Blinking statistics of a molecular beacon triggered by end-denaturation of DNA

TL;DR

This paper models the blinking behavior of a molecular beacon during DNA denaturation using a master equation approach, exploring effects of protein binding and potential for nanoscale sensing.

Contribution

It introduces a master equation model based on Poland-Scheraga free energy to analyze DNA denaturation dynamics and blinking behavior of molecular beacons.

Findings

Quantifies blinking dynamics during DNA denaturation.

Shows effects of protein binding on denaturation behavior.

Proposes a nanoscale sensing application.

Abstract

We use a master equation approach based on the Poland-Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA, that is clamped at one end. In particular, we quantify the blinking dynamics of a fluorophore-quencher pair mounted within the denaturation wedge. We also study the behavioural changes in the presence of proteins, that selectively bind to single-stranded DNA. We show that such a setup could be well-suited as an easy-to-implement nanodevice for sensing environmental conditions in small volumes.