Helicase on DNA: A Phase coexistence based mechanism

Abstract

We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch ensemble that entails a coexistence of domains of zipped and unzipped phases of DNA, separated by a domain wall. The motor action of the helicase leads to a change in the position of the fixed constraint thereby shifting the domain wall on dsDNA. We associate this off-equilibrium domain wall motion with the unzipping activity of helicase. We show that this proposal gives a clear and consistent explanation of the main observed features of helicases.

Revtex4. 5 pages. 4 figures. Published version

References in corpus (7)

• Force and kinetic barriers in unzipping of DNA
• Single Molecule Statistics and the Polynucleotide Unzipping Transition
• Dynamical scaling of the DNA unzipping transition
• Roles of stiffness and excluded volume in DNA denaturation
• Phase diagram of force-induced DNA unzipping in exactly solvable models
• Mechanical denaturation of DNA: existence of a low temperature denaturation
• DNA sequence from the unzipping force? : one mutation problem

Cited by in corpus (10)

• Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity
• Opening of DNA double strands by helicases. Active versus passive opening
• Randomly forced DNA
• Out-of-equilibrium critical dynamics at surfaces: Cluster dissolution and non-algebraic correlations
• 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
• Helicase activity on DNA as a propagating front
• DNA Unzipping Transition
• Nonlinear waves in double-stranded DNA