A DNA-centered explanation of the DNA polymerase translocation mechanism

Abstract

DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA complex can work against loads greater than 50 pN. It is not known, on the one hand, how chemical energy is transduced into mechanical motion, accounting for such large forces on sub-nanometer steps, and, on the other hand, how energy consumption in fidelity maintenance integrates in this non-equilibrium cycle. Here, we propose a translocation mechanism that points to the flexibility of the DNA, including its overstretching transition, as the principal responsible for the DNA polymerase ratcheting motion. By using thermodynamic analyses, we then find that an external load hardly affects the fidelity of the copying process and, consequently, that translocation and fidelity maintenance are loosely coupled processes. The proposed translocation mechanism is compatible with single-molecule experiments, structural data and stereochemical details of the DNA-protein complex that is formed during replication, and may be extended to RNA transcription.

Thermodynamic framework for information in nanoscale systems with memory

“…9 Replication and transcription are enzymatic reactions that involve an energy source responsible for driving these processes in a certain direction, either forward or backward. 10 The mechanisms used by DNA and RNA polymerases, their respective enzymes, naturally introduce a time arrow.…”

“…We will use the toy model developed in a previous study, 14 which was later on applied to explain the energetic contribution of fidelity to the thermodynamic efficiency of polymerases. 10 We propose partial energy functions with linear dependence on the energies of each object in the absence of neighboring interactions,…”

“…6,7 a) Author to whom correspondence should be addressed: ricardo.arias@ imdea.org Information theory and thermodynamics are converging to each other 8 in their interpretation of phenomena that involve order because physical entropy and information entropy may appear together in many systems like the biomolecular ones. 9,10 In this regard, several efforts have been made to use DNA as a practical, high-capacity, and low maintenance information storage drive. 11,12 Concepts like proofreading, edition, and correction, which can be comprised under the most general paradigm of revision, are becoming common across disciplines due to their intuitive meaning.…”

Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers

“…The strength, directionality, and unipolarity of hydrogen bonding and electrostatic interactions between phosphate and protein cause linkage of phosphate association to protein conformation (Rice et al 1999 ; Wittinghofer 2016 ). This coupling of directed molecular displacement (work) to association/dissociation of phosphate, which is in turn linked to pyrophosphate hydrolysis, has been characterized in myosin and kinesin, in the ribosome and in DNA, RNA, and cellulose polymerases (Wang et al 1998 ; Morin et al 2015 ; Morgan et al 2016 ; Arias-Gonzalez 2017 ). During polymerizations of DNA, RNA, protein, and polyglucose, translocations are structurally and energetically coupled to phosphate association/dissociation.…”

Writing, Proofreading and Editing in Information Theory

“…To this end, we adapt a toy model that was previously developed in the context of DNA replication and transcription [3,19,21]. We propose that at each memory position, the introduction of a bit value (0/1) adds a contribution ±ξ (ξ, a real, positive parameter, which we will name stability contrast) to the correctness of the string and that this contribution is affected through the coupling with the previous bit values (memory), as modeled by a power law (see Supplementary Materials).…”