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… 
Bubble dynamics in DNA
TLDR
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.
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
Direct observation of breathing dynamics at the mismatch induced DNA bubble with nanometre accuracy: a smFRET study.
The detailed conformational dynamics of the melted region in double-stranded DNA has been studied using a combination of ensemble and single-molecule FRET techniques. We monitored the millisecond
Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA.
TLDR
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.
TLDR
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
TLDR
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.
TLDR
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
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.
TLDR
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.
TLDR
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.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 28 REFERENCES
Nucleic Acids: Structures, Properties, and Functions
Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text is for those with only a basic
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
Proc
  • Natl. Acad. Sci. U.S.A. 95, 8602
  • 1998
A 34
  • 3191
  • 2001
Phys
  • Rev. E 63, 21901
  • 2001
Phys. Rev. E
  • Phys. Rev. E
  • 2001
Nucleic Acids: Structures
  • Properties, and Functions
  • 2000
Phys
  • Rev. Lett. 85, 4988
  • 2000
Phys. Rev. Lett
  • Phys. Rev. Lett
  • 2000
Phys
  • Rev. E 59, 3408
  • 1999
...
1
2
3
...