The ability to reshape nanopores and observe their shrinkage under an electron microscope is a powerful and novel technique. It increases the sensitivity of the resistive pulse sensing and enables to detect very short and small molecules. However, this has not yet been shown for glass nanocapillaries. In contrast to their solid-state nanopore counterparts, nanocapillaries are cheap, easily fabricated and in the production do not necessitate clean room facilities. We show for the first time that quartz nanocapillaries can be shrunken under a scanning electron microscope beam. Since the shrinking is caused by the thermal heating of the electrons, increasing the beam current increases the shrink rate. Higher acceleration voltage on the contrary increases the electron penetration depth and reduces the electron density causing slower shrinkage. This allows us to fine control the shrink rate and to stop the shrinking process at any desired diameter. We show that a shrunken nanocapillary detects DNA translocation with six times higher signal amplitudes than an unmodified nanocapillary. This will open a new path to detect small and short molecules such as proteins or RNA with nanocapillaries.

ABSTRACT:The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations. KEYWORDS: Single molecule measurements, nanocapillary, solid-state nanopore, DNA translocation, optical tweezers, force measurements S olid-state nanopores are label-free sensing platforms for the detailed characterization of single molecules. They have found applications as detectors of DNA, 1 RNA, 2 proteins, 3 and DNA−protein complexes 4 and are currently promising candidates for next generation DNA sequencing. 5,6 Furthermore, when combined with optical tweezers, solid-state nanopores can answer fundamental questions by revealing single molecule mechanisms. This technique was first applied to measure the charge of DNA in solution. 7 Later, Van Dorp et al. used optical tweezers in combination with nanopores to estimate the impact of electroosmotic flow during translocation of DNA molecules through nanopores of different sizes. 8 Biological applications of this method include calculation of the charge of single RNA molecules 9 and DNA-protein complexes 10 and the detection of single proteins bound to DNA. 11,12 To produce a classical solid-state nanopore, first a Si 3 N 4 or SiO 2 membrane is fabricated using lithography techniques. Next, a pore of desired diameter is drilled by transmission electron microscopy (TEM) 13 or focused-ion beam (FIB). 14 A cheaper and faster alternative to nanopore fabrication is laser pulling of glass capillaries, a technique that does not require cleanroom facilities. This process results in nanocapillaries with openings as small as 50 nm. 15 Similar to solid-state nanopores, glass nanocapillaries can detect single molecules of DNA 15 and proteins. 16 They can also be combined with optical tweezers for ultrasensitive force measurement experiments. 17,18 In this combination, nanocapillaries have advantages over nanopores due to a simpler design of the microfluidic cell, more sensitive lateral displacement of the optically trapped bead during DNA capturing, and easier determination of the proximal location of the pore. Keyser et al. used this setup in a variety of applications including studying the mechanism of DNA relaxation, 19 investigating the behavior of charged polymers in crowded environments, 20 and measuring electroosmoti...