Sensing and characterization of water-soluble peptides is of critical importance in a wide variety of bioapplications. Single molecule nanopore spectrometry (SMNS) is based on the idea that one can use biological protein nanopores to resolve different sized molecules down to limits set by the blockade duration and noise. Previous work has shown that this enables discrimination between polyethylene glycol (PEG) molecules that differ by a single monomer unit. This paper describes efforts to extend SMNS to a variety of biologically relevant, water-soluble peptides. We describe the use of Au(SG) clusters, previously shown to improve PEG detection, to increase the on- and off-rate of peptides to the pore. In addition, we study the role that fluctuations play in the single molecule nanopore spectrometry (SMNS) methodology and show that modifying solution conditions to increase peptide flexibility (via pH or chaotropic salt) leads to a nearly 2-fold reduction in the current blockade fluctuations and a corresponding narrowing of the peaks in the blockade distributions. Finally, a model is presented that connects the current blockade depths to the mass of the peptides, which shows that our enhanced SMNS detection improves the mass resolution of the nanopore sensor more than 2-fold for the largest cationic peptides studied.

Recently proposed methods for DNA sequencing involve the use of cleavage-based enzymes attached to the opening of a nanopore. The idea is that DNA interacting with either an exonuclease or polymerase protein will lead to a small molecule being cleaved near the mouth of the nanopore, and subsequent entry into the pore will yield information about the DNA sequence. The prospects for this approach seem promising, but it has been shown that diffusion related effects impose a limit on the capture probability of molecules by the pore, which limits the efficacy of the technique. Here, we revisit the problem with the goal of optimizing the capture probability via a step decrease in the nucleotide diffusion coefficient between the pore and bulk solutions. It is shown through random walk simulations and a simplified analytical model that decreasing the molecule's diffusion coefficient in the bulk relative to its value in the pore increases the nucleotide capture probability. Specifically, we show that at sufficiently high applied transmembrane potentials (≥100 mV), increasing the potential by a factor f is equivalent to decreasing the diffusion coefficient ratio D(bulk)/D(pore) by the same factor f. This suggests a promising route toward implementation of cleavage-based sequencing protocols. We also discuss the feasibility of forming a step function in the diffusion coefficient across the pore-bulk interface.

Recent work described the use of thiolate-capped gold clusters (Au25(SG)18) with nanopore sensing to increase the residence time of polyethylene glycol (PEG) in an alpha hemolysin pore [Anal. Chem., 2014, 86, 11077]. It was shown that the residence time enhancement narrows the peaks in the PEG-induced current blockade distribution, thus increasing the resolving power of the single molecule nanopore spectrometry (SMNS) technique. Here, we further study the interaction between the cluster and PEG with the goal of optimizing the residence time enhancement for SMNS detection. Specifically, we report the voltage dependence of the enhancement effect and show that, under the conditions studied, the cluster-enhanced residence time is maximized at an applied transmembrane potential near 60 mV. Additionally, we show that the PEG residence time depends on the degree to which the cluster blocks current through the pore and that the PEG on-rate to the pore can be more accurately measured with a cluster in the pore. Finally, we develop a model that describes the cluster-induced shift of the PEG current blockade distribution. We use this model to characterize the interaction between the cluster and PEG and show that it scales linearly with the applied voltage as expected from the proposed enhancement mechanism.

Potentiometric redox measurements were made in subnanoliter droplets of solutions using an optically transparent nanoporous gold electrode strategically mounted on the stage of an inverted microscope. Nanoporous gold was prepared via dealloying gold leaf with concentrated nitric acid and was chemisorbed to a standard microscope coverslip with (3-mercaptopropyl)trimethoxysilane. The gold surface was further modified with 1-hexanethiol to optimize hydrophobicity of the surface to allow for redox measurements to be made in nanoscopic volumes. Time traces of the open-circuit potential (OCP) were used to construct Nernst plots to evaluate the applicability of the droplet-based potentiometric redox measurement system. Two poised one-electron transfer systems (potassium ferricyanide/ferrocyanide and ferrous/ferric ammonium sulfate) yielded Nernstian slopes of -58.5 and -60.3 mV, respectively, with regression coefficients greater than 0.99. The y-intercepts of the two agreed well to the formal potential of the two standard oxidation-reduction potential (ORP) calibrants, ZoBell's and Light's solution. The benzoquinone and hydroquinone redox couple was examined as a representative two-electron redox system; a Nernst slope of -30.8 mV was obtained. Additionally, two unpoised systems (potassium ferricyanide and ascorbic acid) were studied to evaluate the system under conditions where only one form of the redox couple is present in appreciable concentrations. Again, slopes near the Nernstian values of -59 and -29 mV, respectively, were obtained. All experiments were carried out using solution volumes between 280 and 1400 pL with injection volumes between 8 and 100 pL. The miniscule volumes allowed for extremely rapid mixing (<305 ms) as well. The small volumes and rapid mixing along with the high accuracy and sensitivity of these measurements lend support to the use of this approach in applications where time is a factor and only small volumes are available for testing.

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