Large bubble drives melting in circular DNA
arXiv:2404.08244 · doi:10.1039/D4CP01536C
Abstract
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulation. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which agrees with the previous predictions of circular DNA melting in the presence of supercoiling. By analyzing sector-wise changes in average base-pair distance, our study reveals that the melting behavior of circular DNA closely resembles that of linear DNA. Additionally, we find a marked difference in the thermal stability of circular DNA over linear DNA at very short length scales, an effect that diminishes as the length of circular DNA increases. The stability of smaller circular DNA is linked to the occurrence of transient small bubbles, characterized by a lower probability of growth.
11 figures
References in corpus (19)
- Why is the DNA Denaturation Transition First Order?
- DNA unzipped under a constant force exhibits multiple metastable intermediates
- Order of the phase transition in models of DNA thermal denaturation
- Theory of Bubble Nucleation and Cooperativity in DNA Melting
- Measurement of the Phase Diagram of DNA Unzipping in the Temperature- Force Plane
- Bend-Induced Twist Waves and the Structure of Nucleosomal DNA
- Mechanical denaturation of DNA: existence of a low temperature denaturation
- Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance
- Role of loop entropy in the force induced melting of DNA hairpin
- Pause Point Spectra in DNA Constant-Force Unzipping
- DNA denaturation bubbles at criticality
- Dynamical phase transition of a periodically driven DNA
- Distributions of Bubble Lifetimes and Bubble Lengths in DNA
- Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting
- Free energy landscape and characteristic forces for the initiation of DNA unzipping
- Macroscopic loop formation in circular DNA denaturation
- Softening of DNA near Melting as Disappearance of an Emergent Property
- Denaturation of Circular DNA: Supercoils and Overtwist
- Helix-coil Transition in Closed Circular DNA