Denaturation Patterns in Heterogeneous DNA

Abstract

The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes are consistent with the model potential for the hydrogen bonds between complementary strands. The portion of configuration space contributing to the partition function is determined, at any temperature, by selecting the ensemble of paths which fulfill the second law of thermodynamics. For a short DNA fragment, the denaturation is signaled by a succession of peaks in the specific heat plots while the entropy grows continuously versus $T$. Thus, the opening of the double strand with bubble formation appears as a smooth crossover due to base pair fluctuation effects which are accounted for by the path integral method. The multistep transition is driven by the AT-rich regions of the DNA fragment. The base pairs path ensemble shows an enhanced degree of cooperativity at about the same temperatures for which the specific heat peaks occur. These findings establish a link between microscopic and macroscopic signatures of the transition. The fractions of mean base pair stretchings are computed by varying the AT base pairs content and taking some threshold values for the occurrence of the molecule denaturation.

Physical Review E (in press)

References in corpus (11)

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Cited by in corpus (9)

• The probability analysis of opening of DNA
• Stacking Interactions in Denaturation of DNA Fragments
• Entropic Penalties in Circular DNA Assembly
• Twisting short dsDNA with applied tension
• Anharmonic stacking in supercoiled DNA
• Twist-stretch profiles of DNA chains
• Unwinding of circular helicoidal molecules versus size
• Modeling DNA Dynamics by Path Integrals
• Helical Disruptions in Small Loops of DNA