, p. 2692-2704, Vol. 79, No. 5
© 2000 by the Biophysical Society 0006-3495/00/11/2692/13 $2.00
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