2001
DOI: 10.1073/pnas.131477798
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Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins

Abstract: Elucidating the mechanism of folding of polynucleotides depends on accurate estimates of free energy surfaces and a quantitative description of the kinetics of structure formation. Here, the kinetics of hairpin formation in single-stranded DNA are measured after a laser temperature jump. The kinetics are modeled as configurational diffusion on a free energy surface obtained from a statistical mechanical description of equilibrium melting profiles. The effective diffusion coefficient is found to be strongly tem… Show more

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Cited by 175 publications
(300 citation statements)
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“…1). Previous work shows that this addition is sufficient to buffer the core of the hairpin stem against thermal end-fraying of the duplex and against deviations from B-form DNA resulting from the presence of the loop (26). There is good evidence that the core of a hairpin stem interacts with proteins and small molecule ligands indistinguishably from DNA duplexes composed of two individual complementary strands (27,28).…”
Section: Resultsmentioning
confidence: 99%
“…1). Previous work shows that this addition is sufficient to buffer the core of the hairpin stem against thermal end-fraying of the duplex and against deviations from B-form DNA resulting from the presence of the loop (26). There is good evidence that the core of a hairpin stem interacts with proteins and small molecule ligands indistinguishably from DNA duplexes composed of two individual complementary strands (27,28).…”
Section: Resultsmentioning
confidence: 99%
“…Our T-jump spectrometer consists of a multimode Q-switched Nd:YAG laser (Continuum Surelite II, Santa Clara, CA; fwhm ϭ 6 ns, 300 mJ per pulse at 1.06 m) that is used to pump a 1-m-long Raman cell consisting of high pressure methane gas (27,48). The first Stokes line is separated from the fundamental by using a Pellin-Broca prism.…”
Section: Methodsmentioning
confidence: 99%
“…In the last decade, laser T-jump has emerged as a powerful tool whereby conformational changes in biomolecules can be monitored on time scales of submicroseconds-tomilliseconds (23)(24)(25)(26)(27)(28)(29). The T-jump measurements, in combination with stopped-flow measurements, demonstrate that the binding of IHF to its cognate DNA site involves an intermediate state with straight or, possibly, partially bent DNA (Fig.…”
mentioning
confidence: 99%
“…Recently, the studies of the folding kinetics for RNA hairpins (11), peptide ␤-hairpin (12)(13)(14)(15)(16)(17)(18), and DNA hairpins (19)(20)(21)(22)(23)(24)(25) have become highly active. However, despite the active efforts on the modeling of RNA folding (26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39), quantitative analysis based on the first principle calculations has not been explored very much for RNA hairpin-folding kinetics.…”
mentioning
confidence: 99%