# Bubble dynamics in double-stranded DNA.

@article{AltanBonnet2003BubbleDI, title={Bubble dynamics in double-stranded DNA.}, author={Gr{\'e}goire Altan-Bonnet and Albert Libchaber and Oleg Krichevsky}, journal={Physical review letters}, year={2003}, volume={90 13}, pages={ 138101 } }

We report the first measurement of the dynamics of bubble formation in double-stranded DNA. Fluctuations of fluorescence of a synthetic DNA construct, internally tagged with a fluorophore and a quencher, are monitored by fluorescence correlation spectroscopy. The relaxation dynamics follow a multistate relaxation kinetics, with a characteristic time scale of 50 microseconds. A simple model of bubble dynamics based on constant zipping-unzipping rates is proposed to account for our experimental…

## 209 Citations

### Bubble dynamics in DNA

- Physics
- 2003

The dynamics of bubble formation in double-stranded DNA is studied in terms of a Fokker–Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland–Scheraga model.

### The dynamics of intermittent strand separation in double-stranded DNA.

- PhysicsThe Journal of chemical physics
- 2007

The transient rupture and reformation of hydrogen bonds between base pairs on distinct chains of double-stranded DNA ("bubble" dynamics) is modeled in terms of the fluctuating distance between the…

### Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA.

- Biology, PhysicsPhysical review. E, Statistical, nonlinear, and soft matter physics
- 2005

The effective free-energy landscape of the DNA bubble is determined and the system can be driven from undisturbed bubble fluctuations to full, binding-protein-induced denaturation by tuning the physical parameters.

### Breathing dynamics in heteropolymer DNA.

- Biology, PhysicsBiophysical journal
- 2007

The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.

### Dynamic Approach to DNA Breathing

- PhysicsJournal of biological physics
- 2005

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 is presented.

### Dynamics of the DNA duplex formation studied by single molecule force measurements.

- BiologyBiophysical journal
- 2004

Comparing different measurements, it is found that both DNA unzipping and the relaxation of tension in DNA are faster than the formation of the double helix.

### Stochastic approach to DNA breathing dynamics

- Physics
- 2005

We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single-molecule time series. It is demonstrated that the model…

### A semiflexible chain model of local denaturation in double-stranded DNA.

- ChemistryThe Journal of chemical physics
- 2006

The results show that the entropy associated with semiflexibility of DNA sensitively affects the size distribution and lifetime of bubble, and the lifetime grows with bubble size m as m(2.7) at temperature close to T(c), which is consistent with the analysis based on a stochastic model of bubble size dynamics.

### Master equation approach to DNA breathing in heteropolymer DNA.

- PhysicsPhysical review. E, Statistical, nonlinear, and soft matter physics
- 2007

A dynamic description of this DNA breathing in a heteropolymer DNA with given sequence in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence is established.

### Strand diffusion-limited closure of denaturation bubbles in DNA

- Physics
- 2012

The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible…

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