Reparametrizing loop entropy weights: effect on DNA melting curves
Ralf Blossey1, Enrico Carlon2
1blossey@bioinf.uni-sb.de, IRI; 2carlon@lusi.uni-sb.de, IRI
Motivation: Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior loop melting. These corrected weighting factors affect the computation of DNA melting temperatures based on bioinformatics software packages.
Results: We report an analysis of DNA melting curves for DNA of genomic length, calculated by a program based on the algorithms underlying MELTSIM for a fragment of D. Discoideum and for tandemly repeated synthetic sequences inserted on a linearized plasmid, for which well-documented experimental results are available. Using the correct input parameters for the loop statistics we find that the cooperativity parameter may be one order of magnitude larger than current estimates.We report on an the algorithms underlying MELTSIM which employs novel estimates for the weights of loop entropy factors. As test-cases, we studied a fragment of D. Discoideum and tandemly repeated synthetic sequences inserted in a linearized plasmid, for which well-documented experimental results are available. We find that the cooperativity parameter may be about analysis of melting curves for DNA of genomic length, calculated by an in-house software based on one order of magnitude larger than its consensus value.