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

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.

14 pages, 5 figures, LaTeX, IOP style. Accepted to J Phys Cond Mat special issue on diffusion

References in corpus (2)

• Entropy production along a stochastic trajectory and an integral fluctuation theorem
• Stochastic approach to DNA breathing dynamics

Cited by in corpus (4)

• Sequence sensitivity of breathing dynamics in heteropolymer DNA
• Breathing dynamics in heteropolymer DNA
• Bubble merging in breathing DNA as a vicious walker problem in opposite potentials
• Hybridization to surface-bound oligonucleotide probes: Influence of point defects