Control of DNA denaturation bubble nucleation to advance nano-biosensing

TL;DR

This paper explores how controlling DNA denaturation bubbles in minicircles can improve nano-biosensing, using modeling and simulations to understand bubble dynamics for enhanced biosensor design.

Contribution

It introduces a method to control DNA denaturation bubbles in minicircles, advancing biosensing technology through detailed thermodynamic and dynamical analysis.

Findings

DNA minicircle length and superhelical density influence bubble formation

Long-lived nanometer-sized denaturation bubbles can be stabilized

Results enable development of more selective DNA biosensors

Abstract

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.