Journal: The Journal of Physical Chemistry. B

Article Title: Dynamics of DNA Clogging in Hafnium Oxide Nanopores

doi: 10.1021/acs.jpcb.0c07756

Figure Lengend Snippet: Behavior of DNA clogging in HfO 2 -coated nanopore arrays. (a) Fluorescence frames of the 10 kbp dsDNA clogged nanopore array biased at 600 mV. Images are extracted from a real-time recording for 300 s at 3.45 fps frame rate. The white dashed ovals mark two pores that are released from clogging by comparing with the respective state in the previous frames. Scale bar: 2 μm. (b) Images showing the integrated fluorescent signals from 1034 frames (taken in 300 s) for the 10 kbp dsDNA molecules at the pore positions at 200 (i), 400 (ii), and 600 mV (iii). The color scales are set identical and coincide with the intensity range of the integrated gray scale. (c) Mean intensity of the integrated fluorescence signals at different bias voltages in the region of pore positions obtained from (b). (d) Plots of the number of clogged pores by the 10 kbp dsDNA molecules vs time at different bias voltages. The clogging state is evaluated every 3 s. (e) Statistical results of the clogging percentage for 1 kbp, 5 kbp, 10 kbp, and 20 kbp dsDNA measured at 200, 400, and 600 mV. The clogging percentage is extracted from the last frames at the end of the 300 s recording. Mean values and standard deviations from four independent experiments are presented.

Article Snippet: DNA ladders with various lengths of 1 kbp, 5 kbp, 10 kbp, and 20 kbp were purchased from Fisher Scientific.

Techniques: Fluorescence

Journal: The Journal of Physical Chemistry. B

Article Title: Dynamics of DNA Clogging in Hafnium Oxide Nanopores

doi: 10.1021/acs.jpcb.0c07756

Figure Lengend Snippet: Time-resolved study of temporary clogging of DNA HfO 2 nanopore arrays by confocal x – t scans. (a) Fluorescence images of pore clogging acquired by an x – y scan (left) and an x – t scan (right). The white dashed line in the x – y scan marks a row of nanopores that is scanned in the x – t scan mode. In the x – t scan image, the horizontal dimension represents the temporal evolution, where the length of the clogging fluorescent signal denotes the lifetime. The scanning rate of the x – t scan is 0.56 ms/line. The white arrows mark the typical events that can be observed by an x – t scan: persistent clogging, temporary clogging, and probable translocation of DNA. (b) Histograms of the temporary clogging lifetime of 5 kbp and 10 kbp dsDNA at 200, 400, and 600 mV. Curve fitting of the histograms with an exponential function is marked as solid lines, with the fitting parameters given in the figures. Each set of data is analyzed from over 30 clogging events.

Article Snippet: DNA ladders with various lengths of 1 kbp, 5 kbp, 10 kbp, and 20 kbp were purchased from Fisher Scientific.

Techniques: Fluorescence, Translocation Assay

Journal: The Journal of Physical Chemistry. B

Article Title: Dynamics of DNA Clogging in Hafnium Oxide Nanopores

doi: 10.1021/acs.jpcb.0c07756

Figure Lengend Snippet: Evolvement of total energy during translocation and dependence of translocation time on a few representative parameters. (a) Energy landscape of DNA translocation at V = 0 mV and at V = 100 mV, M = 200 (corresponding to a pore length of 68 nm), N = 5000 (corresponding to 5 kbp dsDNA), d p = 15 nm, θ = 54.7°, σ = +10 mC/m 2 . Different regimes are denoted: (i) DNA entering the pore; (ii) DNA translocating across the pore; and (iii) DNA exiting from the pore. (b) τ as a function of d p with different N strand , V = 50 mV, and σ = +10 mC/m 2 . (c) τ as a function of V with different N strand , d p = 15 nm, and σ = +10 mC/m 2 . (d) τ as a function of σ with different N strand , V = 50 mV and d p = 15 nm.

Article Snippet: DNA ladders with various lengths of 1 kbp, 5 kbp, 10 kbp, and 20 kbp were purchased from Fisher Scientific.

Techniques: Translocation Assay