2018/05/11 by François Sicard, Sicard, François, Nicolas Destainville +7
Biochemistry, Genetics and Molecular Biology · Environmental Science · Physics and Astronomy · #Advanced biosensing and bioanalysis techniques #Bacteriophages and microbial interactions #Biological Physics (physics.bio-ph) #DNA and Nucleic Acid Chemistry #FOS: Physical sciences #Soft Condensed Matter (cond-mat.soft) #cond-mat.soft #physics.bio-ph
paper · pdf · doi:10.48550/arxiv.1805.04287
5 pages, 1 figure, and Supporting Information (8 pages, 3 figures). arXiv admin note: text overlap with arXiv:1803.03490
arxiv created 2018/05/11 · openalex publication_date 2018/05/11 · arxiv updated 2018/05/14 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the supercoiled DNA loops found in nature. Their short size makes them extremely susceptible to writhe and twist, which is known to play a central role in DNA denaturation. We investigate minicircle lengths and superhelical densities that induce DNA denaturation bubbles of nanometer size and control well-defined long-life. Mesoscopic modeling and accelerated dynamics simulations allow us to study accurately the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived denaturation bubbles. Our results pave the way for new types of DNA biosensors with enhanced selectivity for specific DNA binding proteins.