Smooth DNA Transport through a Narrowed Pore Geometry

Abstract

Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35-20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics.

Direct and Scalable Deposition of Atomically Thin Low-Noise MoS2 Membranes on Apertures

“…Power spectral density plots shown in Figure 4b for different applied voltages in range 0–200 mV show that the noise is comparable to nanopores in SiN x membranes at this bandwidth. 35 Both pores exhibit typical 1/ f noise regions that decrease with frequency until overwhelmed by capacitive noise at f > 10 4 Hz, which is dampened using the 200 kHz digital low-pass filter (shoulders on right). The 1/ f noise in our MoS 2 membranes is atypical of 2D pores.…”

Detection of short ssDNA and dsDNA by current-voltage measurements using conical nanopores coated with Al2O3 by atomic layer deposition

“…This result seems counterintuitive regarding the literature [26]. Indeed, it was commonly reported an increase of the dwell time with the length of the DNA strands [15]. Thus, this point should be clarified.…”

“…As previously mentioned, DNA detection is commonly performed by SiN nanopore. The latter is limited for the detection of DNA strand with more or less Carson and co-worker [15] have successfully detected dsDNA 35 bp using a high resolution amplifier with a dwell time close to 10 μs. In the case of graphene nanopore, the dwell time for DNA 25 bp is 12.5 μs [13].…”

“…The measurement of short time events is difficult using patch-clamp amplifier with sample rate of 200 kHz. Using a fast amplifier, 35 bp DNA have been successfully detected by Carson et al [15]. In order to increase the DNA dwell time inside nanopore from μs to ms scale, two strategies are considered.…”

Flow of DNA in micro/nanofluidics: From fundamentals to applications

“…Yet, the typical velocity in biological pores and solid-state nanopores with comparable diameter is on the order of 1 nt or bp per ls. 174,188 Other difficulties limiting the sensitivity of the measurements are the random thermal motion of DNA within the pore, The demands for parallelization of the nanopore readings are indeed high, since a single nanopore working at 10 ms/bp would take about 20 years to sequence a human genome. 200 In order to achieve the required high-throughput parallelized sequencing, Huang et al 201 recently demonstrated that it would be feasible to replace electric current measurements with fluorescence imaging of the ionic current through the nanopores.…”