Physics – Condensed Matter – Statistical Mechanics
Scientific paper
2011-05-24
Biophysical Journal, 100 : 1765-1774 (2011)
Physics
Condensed Matter
Statistical Mechanics
Main paper: 20 pages and 6 figures. Supplementary Material: 25 pages
Scientific paper
10.1016/j.bpj.2011.01.071
We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness of the molecular setup moderately enhances the signal-to-noise ratio (SNR) in hopping experiments as compared to conventional long handles constructs (approximately 700 bp). The shorter construct results in a signal of higher SNR and slower folding/unfolding kinetics, thereby facilitating the detection of otherwise fast structural transitions. A novel analysis of the elastic properties of the molecular setup, based on high-bandwidth measurements of force fluctuations along the folded branch, reveals that the highest SNR that can be achieved with short handles is potentially limited by the marked reduction of the effective persistence length and stretch modulus of the short linker complex.
Forns Nuria
Hayashi Kumiko
Huguet Josep Maria
Lorenzo Sara de
Manosas Maria
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