Introducing a model of pairing based on base pair specific interactions between identical DNA sequences

@article{Lee2017IntroducingAM,
  title={Introducing a model of pairing based on base pair specific interactions between identical DNA sequences},
  author={Dominic J O' Lee},
  journal={Journal of Physics: Condensed Matter},
  year={2017},
  volume={30},
  pages={075102}
}
  • D. Lee
  • Published 2 November 2017
  • Physics
  • Journal of Physics: Condensed Matter
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model… 
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References

SHOWING 1-10 OF 35 REFERENCES

Homologous Pairing between Long DNA Double Helices.

  • A. Mazur
  • Biology
    Physical review letters
  • 2016
It is shown here that direct recognition between homologous dsDNA is possible through the formation of short quadruplexes due to direct complementary hydrogen bonding of major-groove surfaces in parallel alignment.

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments.

This work probes how the recognition energy changes when one DNA fragment slides past another, and considers, for the first time, homologous sequences in antiparallel alignment, as well as testing previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations and considering more rigorously the optimization of the orientations of the fragments about their long axes upon calculating these recognition energies.

Direct recognition of homology between double helices of DNA in Neurospora crassa

It is shown that a pair of DNA segments can be recognized as homologous if they share triplets of base pairs arrayed with the matching periodicity of 11 or 12 base pairs, which suggests direct interactions between slightly underwound co-aligned DNA duplexes engaging once per turn and over many consecutive turns.

DNA double helices recognize mutual sequence homology in a protein free environment.

Experimental evidence and possible mechanisms for the recognition of homologous DNAs from a distance are reported and discussed, which reveal that nucleotide sequence recognition occurs between double helices separated by water in the absence of proteins.

Evidence of protein-free homology recognition in magnetic bead force–extension experiments

Single-molecule force experiments with a designed 60 kb long dsDNA construct with simple semi-phenomenological models of the unfolding mechanics are reported, and their predictions are compared with the data.

The homology recognition well as an innate property of DNA structure

A theoretical investigation of the form of the potential well that DNA molecules may feel sliding along each other, the bottom of which is determined by the recognition energy, leads to trapping of the molecular tracks of the same homology in direct juxtaposition.

Torsional deformation of double helix in interaction and aggregation of DNA.

It is found that interaction between double helical DNA may result in sequence homology recognition and selective pairing of homologous fragments containing more than 100-200 base pairs and a weak, but potentially measurable, increase in the expected counterion concentration required for aggregation of nonhomologous DNA.

Sequence recognition in the pairing of DNA duplexes.

Modulation of the DNA surface charge pattern enables duplexes longer than approximately 50 base pairs to recognize sequence homology electrostatically at a distance of up to several water layers, which may explain the local recognition observed in pairing of homologous chromosomes and the observed length dependence of homologueous recombination.

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

It is found that AT-rich DNA Duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology, and methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA–DNA attraction.

Helical coherence of DNA in crystals and solution

This article approaches the problem of sequence-dependent DNA conformation by statistical analysis of X-ray and NMR structures of DNA oligomers and finds that the solution structure of synthetic oligomers is characterized by 100–200 Å coherence length, which is similar to ∼150 ÅCoherence length of natural, salmon-sperm DNA.