Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting

  title={Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting},
  author={Yair A. G. Fosado and Davide Michieletto and Davide Marenduzzo},
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an important role of topology in the physics of DNA denaturation, which is however poorly understood. Here, we shed light on this issue by combining large-scale Brownian Dynamics simulations with an analytically solvable phenomenological Landau mean field theory. We find that the competition… 
Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids
A way to topologically tune DNA mobility via supercoiling is suggested, thus enabling topological control over the (micro)rheology of DNA-based complex fluids.
Simulations of DNA denaturation dynamics under constrained conditions
This work uses a coarse-grained single nucleotide model for dsDNA which considers the helix structure and finds that free DNA melts at faster rate because the entropic gain associated with denaturation is larger.
Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles.
We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of
Double-stranded coarse grained model for DNA: applications to supercoiling and denaturation
A single-nucleotide resolution coarse-grained computational model of DNA is introduced, that faithfully reproduces the geometry of the double-stranded helix and also part of its elastic behaviour, and is employed to study DNA supercoiling.
Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling
It is shown that supercoiling can be exploited to act at a distance on DNA-binding proteins, for instance, unwrapping a nucleosome long before the polymerase reaches it, and the relaxation dynamics of supercoiled double-stranded DNA are analyzed.
Physical principles of retroviral integration in the human genome
A biophysical model for retroviral integration as stochastic and quasi-equilibrium topological reconnections between polymers is developed, identifying previously unnoticed universal principles that regulate this phenomenon.
A review on nonlinear DNA physics
A theory based on the mechanism of ‘self-trapping’ of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure is reviewed and some conjectures on potential future directions for this field are provided.
Integrating transposable elements in the 3D genome
It is argued that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns and suggested that these models may offer orthogonal and generic insights into the integration profiles (or “topography”) of TEs across organisms.
Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus.
It is shown that equilibrium models are not compatible with experiments and a qualitative agreement is recovered by accounting for nonequilibrium processes that can stabilize microphase separated epigenomic domains, and a theory that assumes a coupling between epigenetic mark and genome densities is proposed and studied.
Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance
A striking separation of timescales is found between twist diffusion, which is a simple and fast process, and writhe relaxation, which was slow and entails multiple steps, is found in the relaxation dynamics of supercoiled DNA.


Why is the DNA denaturation transition first order?
The phase transition is found to be first order in d = 2 dimensions and above, in agreement with experiments and at variance with previous theoretical results, in which only excluded-volume interactions within denaturated loops were taken into account.
Torsional stress and local denaturation in supercoiled DNA.
  • C. Benham
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1979
It is shown that local denaturation can be a natural consequence of supercoiling, even in environments where base pairing of linear DNA is energetically favored, and that control of local melting by DNA topoisomerases and DNA gyrases could regulate diverse events involved in transcription, replication, recombination, and repair.
Supercoiling induces denaturation bubbles in circular DNA.
It is shown that in vivo sustained DNA bubbles are likely to occur due to partial twist release in regions rich in weaker AT base pairs, and an analytical derivation of the probability distribution to find multiple bubbles is derived.
A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA
A mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules for time-scales which are relevant to physiological processes is presented.
Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting
This new insight indicates that an increased GC-content adjacent to AT-rich DNA regions will enhance local opening of the double-stranded DNA helix, and is provided by the realization that supercoiling densities of a few percent only induce melting of afew percent of the base pairs.
Stochastic Model of Supercoiling-Dependent Transcription.
There is a sharp crossover from a regime where torsional stresses relax quickly and gene transcription is random, to one where gene expression is highly correlated and tightly regulated by supercoiling.
The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA.
The results differ considerably from expectations based solely upon considerations of chain configuration in vacuo, indicating the importance of solvent-dependent factors in determining the structure of closed circular DNA.
Topological challenges to DNA replication: Conformations at the fork
The importance of replicating DNA conformations and the roles of topoisomerases are discussed, focusing on recent work from the laboratory.
Occurrence of a phase transition in nucleic acid models.
It is found that this happens if c>2, in which case both U(x) (the sequence generating function for loops) and ∂U(x)/∂x converge at the point where x1 (the unit partition function) equals u2 (the statistical weight per unit of an infinite loop, i.e., a free chain).