Directly Characterizing\nthe Capture Radius of Tethered\nDouble-Stranded DNA by Single-Molecule Nanopipette Manipulation

The tethered molecule exhibits characteristics of both\nfree and\nfixed states, with the electrodynamics involved in its diffusion,\nelectrophoresis, and stretching processes still not fully understood.\nWe developed a Single-Molecule Manipulation, Identification, and Length\nExamination (SMILE) system by integrating piezoelectric devices with\nnanopipettes. This system enabled successful capture and stretching\nof tethered double-stranded DNA within the nanopore. Our research\nunveiled distinct capture (<i>r</i><sub>capture</sub>) and\nstretch radii (<i>r</i><sub>stretch</sub>) surrounding the\nDNA’s anchor point. Notably, consistent ratios of capture radius\nfor DNA of varying lengths (2k, 4k, and 6k base pairs) were observed\nacross different capturing voltages, approximately 1:1.4:1.83, showing\na resemblance to their gyration radius ratios. However, the ratios\nof stretch radius are consistent to their contour length (<i>L</i><sub>0</sub>), with the stretching ratio (<i>r</i><sub>stretch</sub>/<i>L</i><sub>0</sub>) increasing from\n70 to 90% as the voltage rose from 100 to 1000 mV. Additionally, through\nnumerical simulations, we identified the origin of capture and stretch\nradii, determined by the entropic elasticity-induced capture barrier\nand the electric field-dominant escape barrier. This research introduces\nan innovative methodology and outlines research perspectives for a\ncomprehensive exploration of the conformational, electrical, and diffusion\ncharacteristics of tethered molecules.