Helicoidal transfer matrix model for inhomogeneous DNA melting.
An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically stressed DNA with a fixed linking number constraint. Without loss of accuracy, the continuous degrees of freedom can be discretized using a minimal number of discretization points, yielding an effective transfer matrix model of modest dimension (d=36). The resulting algorithms to compute DNA melting profiles are both simple and efficient.
Bioinformatics and Evolutionary Genomics, Department of Plant Systems Biology, VIB/Ghent University, Technologiepark 927, B-9052 Gent, Belgium. tom.michoel@psb.ugent.be
Tom
T
Michoel
Yves
Y
Van de Peer