Calculation of the hole mobilities of the three homopolynucleotides, poly(guanilic acid), poly(adenilic acid), and polythymidine in the presence of water and Na+ ions

Attila Bende, F. Bogár, Ferenc Beleznay, János Ladik

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4 Citations (Scopus)

Abstract

Recent high resolution x-ray diffraction experiments have determined the structure of nucleosomes. In it 147 base pair long DNA B superhelix is wrapped around the eight nucleohistone proteins. They have found that there are many hydrogen-bonds (H-bonds) between the negative sites phosphate (P O4-) groups DNA, and first of all there is the positively charged lysine and arginine side chains of the histones. This means that there is a non-negligible charge transfer from DNA to the proteins causing a hole current in DNA and an electronic one in the proteins. If the relative positions of the two macromolecules change due to some external disturbances, the DNA moves away from the protein and can be read. If this happens simultaneously at several nucleosomes and at many places in chromatin (built up from the nucleosomes), undesired genetic information becomes readable. This final end can cause the occurrence of oncoproteins at an undesired time point which most probably disturbs the self-regulation of a differentiated cell. The connection of these chain of events with the initiation of cancer is obvious. To look into the details of these events we have used the detailed band structures of the four homopolynucleotides in the presence of water and natrium (Na+) ions calculated previously with the help of the ab initio Hartree-Fock crystal orbital method. We have found that in the case of three homopolynucleotides the width of their valence band is broad enough (∼10 times broader than the thermal energy at 300 K) for the application of the simple deformation potential approximation for transport calculations. With the help of this we have determined the hole mobilities at 300 K and 180 K of poly(guanilic acid), poly(adenilic acid), and polythimidine (polycytidine has a too narrow valence band for the application of the deformation potential method). The obtained mobilities are large enough to allow Bloch-type conduction in these systems. At the end of the paper we discuss briefly the possible mechanism of charge transport in aperiodic DNA as a combination of Bloch-type conduction, hopping, and tunneling.

Original languageEnglish
Article number061923
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume78
Issue number6
DOIs
Publication statusPublished - Dec 1 2008

Fingerprint

hole mobility
deoxyribonucleic acid
Protein
Water
acids
Conduction
water
proteins
ions
Charge Transport
Charge Transfer
Hydrogen Bonds
Chromatin
Band Structure
P-groups
Phosphate
X-ray Diffraction
valence
conduction
Cancer

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Statistical and Nonlinear Physics
  • Statistics and Probability

Cite this

@article{2336a5f0ae454f1fb1ec63c93e129af6,
title = "Calculation of the hole mobilities of the three homopolynucleotides, poly(guanilic acid), poly(adenilic acid), and polythymidine in the presence of water and Na+ ions",
abstract = "Recent high resolution x-ray diffraction experiments have determined the structure of nucleosomes. In it 147 base pair long DNA B superhelix is wrapped around the eight nucleohistone proteins. They have found that there are many hydrogen-bonds (H-bonds) between the negative sites phosphate (P O4-) groups DNA, and first of all there is the positively charged lysine and arginine side chains of the histones. This means that there is a non-negligible charge transfer from DNA to the proteins causing a hole current in DNA and an electronic one in the proteins. If the relative positions of the two macromolecules change due to some external disturbances, the DNA moves away from the protein and can be read. If this happens simultaneously at several nucleosomes and at many places in chromatin (built up from the nucleosomes), undesired genetic information becomes readable. This final end can cause the occurrence of oncoproteins at an undesired time point which most probably disturbs the self-regulation of a differentiated cell. The connection of these chain of events with the initiation of cancer is obvious. To look into the details of these events we have used the detailed band structures of the four homopolynucleotides in the presence of water and natrium (Na+) ions calculated previously with the help of the ab initio Hartree-Fock crystal orbital method. We have found that in the case of three homopolynucleotides the width of their valence band is broad enough (∼10 times broader than the thermal energy at 300 K) for the application of the simple deformation potential approximation for transport calculations. With the help of this we have determined the hole mobilities at 300 K and 180 K of poly(guanilic acid), poly(adenilic acid), and polythimidine (polycytidine has a too narrow valence band for the application of the deformation potential method). The obtained mobilities are large enough to allow Bloch-type conduction in these systems. At the end of the paper we discuss briefly the possible mechanism of charge transport in aperiodic DNA as a combination of Bloch-type conduction, hopping, and tunneling.",
author = "Attila Bende and F. Bog{\'a}r and Ferenc Beleznay and J{\'a}nos Ladik",
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AU - Bogár, F.

AU - Beleznay, Ferenc

AU - Ladik, János

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