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Journal of Biomedicine and Biotechnology
Volume 2009, Article ID 516723, 8 pages
Research Article

DNA Loci Cross-Talk through Thermodynamics

1Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, 80126 Napoli, Italy
2INFN Sezione di Napoli, 80126 Napoli, Italy
3Department of Physics and Complexity Science, University of Warwick, Coventry CV4 7AL, UK

Received 26 March 2009; Revised 5 June 2009; Accepted 8 July 2009

Academic Editor: Serdar Kuyucak

Copyright © 2009 Antonio Scialdone and Mario Nicodemi. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The recognition and pairing of specific DNA loci, though crucial for a plenty of important cellular processes, are produced by still mysterious physical mechanisms. We propose the first quantitative model from Statistical Mechanics, able to clarify the interaction allowing such “DNA cross-talk” events. Soluble molecules, which bind some DNA recognition sequences, produce an effective attraction between distant DNA loci; if their affinity, their concentration, and the relative DNA binding sites number exceed given thresholds, DNA colocalization occurs as a result of a thermodynamic phase transition. In this paper, after a concise report on some of the most recent experimental results, we introduce our model and carry out a detailed “in silico” analysis of it, by means of Monte Carlo simulations. Our studies, while rationalize several experimental observations, result in very interesting and testable predictions.