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

Abstract

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.

Graphene nanodevices for DNA sequencing

“…The idea of this 'recognition tunneling' originates from successful experiments performed to slow down DNA while it moves through a gap [52][53][54]. Much efforts were focussed on measuring DNA with metallic tunneling electrodes embedded in silicon nitride pores [52,[55][56][57][58][59], and indeed, some sequence information could be extracted when the DNA was pulled through the gap by an electric field [56,57].…”

DNA Base-Specific Modulation of Microampere Transverse Edge Currents through a Metallic Graphene Nanoribbon with a Nanopore

“…An alternative scheme is to adapt the transverse current approach to graphene-based biosensors. 8–11 The past several years have seen a number of theoretical proposals 12–16 and experiments 17,18 on nanogaps between two metallic electrodes (typically gold 12–14 or carbon nanotubes 15,16 ) where the longitudinally translocated DNA through the gap modulates the transverse tunneling current. Also, recent first-principles simulations have analyzed modulation of the tunneling current for a nanogap 9,10 between metallic GNRs with zigzag edges (ZGNR) or a nanopore 11 within semiconducting graphene nanoribbons with armchair edges (AGNR).…”

“…The theoretical proposals to increase the transverse current across the nanogap in vacuum, as in the case of carbon nanotube (CNT) electrodes terminated with nitrogen 15 or close-ended CNT electrodes separated by an ultra-short gap, 16 offer only moderate improvement (~ 1–10 nA currents at ≃ 0.5 V bias voltage 15,16 ). Applying higher bias voltage to increase the current signal is detrimental since it can lead to attraction of the negatively charged DNA backbone toward one of the electrodes thereby impeding the translocation, or even a breakdown of the electrodes or the substrate at sufficiently high electric fields.…”

“…These effects were not taken into account in our proof-of-concept calculations. While time-dependent simulations to capture these effects within fully quantum transport framework are far beyond present capabilities of NEGF-DFT codes, using molecular dynamics (MD) simulations 38 to obtain snapshots of translocated DNA within the pore in the presence of solvent and substrate makes it possible to feed 10,13,14,16 real-time atomic coordinates (of the nucleobases, water 39 and ions) into NEGF-DFT methodology, which is something we leave for future investigation.…”

Sensitive DNA detection based on the capacitance properties of graphene

“…In the proposals [31][32][33][34][35][36] on nanogaps between two metallic electrodes, the longitudinally translocated DNA through the gap modulates the transverse tunneling current. Moreover, recent first-principles simulations have evaluated modulation of the tunneling current for a nanogap [27,37] between metallic GNRs with zigzag edges (ZGNR) or a nanopore [28] within semiconducting graphene nanoribbons with armchair edges (AGNR).…”