Unzipping of DNA with correlated base sequence.

  title={Unzipping of DNA with correlated base sequence.},
  author={Armen E. Allahverdyan and Zh. S. Gevorkian and Chin-Kun Hu and Ming-Chya Wu},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  volume={69 6 Pt 1},
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase stability of DNA with respect to the external unzipping force. Due to long-range correlations the number of unzipped base pairs displays two widely different scenarios depending on the details of the base sequence: either there is no unzipping phase transition at… 

Force induced unzipping of DNA with long range correlated noise

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Interfacial instability and DNA fork reversal by repair proteins

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  • 2010
It is proposed here that a softening of the zipped-unzipped interface at the fork results in the front propagating towards the unzipped side.

Impacts of magnesium ions on the unzipping of λ-phage DNA

We used magnetic tweezers to exert a constant force to separate double stranded λ-phage DNA as a function of temperature and buffer content. The separation was performed at temperatures ranging from

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Single molecule statistics and the polynucleotide unzipping transition.

  • D. LubenskyD. Nelson
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    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2002
Despite their unusual form, the extension versus force curves for single molecules still reveal remnants of the disorder-averaged critical behavior, which should reappear in micromanipulation experiments on proteins and on folded RNA molecules.

Phase diagram of force-induced DNA unzipping in exactly solvable models.

It is confirmed the existence of a cold denaturation transition recently observed in numerical simulations: for a finite range of forces, the system is unzipped by decreasing the temperature.

Dynamical scaling of the DNA unzipping transition.

These models enable us to characterize the dynamics of the process starting from a nonequilibrium initial condition and show that the dynamical mechanism for the unzipping by force is very robust and the scaling behavior is independent of the details of the description and, hence, superuniversal.

Pulling pinned polymers and unzipping DNA.

For random DNA sequences with short-ranged correlations, exact results for the number of monomers liberated and the specific heat are obtained, including the critical behavior at the transition.


This paper aims at understanding the statistical features of nucleic acid sequences from the knowledge of the dynamical process that produces them, and it is observed that intron sequences (noncoding sequences) tend to have longer correlation lengths than exon sequences (protein-c coding sequences).

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This work proposes a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which it refers to as a 'DNA walk', and uncovers a remarkably long-range power law correlation.

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    Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
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This work considers the problem of pulling a polymer out of a potential well by a force applied to one of its ends by using the Rouse model for a description of the dynamics of the peeling out, and studies the average behavior of the chain by replacing the random noise by its mean.

Long-range correlations in genomic DNA: a signature of the nucleosomal structure.

A comparative statistical analysis of DNA bending profiles and of the corresponding DNA texts suggests that small-scale PLC are related to the mechanisms underlying the wrapping of DNA in the nucleosomal structure and speculate that the large scale P LC are the signature of the higher-order structure and dynamics of chromatin.

Generalized Lévy-walk model for DNA nucleotide sequences.

The generalized Lévy-walk model simultaneously accounts for the long-range correlations in noncoding DNA sequences and for the apparently paradoxical finding of long subregions of biased random walks (length lj) within these correlated sequences.

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Mutual information function, which is an alternative to correlation function for symbolic sequences, and a "symbolic spectrum" are calculated for a human DNA sequence containing mostly intron