Dependence on temperature and GC content of bubble length distributions in DNA

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bubble sizes up to the order of a hundred base pairs. The dependence of the parameters of bubble length distribution on temperature and the GC content is investigated. We provide simple expressions which approximately describe these relations. The variation of the average bubble length is also presented. We find a temperature dependence of the exponent c that appears in the distribution of bubble lengths. If an analogous dependence exists in the loop entropy exponent of real DNA, it may be relevant to understand overstretching in force-extension experiments.

💡 Research Summary

The paper investigates how temperature and guanine‑cytosine (GC) content affect the statistical distribution of denaturation bubbles—contiguous stretches of opened base pairs—in double‑stranded DNA. The authors employ the Peyrard‑Bishop‑Dauxois (PBD) model, a mesoscopic Hamiltonian that represents hydrogen‑bond stretching with a Morse potential and stacking interactions with an anharmonic coupling term. By performing extensive Metropolis Monte Carlo simulations at thermal equilibrium, they generate ensembles of DNA configurations for a range of temperatures (from well below the melting temperature up to near‑melting) and for several GC fractions (from AT‑rich to GC‑rich sequences).

From each configuration they identify bubbles, defined as consecutive base pairs whose separation exceeds a chosen opening threshold, and they record the bubble length (l) (number of opened base pairs). The resulting probability distribution (P(l)) is found to follow a combined power‑law and exponential form:

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