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Literature DB >> 12672955

Localization of denaturation bubbles in random DNA sequences.

Terence Hwa¹, Enzo Marinari, Kim Sneppen, Lei-han Tang.

Abstract

We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to AT-rich segments. In the localized regime, the bubbles exhibit "aging" and move around subdiffusively with continuously varying dynamic exponents. These properties are derived by using results of large-deviation theory together with scaling arguments and are verified by Monte Carlo simulations.

Mesh：

Substances：
DNA

Year: 2003 PMID： 12672955 PMCID： PMC404689 DOI： 10.1073/pnas.0736291100

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

17 in total

Localization of denaturation bubbles in random DNA sequences.

1. Rare-event induced binding transition of heteropolymers.

2. Why is the DNA denaturation transition first order?

Review 3. Stress-induced structural transitions in DNA and proteins.

4. Statistical significance of probabilistic sequence alignment and related local hidden Markov models.

5. Single molecule statistics and the polynucleotide unzipping transition.

6. Subdiffusion and localization in the one-dimensional trap model.

7. Physical constraints and functional characteristics of transcription factor-DNA interaction.

8. Improved nearest-neighbor parameters for predicting DNA duplex stability.

9. Statistical mechanics of supercoiled DNA.

10. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.

1. Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping.

2. DNA dynamically directs its own transcription initiation.

3. Breathing dynamics in heteropolymer DNA.

4. Formation and positioning of nucleosomes: effect of sequence-dependent long-range correlated structural disorder.

5. Localization and delocalization of energy in a Peyrard-Bishop chain.

6. Dynamic approach to DNA breathing.

7. Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites.

8. Observation of universal ageing dynamics in antibiotic persistence.

9. Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking.

10. Real-time detection of cruciform extrusion by single-molecule DNA nanomanipulation.