2012/08/09 by J. Ricardo Arias‐Gonzalez, J. Ricardo Arias-Gonzalez
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Advanced Thermodynamics and Statistical Mechanics #Biology #Computational biology #DNA #DNA polymerase #DNA replication #Entropy (arrow of time) #Gene Regulatory Network Analysis #Genetics #Physics #Polymerase #Quantum Mechanics and Applications #Quantum mechanics #Statistical physics #cond-mat.stat-mech #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.1371/journal.pone.0042272
published as PLoS ONE 7(8): e42272 (2012) · 25 pages, 5 figures
openalex publication_date 2012/08/09 · arxiv created 2012/08/14 · arxiv updated 2012/08/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Information has an entropic character which can be analyzed within the framework of the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. Here, we introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorporation of the nucleotides. The copied strand is, to first order of approximation, a state of independent and non-indentically distributed random variables for which the nucleotide that is incorporated by the polymerase at each step is dictated by the template strand, and to second order of approximation, a state of non-uniformly distributed random variables with nearest-neighbor interactions for which the recognition of secondary structure by the polymerase in the resultant double-stranded polymer determines the entropy of the replicated strand. Two incorporation mechanisms arise naturally and their biological meanings are explained. It is known that replication occurs far from equilibrium and therefore the Shannon entropy here derived represents an upper bound for replication to take place. Likewise, this entropy sets a universal lower bound for the copying fidelity in replication.