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Title: Benzo-homologated nucleobases in a nanotube-electrodes setup for DNA sequencing

Abstract

Motivated by the possibility that the conductivity signatures of benzo-homologated DNA bases could be used to sequence DNA, we have investigated the conductivity properties of these bases when they are non-covalently sandwiched between two (5,5) nanotube electrodes. It is found that these bases conduct poorly, making it very difficult to distinguish them. An analysis of the changes in the conductivity of benzo-adenine as a function of the distance between the tips of the nanotubes revealed that, even though the conductance increases by four orders of magnitude when the electrodes are brought closer together, the net conductance remains rather small. These results suggest that benzo-homologated bases, despite having smaller HOMO-LUMO gaps than their natural counterparts, when non-covalently bound to the electrodes cannot be used to sequence DNA by means of conductivity measurements.

Authors:
 [1];  [1];  [1]
  1. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Center for Nanophase Materials Sciences
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
950796
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nanotechnology; Journal Volume: 18; Journal Issue: 42
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DNA; DNA SEQUENCING; ELECTRODES; NANOTUBES

Citation Formats

Fuentes-Cabrera, Miguel A, Meunier, Vincent, and Sumpter, Bobby G. Benzo-homologated nucleobases in a nanotube-electrodes setup for DNA sequencing. United States: N. p., 2007. Web. doi:10.1088/0957-4484/18/42/424019.
Fuentes-Cabrera, Miguel A, Meunier, Vincent, & Sumpter, Bobby G. Benzo-homologated nucleobases in a nanotube-electrodes setup for DNA sequencing. United States. doi:10.1088/0957-4484/18/42/424019.
Fuentes-Cabrera, Miguel A, Meunier, Vincent, and Sumpter, Bobby G. Mon . "Benzo-homologated nucleobases in a nanotube-electrodes setup for DNA sequencing". United States. doi:10.1088/0957-4484/18/42/424019.
@article{osti_950796,
title = {Benzo-homologated nucleobases in a nanotube-electrodes setup for DNA sequencing},
author = {Fuentes-Cabrera, Miguel A and Meunier, Vincent and Sumpter, Bobby G},
abstractNote = {Motivated by the possibility that the conductivity signatures of benzo-homologated DNA bases could be used to sequence DNA, we have investigated the conductivity properties of these bases when they are non-covalently sandwiched between two (5,5) nanotube electrodes. It is found that these bases conduct poorly, making it very difficult to distinguish them. An analysis of the changes in the conductivity of benzo-adenine as a function of the distance between the tips of the nanotubes revealed that, even though the conductance increases by four orders of magnitude when the electrodes are brought closer together, the net conductance remains rather small. These results suggest that benzo-homologated bases, despite having smaller HOMO-LUMO gaps than their natural counterparts, when non-covalently bound to the electrodes cannot be used to sequence DNA by means of conductivity measurements.},
doi = {10.1088/0957-4484/18/42/424019},
journal = {Nanotechnology},
number = 42,
volume = 18,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}
  • We investigated the interfacial electronic structures of Al/adenine/indium-tin-oxide (ITO) and Al/thymine/ITO using in situ ultraviolet and x-ray photoemission spectroscopy and density functional theory calculations. Adenine shows both an interface dipole and level bending, whereas thymine shows only an interface dipole in contact with ITO. In addition, thymine possesses a larger ionization energy than adenine. These are understood with delocalized {pi} states confirmed with theoretical calculations. For the interface between nucleobases and Al, both nucleobases show a prominent reduction of the electron injection barrier from Al to each base in accordance with a downward level shift.
  • Calculations of the direct ionization potentials (DIP) of DNA nucleobases in the fully solvated DNA helix are reported. The results show an unexpected large shift of roughly 3.2-3.3 eV compared to the corresponding gas-phase IP values. The DIP shift is nearly the same for all the four DNA bases and appears to vary slowly with the stacking and H-bonding interactions of the nucleobases. We demonstrate that the large shift in the DIP of bases is due to the electric potential around the DNA resulting from the long range solvent structure created by the negative phosphate groups and positive counterions ofmore » the DNA helical structure. Thermal fluctuations in the fluid can result in DIP changes of roughly 1ev on a picosecond time scale. The model used in this work is based on a QM/MM approach in which the base (or clusters of bases) are chosen as the QM system and calculated using a high-level quantum chemistry method. The remaining DNA fragment and the species in solution are included in an exact molecular mechanics (MM) model. The expected high accuracy of the QM/MM model is defended in terms of the essentially Columbic nature of the interactions of the solvent (the MM region) with isolated base in the quantum region. For the test anion, Cl-, the QM/MM approach yields the 3.4 eV (gas-phase) to 9.3 eV (aqueous solution) shift of the ionization energy in agreement with experimental values (3.6 and 9.6 eV). The localization of the electronic excitation inside the QM region is supported by current experimental and theoretical evidence indicating that the HOMO of the nucleotide is localized on the base rather than the sugar or the phosphate backbone. Our calculations performed in the native DNA environment support this localization. The QM/MM model presented in this work provides an important simplification to the difficult problem of incorporating a detailed structural model of the physiological conditions into investigations of the electronic processes in DNA.« less
  • Among the distinct strategies proposed to expand the genetic alphabet, sizeexpanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examinedmore » by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. Themost relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMOLUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.« less
  • Among the distinct strategies proposed to expand the genetic alphabet, size-expanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examinedmore » by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMO-LUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.« less
  • Exciton delocalization and singlet excitation energy transfer have been systematically studied for the complete set of 16 DNA nucleobase dimers in their ideal, single-strand stacked B-DNA conformation, at the MS-CASPT2 level of theory. The extent of exciton delocalization in the two lowest (π,π{sup *}) states of the dimers is determined using the symmetrized one-electron transition density matrices between the ground and excited states, and the electronic coupling is calculated using the delocalization measure and the energy splitting between the states [see F. Plasser, A. J. A. Aquino, W. L. Hase, and H. Lischka, J. Phys. Chem. A 116, 11151–11160 (2012)].more » The calculated couplings lie between 0.05 eV and 0.14 eV. In the B-DNA conformation, where the interchromophoric distance is 3.38 Å, our couplings deviate significantly from those calculated with the transition charges, showing the importance of orbital overlap components for the couplings in this conformation. The calculation of the couplings is based on a two-state model for exciton delocalization. However, in three stacks with a purine in the 5{sup ′} position and a pyrimidine in the 3{sup ′} one (AT, GC, and GT), there is an energetically favored charge transfer state that mixes with the two lowest excited states. In these dimers we have applied a three-state model that considers the two locally excited diabatic states and the charge transfer state. Using the delocalization and charge transfer descriptors, we obtain all couplings between these three states. Our results are important in the context of DNA photophysics, since the calculated couplings can be used to parametrize effective Hamiltonians to model extended DNA stacks. Our calculations also suggest that the 5{sup ′}-purine-pyrimidine-3{sup ′} sequence favors the formation of charge transfer excited states.« less