| 1. |
- He, Yuhui, et al.
(author)
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Mechanism of How Salt-Gradient-Induced Charges Affect the Translocation of DNA Molecules through a Nanopore
- 2013
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In: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 105:3, s. 776-782
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Journal article (peer-reviewed)abstract
- Experiments using nanopores demonstrated that a salt gradient enhances the capture rate of DNA and reduces its transfocation speed. These two effects can help to enable electrical DNA sequencing with nanopores. Here, we provide a quantitative theoretical evaluation that shows the positive net charges, which accumulate around the pore entrance due to the salt gradient, are responsible for the two observed effects: they reinforce the electric capture field, resulting in promoted molecule capture rate; and they induce cationic electroosmotic flow through the nanopore, thus significantly retarding the motion of the anionic DNA through the nanopore. Our multiphysical simulation results show that, during the polymer trapping stage, the former effect plays the major role, thus resulting in promoted DNA capture rate, while during the nanopore-penetrating stage the latter effect dominates and consequently reduces the DNA translocation speed significantly. Quantitative agreement with experimental results has been reached by further taking nanopore wall surface charges into account.
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| 2. |
- He, Yuhui, et al.
(author)
-
Thermophoretic Manipulation of DNA Translocation through Nanopores
- 2013
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In: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 7:1, s. 538-546
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Journal article (peer-reviewed)abstract
- Manipulating DNA translocation through nanopore is one crucial requirement for new ultrafast sequencing methods in the sense that the polymers have to be denatured, unraveled, and then propelled through the pore with very low speed. Here we propose and theoretically explore a novel design to fulfill the demands by utilizing cross-pore thermal gradient. The high temperature in the cis reservoir is expected to transform double-stranded DNA into single strands and that temperature would also prevent those single strands from intrastrand base-pairing, thus, achieving favorable polymer conformation for the subsequent translocation and sequencing. Then, the substantial temperature drop across the pore caused by the thermal-insulating membrane separating cis and trans chambers would stimulate thermophoresis of the molecules through nanopores. Our theoretical evaluation shows that the DNA translocation speeds will be orders smaller than the electrophoretic counterpart, while high capture rate of DNA Into nanopore Is maintained, both of which would greatly benefit the sequencing.
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