Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient

Abstract

Solid-state nanopores are sensors capable of analyzing individual unlabelled DNA molecules in solution. While the critical information obtained from nanopores (e.g., DNA sequence) is the signal collected during DNA translocation, the throughput of the method is determined by the rate at which molecules arrive and thread into the pores. Here we study the process of DNA capture into nanofabricated silicon nitride pores of molecular dimensions. For fixed analyte concentrations we find an increase in capture rate as the DNA length increases from 800 to 8,000 basepairs, a length-independent capture rate for longer molecules, and increasing capture rates when ionic gradients are established across the pore. In addition, we show that application of a 20-fold salt gradient enables detection of picomolar DNA concentrations at high throughput. The salt gradients enhance the electric field, focusing more molecules into the pore, thereby advancing the possibility of analyzing unamplified DNA samples using nanopores.

Current rectification by nanoparticle blocking in single cylindrical nanopores

“…4(a)). This fact enhances the electrostatic focusing 18 of the NP to the pore and subsequent blocking. Also, the rectification increases with decreasing the pore radius because of the increased pore blocking effect (Fig.…”

Stiff filamentous virus translocations through solid-state nanopores

“…It senses when a single biopolymer threads it by registering a change in its ionic conductance 1,2 . The possibility of applying nanopores to the analysis of nucleic acids, in particular DNA sequencing, has generated interest 3 , and motivated fundamental studies of the physics of nanopore translocations [4][5][6][7][8][9][10][11][12][13][14][15][16][17] . The uses of solid-state nanopores have recently expanded to include detecting single proteins 18 , mapping structural features along RecA-bound DNA-protein complexes 19 and detecting spherical and icosahedral virus strains [20][21][22] .…”

Single Molecule Localization and Discrimination of DNA–Protein Complexes by Controlled Translocation Through Nanocapillaries

“…We also note here that the process of threading the free end of DNA is harder to predict and thus the entrance of DNA cannot be used instead of the exit as a reference point 3,4 . It remains to determine the DNA extension.…”