DNA Translocations through Nanopores under Nanoscale Preconfinement

Abstract

To reduce unwanted variation in the passage speed of DNA through solid-state nanopores, we demonstrate nanoscale pre-confinement of translocating molecules using an ultra-thin nanoporous silicon nitride membrane separated from a single sensing nanopore by a nanoscale cavity. We present comprehensive experimental and simulation results demonstrating that the presence of an integrated nanofilter within nanoscale distances of the sensing pore eliminates the dependence of molecular passage time distributions on pore size, revealing a global minimum in the coefficient of variation of the passage time. These results provide experimental verification that the inter- and intra-molecular passage time variation depends on the conformational entropy of each molecule prior to translocation. Furthermore, we show that the observed consistently narrower passage time distributions enables a more reliable DNA length separation independent of pore size and stability. We also demonstrate that the composite nanofilter/nanopore devices can be configured to suppress the frequency of folded translocations, ensuring single-file passage of captured DNA molecules. By greatly increasing the rate at which usable data can be collected, these unique attributes will offer significant practical advantages to many solid-state nanopore-based sensing schemes, including sequencing, genomic mapping, and barcoded target detection.

TEM Tomography of Pores with Application to Computational Nanoscale Flows in Nanoporous Silicon Nitride (NPN)

“…The method of manufacture will create silicon nanomembranes with different nanopore features, especially when comparing self-assembly processes [ 1 , 2 , 19 ] to direct patterning techniques [ 18 , 20 ]. In biological applications, the shapes and sizes of nanopores in silicon nanomembranes are particularly important in DNA sensing [ 18 , 19 , 21 ], dielectrophoretic applications [ 22 ], and ultrafiltration [ 8 ]. Many software tools have been developed to aid the reconstruction of electron tomography data, such as TomoJ [ 23 ] or IMOD [ 24 ], and these packages are often freely accessible online.…”

“…This permits a more realistic analysis of flow behavior than can be achieved with simple cylindrical or conical models that have been used [ 6 , 7 , 25 ]. Our method of reconstruction and simulation could readily be adapted to the detailed study of electric field lines around pores, providing insights for applications such as electroosmostic pumping [ 26 ], dielectrophoresis [ 22 ], and molecular sensing [ 21 ].…”

Functionalized Boron Nitride Applications in Biotechnology

“…The selected conformation positions within a tridimensional space, regarding to its rotation, torsion, or twist which needs to be lower than its initial conformation in study [65]. About the computational methods used in nanotechnology, we can highlight several studies in different nanostructures, such as h-BN and BNNTs, explored in several technology areas such as DNA sequencing [66][67][68][69][70], water treatment [71][72][73][74], piezoelectric properties [75,76], and drug delivery [77][78][79], among others. For instance, the cisplatin (CP) is a well-known agent chemotherapeutic that acts directly on DNA causing defects in the cell repair mechanism and leading to apoptosis.…”

Microfluidic Devices for Label-Free DNA Detection

“…The nanofabrication of a complete, high performing nanopore-based DNA sequencing system is currently the main focus of researchers [73,74], with the objective of combining solid state nanopores, sensing nanoelectrodes for the detection of the electrical signal and sample delivery nanofluidics into a rapid and reliable DNA sequencing microchip. The commercial success of Oxford Nanopore Ltd. (see the following paragraph), launching MinION as the first portable commercial label-free sequencer [75], has led researchers to assess its performance in several real-life applications, and to try to identify its current limitations [76][77][78].…”