Nucleotide correlations and electronic transport of DNA sequences

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Feb;71(2 Pt 1):021910. doi: 10.1103/PhysRevE.71.021910. Epub 2005 Feb 23.

Abstract

We use a tight-binding formulation to investigate the transmissivity and wave-packet dynamics of sequences of single-strand DNA molecules made up from the nucleotides guanine G , adenine A , cytosine C , and thymine T . In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for the genomic DNA sequence with those of two artificial sequences: (i) the Rudin-Shapiro one, which has long-range correlations; (ii) a random sequence, which is a kind of prototype of a short-range correlated system, presented here with the same first-neighbor pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the persistence of resonances of finite segments. On the other hand, the wave-packet dynamics seems to be mostly influenced by the short-range correlations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Computer Simulation
  • DNA / analysis*
  • DNA / chemistry*
  • Electric Conductivity
  • Electron Transport*
  • Models, Chemical*
  • Models, Molecular*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleotides / chemistry*
  • Sequence Analysis, DNA / methods*
  • Statistics as Topic
  • Structure-Activity Relationship

Substances

  • Nucleotides
  • DNA