We demonstrate for the first time the detection of the folding state of double-stranded DNA in nanocapillaries with the resistive pulse technique. We show that glass capillaries can be pulled into nanocapillaries with diameters down to 45 nm. We study translocation of lambda -DNA which is driven by an electrophoretic force through the nanocapillary. The resulting change in ionic current indicates the folding state of single lambda -DNA molecules. Our experiments prove that nanocapillaries are suitable for label-free analysis of DNA in aqueous solutions and viable alternatives to solid-state nanopores made by silicon nanotechnology.

We have developed a method to analyze in detail, translocation events providing a novel and flexible tool for data analysis of nanopore experiments. Our program, called OpenNanopore, is based on the cumulative sums algorithm (CUSUM algorithm). This algorithm is an abrupt change detection algorithm that provides fitting of current blockages, allowing the user to easily identify the different levels in each event. Our method detects events using adaptive thresholds that adapt to low-frequency variations in the baseline. After event identification, our method uses the CUSUM algorithm to fit the levels inside every event and automatically extracts their time and amplitude information. This facilitates the statistical analysis of an event population with a given number of levels. The obtained information improves the interpretation of interactions between the molecule and nanopore. Since our program does not require any prior information about the analyzed molecules, novel moleculenanopore interactions can be characterized. In addition our program is very fast and stable. With the progress in fabrication and control of the translocation speed, in the near future, our program could be useful in identification of the different bases of DNA.

No abstract

The DNA uptake of naturally competent bacteria has been attributed to the action of DNA uptake machineries resembling type IV pilus complexes. However, the protein(s) for pulling the DNA across the outer membrane of Gram-negative bacteria remain speculative. Here we show that the competence protein ComEA binds incoming DNA in the periplasm of naturally competent Vibrio cholerae cells thereby promoting DNA uptake, possibly through ratcheting and entropic forces associated with ComEA binding. Using comparative modeling and molecular simulations, we projected the 3D structure and DNA-binding site of ComEA. These in silico predictions, combined with in vivo and in vitro validations of wild-type and site-directed modified variants of ComEA, suggested that ComEA is not solely a DNA receptor protein but plays a direct role in the DNA uptake process. Furthermore, we uncovered that ComEA homologs of other bacteria (both Gram-positive and Gram-negative) efficiently compensated for the absence of ComEA in V. cholerae, suggesting that the contribution of ComEA in the DNA uptake process might be conserved among naturally competent bacteria.

olid-state nanopores for single-molecule detection of DNA were first used in 2001 by Li et al., who were able to detect double-stranded (ds) DNA when it was translocated through the nanopore. 1 To fabricate this nanopore, an electron beam from a transmission electron microscope (TEM) was focused on a few nanometer thick silicon nitride membrane. The membrane separates two reservoirs containing a salt solution, across which an electric potential was applied. This causes an ionic current that is measured and depends on parameters such as salt concentration and the dimension of the nanopore. Nanopores are a useful technique to detect charged single molecules, which can be forced to translocate through the nanopore by the electric field. The volume displaced by the molecule can be sensed, because when it enters the nanopore, there is a reduction in the ionic current at high salt concentrations. 2 The ability to precisely control the size of the nanopore is crucial to sense small molecules since the amplitude of the conductance drop increases with smaller diameters. An early technique used the electron beam of an already drilled nanopore to shrink it to any desired diameter. 3 The electron beam would heat up the silicon membrane around the nanopore, reducing the size of the pore due to the surface stress and the increased mobility of the heated atoms. The method of pore shrinking with a transmission electron microscope was soon expanded to other instruments such as scanning electron microscopes or lasers, which were able to locally heat up a material. 4À6 An opposite approach was reported by Beamish et al. by enlarging solidstate nanopores using a high electric field. 7 An inexpensive alternative to solid-state nanopores in silicon membranes is laser pulled glass nanocapillaries, which have a conical shape and a very small orifice at their tip. 8 It was shown that they are able to sense the folding state of translocating dsDNA on the single-molecule level. 9

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.

We study the effect of salt concentration on the ionic conductance and translocation of single DNA molecules through nanocapillaries made out of quartz glass. DNA translocation experiments were performed in aqueous solution for concentrations of KCl between 10 mM and 2 M while ion conductance was characterized from 1 mM to 2 M KCl concentration. Here, we develop a model for the conductance of conical nanocapillaries taking into consideration the surface charge of the quartz glass. We demonstrate that the conductance of our nanocapillaries shows similar behavior to silicon oxide nanopores at low and high KCl concentrations. Finally, we show that DNA translocations in high KCl concentrations (400 mM-2 M) cause a reduction in the ionic current. In contrast, DNA translocations at low KCl concentrations (10-300 mM) lead to increases in the ionic current. Our new results, which until now have not been shown for nanocapillaries, can be well understood with an adapted model.

a Single molecule studies using nanopores have gained attention due to the ability to sense single molecules in aqueous solution without the need to label them. In this study, short DNA molecules and proteins were detected with glass nanopores, whose sensitivity was enhanced by electron reshaping which decreased the nanopore diameter and created geometries with a reduced sensing length. Further, proteins having molecular weights (MW) ranging from 12 kDa to 480 kDa were detected, which showed that their corresponding current peak amplitude changes according to their MW. In the case of the 12 kDa ComEA protein, its DNA-binding properties to an 800 bp long DNA molecule was investigated. Moreover, the influence of the pH on the charge of the protein was demonstrated by showing a change in the translocation direction. This work emphasizes the wide spectrum of detectable molecules using nanopores from glass nanocapillaries, which stand out because of their inexpensive, lithography-free, and rapid manufacturing process.