Biomedical subjects

Enrico Carlon

Publications and source records attributed to Enrico Carlon.

5 recordsLinked to original sources

PubMed2005

Exons, introns, and DNA thermodynamics.

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e., stretches of DNA which do not carry useful information for protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights into the physical mechanisms underlying the evolution of genes.

Biophysics↗

PubMed2004

Unbinding of mutually avoiding random walks and two-dimensional quantum gravity.

We analyze the unbinding transition for a two-dimensional lattice polymer in which the constituent strands are mutually avoiding random walks. At low temperatures the strands are bound and form a single self-avoiding walk. We show that unbinding in this model is a strong first order transition. The entropic exponents associated with denaturated loops and end-segment distributions show sharp differences at the transition point and in the high temperature phase. Their values can be deduced from some exact arguments relying on a conformal mapping of copolymer networks into a fluctuating geometry, i.e., in the presence of quantum gravity. An excellent agreement between analytical and numerical estimates is observed for all cases analyzed.

Journal Article↗

PubMed2003

Reparametrizing the loop entropy weights: effect on DNA melting curves.

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. So far, in the modeling of DNA melting, the entropy of denaturated loops has been estimated from the number of configurations of a closed self-avoiding walk. It is well understood now that a loop embedded in a chain is characterized by a loop closure exponent c which is higher than that of an isolated loop. Here we report an analysis of DNA melting curves for sequences of a broad range of lengths (from 10 to 10(6) base pairs) calculated with a program based on the algorithms underlying MELTSIM. Using the embedded loop exponent we find that the cooperativity parameter is one order of magnitude bigger than current estimates. We argue that in the melting region the double helix persistence length is greatly reduced compared to its room temperature value, so that the use of the embedded loop closure exponent for real DNA sequences is justified.

Algorithms↗

PubMed2002

Scaling in DNA unzipping models: denaturated loops and end segments as branches of a block copolymer network.

For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions are consistent with first-order thermal denaturation in both cases. Results for end segments show a coexistence of two distinct power laws in the relative distributions, which is not foreseen by a recent approach in which DNA is treated as a homogeneous network of linear polymer segments. This unexpected feature, and the discrepancies with such an approach, are explained in terms of a refined scaling picture in which a precise distinction is made between network branches representing single-stranded and effective double-stranded segments.

Journal Article↗

PubMed2002

Roles of stiffness and excluded volume in DNA denaturation.

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, P approximately l(-c). If excluded volume effects are fully taken into account, c = 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.

DNA↗