Resistive‐pulse Sensing of DNA with a Polymeric Nanopore Sensor and Characterization of DNA Translocation

Abstract

The ability to detect DNA strands and determine their characteristics in solution plays a critical role to design a sensor in terms of its biophysical properties and receives attention in whole‐ genome sequencing. In this study, we report a simple method to detect 100‐bp DNA based on resistive‐pulse sensing and its characteristics in terms of analyte concentration, potential, tip size. and electrolyte concentration. Track‐etched polyethyleneterephtalate (PET) nanopores were used and modified (w/EDC‐NHS coupling) to decrease the negative surface charge and promote DNA translocation. We tuned up the tip diameters of nanopores by using symmetric and asymmetric chemical etching. The tip diameters ranged from 21 nm to 42 nm. To show the electrophoretic nature of translocation, we investigated the concentration and potential dependence. The current‐pulse events were observed down to 600 mV (4±1 events/min) and 0.25 nM was the minimum concentration. Both potential and concentration dependence showed linear behavior which agreed to previous studies. The effect of tip size was also studied and its effect on translocation frequency was discussed. Finally, the change in current‐pulse amplitude and duration as a function of electrolyte concentration was studied and longer duration values (14.3±1.4 ms) were observed. Our findings provide a guide to translocate the charged molecules more efficiently and help to understand the translocation dynamics of short DNA molecules in resistive‐pulse sensing.

A Comparable Study of Single Stranded DNA Sensing Using Track‐Etched Nanopore Sensors

“…Such behavior in current‐pulse amplitude may originate from the conformational changes which is more possible in ss‐DNA due to its flexible structure respect to double‐strand form [64] . Both duration and current‐pulse amplitude values (for ds‐DNA) are consistent with our previous findings in which 21 nm nanopore were used [65] …”

“…However, the frequency of current‐pulses was low and the minimum concentration was relatively higher than ds‐DNA. The minimum concentration that we observed in our previous study was 0.25 nM for ds‐DNA [65] …”

“…The translocation frequency of ss‐DNA was less than the translocation frequency of ds‐DNA [65] . In addition, the minimum potential in which the events were observed was higher than the potential for ds‐DNA (i. e., 600 mV).…”

“…[64] Both duration and current-pulse amplitude values (for ds-DNA) are consistent with our previous findings in which 21 nm nanopore were used. [65] The concentration dependence was studied between 0.5 nM to 15 nM in which the linear behavior was observed. From 0.50 nM to 15 nM, the frequency increased 6 min À 1 to 78 min À 1 (see Figure 5).…”

“…The minimum concentration that we observed in our previous study was 0.25 nM for ds-DNA. [65] The voltage dependence of ss-DNA between 700 mV to 1000 mV is given in Figure 6. The frequency was found 5 � 2 min À 1 (at 700 mV) and 67 � 9 min À 1 (at 1000 mV).…”