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

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

2005-08-20

arxiv.org/abs/cond-mat/0508492v1

Physics

Condensed Matter

Soft Condensed Matter

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

Scientific paper

10.1088/0953-8984/17/49/022

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.

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