Slowing DNA Translocation through Nanopores Using a Solution Containing Organic Salts

Abstract

One of the key challenges to nanopore DNA sequencing is to slow down DNA translocation. Here, we report that the translocation velocities of various DNA homo- and copolymers through protein pores could be significantly decreased by using electrolyte solutions containing organic salts. Using a butylmethylimidazolium chloride (BMIM-Cl) solution instead of the commonly used KCl solution, DNA translocation rates on the order of hundreds of microseconds per nucleotide base were achieved. The much enhanced resolution of the nanopore coupled with different event blockage amplitudes produced by different nucleotides permits the convenient differentiation between various DNA molecules.

Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore

“…The residual current also has a wide distribution, with a peak at 17.4 ± 0.84 pA (Figure 1c). Others have previously noted that KNO 3 has unknown effects on DNA translocation and some extraordinary long events were seen, with about 10-fold lower occurrence rate constant ( K on ) of ssDNA in KNO 3 than in the KCl buffer8, as well as in certain cations such as Li + 33 and ion liquid34. In order to ensure the ssDNA interactions were excluded, we only considered events longer than 10 ms as the DNA duplexes interact with the nanopore.…”

Applications of biological pores in nanomedicine, sensing, and nanoelectronics

“…It entails the use of proteins that bind single-stranded DNA; these interactions prohibit translocation of the single-stranded DNA until the proteins unbind and reduce the rate of translocation [269]. Other promising techniques include the use of organic salts that interact with DNA [274,275] and nanoparticles that partially obstruct the entrance to a pore [275]. These nanoparticles made it possible to decrease the translocation speed of single-stranded DNA through α-hemolysin pores by a factor of 10–100 [275].…”

Electrokinetic particle translocation through a nanopore containing a floating electrode

“…However, a very fast DNA translocation may result in an inaccurate detection of the ionic current [11]. As a result, several methods, including optical tweezers [12,13], chemical functionalization of the nanopore [14], adjustment of the aqueous solution's property [15][16][17][18], have been proposed to slow down or actively control the DNA translocation through a nanopore, as reviewed in our previous study [19]. In particular, Ai et al utilized a gate electrode to modify the surface potential of the nanopore that in turn actively controls the DNA translocation through a nanopore [19].…”