# Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations

## TL;DR

This paper uses simulations to explain how bent DNA sensors work, showing that magnesium ions stabilize bent DNA and improve its sensitivity.

## Contribution

The study provides a quantitative understanding of bent DNA sensor mechanisms using all-atom molecular dynamics simulations.

## Key findings

- Mg2+ ions reduce DNA strand fluctuations and stabilize bent DNA.
- Computational results are validated by melting curve and FRET experiments.
- Bent DNA is mechanically unstable and sensitive to ion concentration.

## Abstract

Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics of sharply bent DNA molecules in the absence and presence of Mg2+ ions at different concentrations. The simulations show that Mg2+ ions reduce the fluctuations of DNA strands, enhance base-pairing, and stabilize bent DNA molecules. The computational results are further verified by both melting curve experiments and ensemble FRET measurements, highlighting the mechanical instability and sensitivity of bent DNA molecules.