Helicase activity on DNA as a propagating front

Abstract

We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front separates the zipped and unzipped phases of a dsDNA and a drive acts locally around the front. Bounds from variational analysis and numerical estimates for the speed of a helicase are obtained. Different types of helicase behaviours can be distinguished by the nature of the drive.

arXiv comment5 pages, 5 eps figures; replaced by the published version

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Cited by in corpus (13)

• Single-molecule experiments in biological physics: methods and applications
• Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium
• Randomly forced DNA
• Dynamical phase transition of a periodically driven DNA
• Velocity and processivity of helicase unwinding of double-stranded nucleic acids
• Unzipping DNA by force: thermodynamics and finite size behaviour
• Manipulating a single adsorbed DNA for a critical endpoint
• Can a double stranded DNA be unzipped by pulling a single strand?: Phases of adsorbed DNA
• Thermodynamic relations for DNA phase transitions
• Diffusion of Macromolecules across the Nuclear Pore Complex
• Interfacial instability and DNA fork reversal by repair proteins
• Velocity and diffusion coefficient of $A+A\leftrightarrow A$ reaction fronts in one dimension
• DNA Unzipping Transition