Large Scale Parallel DNA Detection by Two-Dimensional Solid-State Multipore Systems

Abstract

We describe a scalable device design of a dense array of multiple nanopores made from nanoscale semiconductor materials to detect and identify translocations of many biomolecules in a massively parallel detection scheme. We use molecular dynamics coupled to nanoscale device simulations to illustrate the ability of this device setup to uniquely identify DNA parallel translocations. We show that the transverse sheet currents along membranes are immune to the crosstalk effects arising from simultaneous translocations of biomolecules through multiple pores, due to their ability to sense only the local potential changes. We also show that electronic sensing across the nanopore membrane offers a higher detection resolution compared to ionic current blocking technique in a multipore setup, irrespective of the irregularities that occur while fabricating the nanopores in a two-dimensional membrane.

3D DNA Walker-Assisted CRISPR/Cas12a Trans-Cleavage for Ultrasensitive Electrochemiluminescence Detection of miRNA-141

“…13−15 In the process of walking, driven by the strand-displacement reaction, the DNA walker can move autonomously along the predetermined orbit through a swing arm probe and track probe, improving the local concentration and achieving the accumulation of signal. 16,17 Furthermore, compared with one-dimensional (1D) 18 and two-dimensional (2D) 19 orbital DNA nanomachines, the three-dimensional (3D) orbital DNA walker 20−22 exhibits satisfactory achievements in the field of nucleic acid amplification with high-throughput cargo loading capacity, high-density walking steps, and faster target recovery rates. Therefore, through the justifiable design of the orbit, the accurate identification and multicycle amplification 23,24 of target miRNA can be realized, and the intensity of ECL signal response can be improved vigorously.…”

“…For the sake of improving the signal strength of ECL detection, some nucleic acid amplification technologies, such as rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), and strand-displacement amplification (SDA), have been manufactured widely. Nevertheless, as a special species of nanomachines, inspired by the biological protein motors, a DNA walker can amplify the signal by providing energy to drive the walking chain, moving along a specific track, which further improves its operability, accuracy, and flexibility. − In the process of walking, driven by the strand-displacement reaction, the DNA walker can move autonomously along the predetermined orbit through a swing arm probe and track probe, improving the local concentration and achieving the accumulation of signal. , Furthermore, compared with one-dimensional (1D) and two-dimensional (2D) orbital DNA nanomachines, the three-dimensional (3D) orbital DNA walker − exhibits satisfactory achievements in the field of nucleic acid amplification with high-throughput cargo loading capacity, high-density walking steps, and faster target recovery rates. Therefore, through the justifiable design of the orbit, the accurate identification and multicycle amplification , of target miRNA can be realized, and the intensity of ECL signal response can be improved vigorously.…”

Electrically Controlled Nanofluidic DNA Sluice for Data Storage Applications

“…One of the most promising avenues in the quest of ultradense storage systems is macromolecular data storage, in which DNA molecules stand out as primary candidates for massive storage media because of well-developed accompanying DNA “writing” (DNA synthesis) − and “reading” technologies (high-throughput DNA sequencing). − Furthermore, DNA and its derivatives are the only known macromolecules that enable random access , to select parts of the information content and large-scale amplification via polymerase chain reactions (PCRs) . DNA has also shown to lend itself to portable storage architectures with controllable data access, rewriting, and management, all in the presence of a large number of insertion–deletion errors inherent to inexpensive nanopore sequencers. , Recently, most research works have been geared toward DNA-based storage systems ,,,,− with very little attention to addressing the most prominent challenges encountered in all practical implementations of DNA-based data storage systems, i.e., the excessively high cost and delay of DNA synthesis and the incompatibility of DNA media with the existing silicon computing architectures that support data access, retrieval, and computing.…”

“…One main challenge in this area is to determine the biodevice architectures enabling the detection of chemical changes in chimeric DNA and structural changes such as DNA nicks. In this perspective, the use of solid-state nanopore FETs, for instance, would offer an attractive solution as they also provide seamless integration to complementary metal oxide–semiconductor (CMOS) devices. ,,,− …”

Selective detections of single-viruses using solid-state nanopores

“…While it was demonstrated previously that viruses of different sizes can be discriminated by the height of resistive pulses using conventional long fluidic channels, the method is anticipated to be not applicable for distinguishing the essentially equi-sized viral nanoparticles of influenza types. The nanopores in the present study were therefore designed to have low thickness-to-diameter aspect-ratio structure 23 – 28 so as to render additional sensitivity to the particle shape and surface charges whereby provide resistive pulses holding complex set of information concerning not only the nanoparticle volume but multiple physical properties of the intact viral particles. Although this would in general complicates the physical interpretation of the electrical signals wherein numerical simulations often play central roles to elucidate the electrokinetic phenomena 29 , 30 , we employed a machine-learning-driven pattern-analysis of the electrical signatures for rapid detection and simultaneous subtype differentiation with an ultimate sensitivity of single-particle discriminations.…”