Fast DNA Sequencing via Transverse Electronic Transport

Abstract

A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, e.g., orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict and cure diseases from the perspective of the genetic makeup of each individual.Recent innovations in manufacturing processes have made it possible to fabricate devices with pores at the nanometer scale [1][2][3][4][5], i.e., the scale of individual nucleotides. This opens up fascinating new venues for sequencing DNA. For instance, one suggested method is to measure the so called blockade current [6][7][8][9][10][11][12][13][14][15][16][17][18][19]. In this method, a longitudinal electric field is applied to pull DNA through a pore. As the DNA goes through, a significant fraction of ions is blocked from simultaneously entering the pore. By continuously measuring the ionic current, single molecules of DNA can be detected. Other methods using different detection schemes, ranging from optical [20] to capacitive [21], have also been suggested. Despite much effort, however, single nucleotide resolution has not yet been achieved [22].In this Letter, we explore an alternative idea which would allow single-base resolution by measuring the electrical current perpendicular to the DNA backbone while a single strand immersed in a solution translocates through a pore. To do this, we envision embedding electrodes in the walls of a nanopore as schematically shown in the inset of Figure 1. The realization of such a configuration, while difficult to achieve in practice, is within reach of present experimental capabilities [1][2][3][4][5]. The DNA is sequenced by using the measured current as an electronic signature of the bases as they pass through the pore. We couple molecular dynamics simulations and quantum mechanical current calculations to examine the feasibility of this approach. We find that if some control is exerted over the DNA dynamics, the distributions of current values for each nucleotide will be sufficiently different to allow for rapid sequencing. We show that a transverse field of the same magnitude as that driving the current provides sufficient control.We first discuss an idealized case of DNA dynamics which sets the foundations for the approach we describe. Second, we look at the distributions of transverse currents through the nucleotides in a realistic setting using a combination of quantum-mechanical calculations of current and molecular dynamics simulations of DNA translocation through the pore. We use a Green's function method to calculate the c...

Single Sub-20 nm Wide, Centimeter-Long Nanofluidic Channel Fabricated by Novel Nanoimprint Mold Fabrication and Direct Imprinting

“…[8][9][10] For example, to explore a new real-time DNA-sequencing device (potentially revolutionary if successful), it requires not only a continuous fluidic channel of a width below 20 nm and a length of a centimeter for stretching and stabilizing DNAs, but also a single channel host for putting electrical or optical sensors inside the channel. 4,5,7,[11][12][13][14][15] Multiple channels will greatly complicate the sensor fabrication and the addressable detection of single DNA. 15,16 These requirements make the fabrication of a single sub-20 nm wide, centimeter-long, continuous fluidic channel extremely challenging due to two main reasons.…”

Single-Molecule Analysis Methods Using Nanogap Electrodes and Their Application to DNA Sequencing Technologies

“…As a result, we predicted that single-base molecules between nanoelectrodes will have conformations that are energetically stable, and as a result, the single-molecule conductance measurements will obtain only single peaks for them. 31,32,102,103 The conductance histograms of all of the base molecules tested by us were found to have large dispersions. The tunneling current flowing through a molecule strongly depends on the distance between the molecule and the electrodes and the conformation of the molecule.…”

“…Theoretical calculations support this prediction. 31,32,102,103 However, because the degrees of freedom of base molecules in DNA are limited by chemical bonds, the variance of the histograms of base molecules in DNA is actually smaller than the variance for individual base molecules. 37 As is shown in Figure 21, there is an order in the various values of the peak conductance of each conductance histogram.…”

“…3 The earliest methods focused on base molecules with π electron systems, as these would allow a large amount of electricity to flow through the single molecules and allow for the base molecules to be identified at single-molecule resolutions; this was considered to be an important step in the sequencing of individual strands of DNA and RNA. 31 36 Currently, it is possible to determine sequences of base molecules in DNA and RNA 37 and partial sequences of amino acids in peptides. 38,39 Moreover, because single-molecule conductance strongly corresponds with the properties of single molecules, single-molecule analysis methods can identify the chemically modified base molecules that traditionally denote cancer or diseases markers; this is despite current DNA sequencing technologies not being able to identify the base molecules directly.…”

Nanopore Integrated Nanogaps for DNA Detection

“…I n 2006, Lagerqvist et al 1 proposed novel modality of nanopore sequencing that exploits quantum mechanical phenomena of electron tunneling allowing identification of individual bases. At the heart of this concept are nanochannels or nanopores that are required to spatially confine DNA molecules whereas two electrodes separated by a few nanometers act as tunneling probes.…”