Generalized PolandScheraga model for DNA hybridization
Abstract
The PolandScheraga (PS) model for the helixcoil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the same index along the strands are allowed to bind. In this paper, we extend this model by relaxing these constraints: We propose a generalization of the PS model which allows for the binding of two strands of unequal lengths $N_{1}$ and $N_{2}$ with unrelated sequences. We study in particular (i) the effect of mismatches on the hybridization of complementary strands (ii) the hybridization of non complementary strands (as resulting from point mutations) of unequal lengths $N_{1}$ and $N_{2}$. The use of a FixmanFreire scheme scales down the computational complexity of our algorithm from $O(N_{1}^{2}N_{2}^{2})$ to $O(N_{1}N_{2})$.The simulation of complementary strands of a few kbps yields results almost identical to the PS model. For short strands of equal or unequal lengths, the binding displays a strong sensitivity to mutations. This model may be relevant to the experimental protocol in DNA microarrays, and more generally to the molecular recognition of DNA fragments. It also provides a physical implementation of sequence alignments.
 Publication:

arXiv eprints
 Pub Date:
 February 2004
 arXiv:
 arXiv:qbio/0402037
 Bibcode:
 2004q.bio.....2037G
 Keywords:

 Quantitative Biology  Biomolecules;
 Condensed Matter  Soft Condensed Matter
 EPrint:
 20 pages