Bubble Dynamics in Double-Stranded DNA

Altan‐Bonnet, Grégoire; Libchaber, Albert; Krichevsky, Oleg

doi:10.1103/physrevlett.90.138101

Cited by 270 publications

(516 citation statements)

References 16 publications

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“…Because these measurements were done below the melting temperature of the AT-rich regions, the observed relaxation times reflect primarily the closing kinetics, with the opening kinetics occurring much slower. These closing times are significantly slower than previously reported closing times for single base pairs, which are found to be in the range of Ϸ10-300 ns (38,(40)(41)(42), and suggest that large bubbles are additionally stabilized, perhaps by stacking interactions in the singlestranded regions (39).…”

Section: Discussioncontrasting

confidence: 66%

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Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF

Kuznetsov¹,

Sugimura

Vivas³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Regulation of gene expression involves formation of specific protein-DNA complexes in which the DNA is often bent or sharply kinked. Kinetics measurements of DNA bending when in complex with the protein are essential for understanding the molecular mechanism that leads to precise recognition of specific DNAbinding sites. Previous kinetics measurements on several DNAbending proteins used stopped-flow techniques that have limited time resolution of few milliseconds. Here we use a nanosecond laser temperature-jump apparatus to probe, with submillisecond time resolution, the kinetics of bending͞unbending of a DNA substrate bound to integration host factor (IHF), an architectural protein from Escherichia coli. The kinetics are monitored with time-resolved FRET, with the DNA substrates end-labeled with a FRET pair. The temperature-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. The DNA bending rates range from Ϸ2 ms ؊1 at Ϸ37°C to Ϸ40 ms ؊1 at Ϸ10°C and correspond to an activation energy of Ϸ14 ؎ 3 kcal͞mol. These rates and activation energy are similar to those of a single A:T base pair opening inside duplex DNA. Thus, our results suggest that spontaneous thermal disruption in base-paring, nucleated at an A:T site, may be sufficient to overcome the free energy barrier needed to partially bend͞kink DNA before forming a tight complex with IHF.DNA bending kinetics ͉ laser temperature jump ͉ protein-DNA interactions ͉ time-resolved FRET measurements

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Section: Discussioncontrasting

confidence: 66%

“…The opening͞closing dynamics of internal bubbles in AT-rich stretches of dsDNA, flanked by GC-rich ''clamps,'' have also been monitored by fluctuation correlation spectroscopy (39). These measurements yield characteristic relaxation time scales of 30-100 s for bubble dynamics in the temperature range of 20-50°C.…”

Section: Discussionmentioning

confidence: 99%

Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF

Kuznetsov¹,

Sugimura

Vivas³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…In fact, without the loop closure term, Eq. (5) exactly equals the expression used to fit the fluorescence correlation data in reference [5]. The Fokker-Planck Eq.…”

Section: Continuous Fokker-planck Equation Approachmentioning

confidence: 94%

“…describe the exponential relaxation of modes whose relative contribution c p is determined by the initial condition. An important experimental quantity is the autocorrelation function A(t) = m(t)m(0) [5]. It can be written in the form [25] …”

Section: Discrete Master Equation Approach: Including the Bubble Initmentioning

confidence: 99%

“…The size of a DNA-bubble changes constantly by successive unzipping or zipping of base-pairs at the zipping forks where the single-stranded bubble connects to the intact doublehelix. As we assume that the (un)zipping dynamics (single zipping events running off on the scale of a few tens of µsec [5]) is slower than the Rouse relaxation time ∼ n 2 of the rather short ssDNA strand making up the bubble [6] (i.e., we neglect dynamic feedback from the rest of the DNA molecule), this DNA breathing can be interpreted as a random walk in the one-dimensional coordinate n, the number of denatured base-pairs. In what follows, we first propose a continuum description to bubble dynamics in terms of a Fokker-Planck equation, that describes a stochastic process for the bubble size n in a potential given by the Poland-Scheraga free energy.…”

Section: Introductionmentioning

confidence: 99%

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Dynamic Approach to DNA Breathing

Metzler¹,

Ambjörnsson²

2005

J Biol Phys

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Abstract.Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quantities such as the lifetime, an important measure for the description of the interaction of a breathing DNA molecule and selectively single-stranded DNA binding proteins. Our approach is consistent with recent single molecule measurements of bubble fluctuation. We also introduce a master equation approach to model DNA breathing, and discuss its differences from the continuous Fokker-Planck description.

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Fluorescence Correlation Spectroscopy in Living Cells: A Practical Approach

Altan‐Bonnet

2009

CP Cell Biology

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Fluorescence correlation spectroscopy (FCS) is a single‐molecule fluorescence technique used to monitor molecular dynamics. It can be applied to living cells expressing fluorescently labeled proteins and lipids to determine the diffusion timescales and the total number of diffusing fluorescent molecules in the cell. A practical step‐by‐step approach to performing FCS with a commercial spectroscopy/microscopy system, the Zeiss Confocor 3, how to set up live‐cell FCS experiments, acquire reliable data, and finally how to analyze the data acquired, are all described in this unit. Curr. Protoc. Cell Biol. 45:4.24.1‐4.24.14. © 2009 by John Wiley & Sons, Inc.

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Bubble Dynamics in Double-Stranded DNA

Cited by 270 publications

References 16 publications

Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF

Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF

Dynamic Approach to DNA Breathing

Fluorescence Correlation Spectroscopy in Living Cells: A Practical Approach

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