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Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials
journal contribution
posted on 2017-02-08, 00:00 authored by László Kékedy-Nagy, Elena E. Ferapontova, Izabella BrandUnique
electronic and ligand recognition properties of the DNA
double helix provide basis for DNA applications in biomolecular electronic
and biosensor devices. However, the relation between the structure
of DNA at electrified interfaces and its electronic properties is
still not well understood. Here, potential-driven changes in the submolecular
structure of DNA double helices composed of either adenine-thymine
(dAdT)25 or cytosine-guanine (dGdC)20 base pairs
tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption
spectroscopy (PM IRRAS) performed under the electrochemical control.
It is shown that the conformation of the DNA duplexes tethered to
gold electrodes via the C6 alkanethiol linker strongly
depends on the nucleic acid sequence composition. The tilt of purine
and pyrimidine rings of the complementary base pairs (dAdT and dGdC)
depends on the potential applied to the electrode. By contrast, neither
the conformation nor orientation of the ionic in character phosphate–sugar
backbone is affected by the electrode potentials. At potentials more
positive than the potential of zero charge (pzc), a gradual tilting
of the double helix is observed. In this tilted orientation, the planes
of the complementary purine and pyrimidine rings lie ideally parallel
to each other. These potentials do not affect the integral stability
of the DNA double helix at the charged interface. At potentials more
negative than the pzc, DNA helices adopt a vertical to the gold surface
orientation. Tilt of the purine and pyrimidine rings depends on the
composition of the double helix. In monolayers composed of (dAdT)25 molecules the rings of the complementary base pairs lie
parallel to each other. By contrast, the tilt of purine and pyrimidine
rings in (dGdC)20 helices depends on the potential applied
to the electrode. Such potential-induced mobility of the complementary
base pairs can destabilize the helix structure at a submolecular level.
These pioneer results on the potential-driven changes in the submolecular
structure of double stranded DNA adsorbed on conductive supports contribute
to further understanding of the potential-driven sequence-specific
electronic properties of surface-tethered oligonucleotides.
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acid sequence compositiondGdCligand recognition propertieshelixIRRASbase pairspotential-driven changesPMgold surface orientationSuch potential-induced mobilitypyrimidine ringspurinehelice20 base pairsdAdTDNAGold Electrodes Probedreflection absorption spectroscopyOligonucleotide Duplexes TetheredInfrared Reflection Absorption Spectroscopysubmolecular structuregold electrodesC 6 alkanethiol linker
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