First-Principles Transversal DNA Conductance Deconstructed

Zhang, Xiaoguang; Krstić, Predrag; Žikić, Radomir; Wells, Jack; Fuentes‐Cabrera, Miguel

doi:10.1529/biophysj.106.085548

Cited by 56 publications

(68 citation statements)

References 17 publications

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“…They concluded that sequencing should be possible and also investigated the effect of water and other environmental factors including dynamics, as well as tunnelling noise characteristics on the device performance 80,81 . Fuentes-Cabrera and coworkers 82,83 stressed that in off-resonant tunnelling regime dynamic effects, such as Brownian motion and the exact geometry of the DNA in the junction, may dominate the tunnelling current, rather than base-specific electronic factors. In essence, however, it has become clear that motion of DNA in the tunnelling junction and in particular the DNA/electrode interaction would have to be controlled carefully to make sequencing-by-tunnelling in nanopore configuration a reality.…”

Section: Small-molecule Sensing By Tunnelling Currentsmentioning

confidence: 99%

Electrochemical tunnelling sensors and their potential applications

Albrecht

2012

Nat Commun

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the quantum-mechanical tunnelling effect allows charge transport across nanometre-scale gaps between conducting electrodes. application of a voltage between these electrodes leads to a measurable tunnelling current, which is highly sensitive to the gap size, the voltage applied and the medium in the gap. applied to liquid environments, this offers interesting prospects of using tunnelling currents as a sensitive tool to study fundamental interfacial processes, to probe chemical reactions at the single-molecule level and to analyse the composition of biopolymers such as Dna, rna or proteins. this offers the possibility of a new class of sensor devices with unique capabilities. E lectrochemical sensors based on measuring the tunnelling current across nanoscale electrode junctions in solution are emerging as a new class of single-molecule sensors. They combine extremely high spatial resolution with sensitivity to the electronic structure of the analyte. This opens up perspectives towards the label-free detection of small molecules, the characterization of catalytic or enzymatic processes at the single-molecule level as well as the analysis of biopolymers with sub-molecular resolution, Fig. 1. To this end, label-free, fast and inexpensive RNA and DNA sequencing may be in reach, potentially revolutionizing the way we perform gene sequencing today.Charge transfer by quantum-mechanical tunnelling is one of the most ubiquitous elementary processes in nature and features in areas as diverse as electron or hydrogen transfer in enzymatic reactions, interfacial charge transfer at metal electrodes in solution, thin-layer devices in electronics, charge transfer between crystal defects and radioactive α-decay 1 . Important applications exploiting tunnelling transport include the Esaki tunnelling diode and the scanning tunnelling microscope (STM)-both recognized with the Nobel Prize in Physics for their inventors, namely Esaki in 1973 (jointly with Josephson), and Binnig and Rohrer in 1986, respectively.'Tunnelling' refers to the transport of electrons (or other light charge carriers) across a nanometre-sized gap, a molecule or even an insulating layer between two electrodes. Upon application of a bias voltage V bias between the two electrodes, negatively charged electrons are more likely to be transported towards the positively biased electrode and a so-called 'tunnelling current' I t is detected. The latter depends exponentially on gap size, which is the reason for the high spatial resolution of STM, the applied voltage V b and the electronic structure of the medium in the gap. To this end, the electrode junction may be represented by a transmission function that characterizes the probability of electrons moving from one electrode across the gap into the second electrode, summarized over all energy levels.Hence, the more accessible the energy levels in the junction, and the better their electronic coupling to the electrodes, the higher current across the junction. This also implies that the tunnelling current is sensitive to ...

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Section: Small-molecule Sensing By Tunnelling Currentsmentioning

confidence: 99%

Electrochemical tunnelling sensors and their potential applications

Albrecht

2012

Nat Commun

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“…52 As an alternative, the layout proposed here can also be used to directly detect voltage fluctuations due to the local and unique dipole moments of the bases. 53,54 This capacitive detection approach is not preferred, however, due to its reliance on the relatively long-range capacitive interaction, possibly limiting the spatial resolution with which individual bases can be resolved.…”

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confidence: 99%

Rapid Sequencing of Individual DNA Molecules in Graphene Nanogaps

2010

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I propose a technique for reading the base sequence of a single DNA molecule using a graphene nanogap to read the DNA's transverse conductance. Because graphene is a single atom thick, single-base resolution of the conductance is readily obtained. The nonlinear current-voltage characteristic is used to determine the base type independent of nanogap-width variations that cause the current to change by 5 orders of magnitude. The expected sequencing error rate is 0% up to a nanogap width of 1.6 nm.

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“…13 On the theoretical front, the transverse tunneling conductance across nucleobases placed between two gold electrodes has been actively investigated and debated. 4,7,[16][17][18][19][20][21] Interestingly, recently some special attention has been dedicated to exploring graphene nanopore, graphene nanoribbon and carbon nanotubes (CNT) as potential electrodes materials. [22][23][24] Despite these many works, a key question still remains largely unanswered, namely, how can one enhance the nucleotide-electrode interaction to a point where the transmigration is still possible, but the geometrical fluctuations are sufficiently suppressed to allow unambiguous single nucleotide recognition.…”

Section: Introductionmentioning

confidence: 99%

First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes

et al. 2012

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Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nanometer-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular, we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore it can both reduce conformational fluctuations and significantly improve the conductance. As such, when the electrodes are closely spaced, the nucleobases can pass through only with their base plane parallel to the plane of CNT end caps. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. These correspond approximately to the lowest energy configurations. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several μA. Below 1 V, the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second largest, cytosine the third and, finally, thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations. Based on these results, we propose a DNA sequencing protocol combining three possible data analysis strategies.

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First-Principles Transversal DNA Conductance Deconstructed

Cited by 56 publications

References 17 publications

Electrochemical tunnelling sensors and their potential applications

Electrochemical tunnelling sensors and their potential applications

Rapid Sequencing of Individual DNA Molecules in Graphene Nanogaps

First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes

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