Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/95816
Title: Exploring the energy landscape of nucleic acid hairpins using laser temperature-jump and microfluidic mixing
Authors: Kuznetsov, Serguei V.
Lapidus, Lisa J.
Narayanan, Ranjani
Zhu, Li
Velmurugu, Yogambigai
Roca, Jorjethe
Prehna, Gerd
Ansari, Anjum
Issue Date: 2012
Source: Narayanan, R., Zhu, L., Velmurugu, Y., Roca, J., Kuznetsov, S. V., Prehna, G., et al. (2012). Exploring the Energy Landscape of Nucleic Acid Hairpins Using Laser Temperature-Jump and Microfluidic Mixing. Journal of the American Chemical Society, 134(46), 18952-18963.
Series/Report no.: Journal of the American chemical society
Abstract: We have investigated the multidimensionality of the free energy landscape accessible to a nucleic acid hairpin by measuring the relaxation kinetics in response to two very different perturbations of the folding/unfolding equilibrium, either a laser temperature-jump or ion-jump (from rapid mixing with counterions). The two sets of measurements carried out on DNA hairpins (4 or 5 base pairs in the stem and 21-nucleotide polythymine loop), using FRET between end labels or fluorescence of 2-aminopurine in the stem as conformational probes, yield distinctly different relaxation kinetics in the temperature range 10–30 °C and salt range 100–500 mM NaCl, with rapid mixing exhibiting slower relaxation kinetics after an initial collapse of the chain within 8 μs of the counterion mixing time. The discrepancy in the relaxation times increases with increasing temperatures, with rapid mixing times nearly 10-fold slower than T-jump times at 30 °C. These results rule out a simple two-state scenario with the folded and unfolded ensemble separated by a significant free energy barrier, even at temperatures close to the thermal melting temperature Tm. Instead, our results point to the scenario in which the conformational ensemble accessed after counterion condensation and collapse of the chain is distinctly different from the unfolded ensemble accessed with T-jump perturbation. Our data suggest that, even at temperatures in the vicinity of Tm or higher, the relaxation kinetics obtained from the ion-jump measurements are dominated by the escape from the collapsed state accessed after counterion condensation.
URI: https://hdl.handle.net/10356/95816
http://hdl.handle.net/10220/11261
DOI: 10.1021/ja301218e
Schools: School of Physical and Mathematical Sciences 
Rights: © 2012 American Chemical Society
Fulltext Permission: none
Fulltext Availability: No Fulltext
Appears in Collections:SPMS Journal Articles

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