Hang Ren

Critical Nuclei Size, Rate, and Activation Energy of H2 Gas Nucleation

Electrochemical measurements of the nucleation rate of individual H2 bubbles at the surface of Pt nanoelectrodes (radius = 7-41 nm) are used to determine the critical size and geometry of H2 nuclei leading to stable bubbles. Precise knowledge of the H2 concentration at the electrode surface, CH2surf, is obtained by controlled current reduction of H+ in a H2SO4 solution. Induction times of single-bubble nucleation events are measured by stepping the current, to control CH2surf, while monitoring the voltage. We find that gas nucleation follows a first-order rate process; a bubble spontaneously nucleates after a stochastic time delay, as indicated by a sudden voltage spike that results from impeded transport of H+ to the electrode. Hundreds of individual induction times, at different applied currents and using different Pt nanoelectrodes, are used to characterize the kinetics of phase nucleation. The rate of bubble nucleation increases by four orders of magnitude (0.3-2000 s-1) over a very small relative change in CH2surf (0.21-0.26 M, corresponding to a ∼0.025 V increase in driving force). Classical nucleation theory yields thermodynamic radii of curvature for critical nuclei of 4.4 to 5.3 nm, corresponding to internal pressures of 330 to 270 atm, and activation energies for nuclei formation of 14 to 26 kT, respectively. The dependence of nucleation rate on H2 concentration indicates that nucleation occurs by a heterogeneous mechanism, where the nuclei have a contact angle of ∼150° with the electrode surface and contain between 35 and 55 H2 molecules.

Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA

Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( kintra-extra) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( kextra-intra) remains unchanged. Both kintra-extra and kextra-intra are on the order of 1 × 10-2 s-1 to 1 × 10-1 s-1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H+ into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for kintra-extra ( kH/ kD ≈ 5) but a limited KIE for kextra-intra ( kH/ kD ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.

Electrochemical Generation of Individual O2 Nanobubbles via H2O2 Oxidation

Herein, we use Pt nanodisk electrodes (apparent radii from 4 to 80 nm) to investigate the nucleation of individual O2 nanobubbles generated by electrooxidation of hydrogen peroxide (H2O2). A single bubble reproducibly nucleates when the dissolved O2 concentration reaches ∼0.17 M at the Pt electrode surface. This nucleation concentration is ∼130 times higher than the equilibrium saturation concentration of O2 and is independent of electrode size. Moreover, in acidic H2O2 solutions (1 M HClO4), in addition to producing an O2 nanobubble through H2O2 oxidation at positive potentials, individual H2 nanobubbles can also be generated at negative potentials. Alternating generation of single O2 and H2 bubbles within the same experiment allows direct comparison of the critical concentrations for nucleation of each nanobubble without knowing the precise size/geometry of the electrode or the exact viscosity/temperature of the solution.

The Nucleation Rate of Single O2 Nanobubbles at Pt Nanoelectrodes

Nanobubble nucleation is a problem that affects efficiency in electrocatalytic reactions since those bubbles can block the surface of the catalytic sites. In this article, we focus on the nucleation rate of O2 nanobubbles resulting from the electrooxidation of H2O2 at Pt disk nanoelectrodes. Bubbles form almost instantaneously when a critical peak current, inbp, is applied, but for lower currents, bubble nucleation is a stochastic process in which the nucleation (induction) time, tind, dramatically decreases as the applied current approaches inbp, a consequence of the local supersaturation level, ζ, increasing at high currents. Here, by applying different currents below inbp, nanobubbles take some time to nucleate and block the surface of the Pt electrode at which the reaction occurs, providing a means to measure the stochastic tind. We study in detail the different conditions in which nanobubbles appear, concluding that the electrode surface needs to be preconditioned to achieve reproducible results. We also measure the activation energy for bubble nucleation, Ea, which varies in the range from (6 to 30)kT, and assuming a spherically cap-shaped nanobubble nucleus, we determine the footprint diameter L = 8–15 nm, the contact angle to the electrode surface θ = 135–155°, and the number of O2 molecules contained in the nucleus (50 to 900 molecules).

γ-Hemolysin Nanopore is Sensitive to Guanine-to-Inosine Substitutions in Double-Stranded DNA at the Single-Molecule Level.

Biological nanopores provide a unique single-molecule sensing platform to detect target molecules based on their specific electrical signatures. The γ-hemolysin (γ-HL) protein produced by Staphylococcus aureus is able to assemble into an octamer nanopore with a ∼2.3 nm diameter β-barrel. Herein, we demonstrate the first application of γ-HL nanopore for DNA structural analysis. To optimize conditions for ion-channel recording, the properties of the γ-HL pore (e.g., conductance, voltage-dependent gating, and ion-selectivity) were characterized at different pH, temperature, and electrolyte concentrations. The optimal condition for DNA analysis using γ-HL corresponds to 3 M KCl, pH 5, and T = 20 °C. The γ-HL protein nanopore is able to translocate dsDNA at about ∼20 bp/ms, and the unique current-signature of captured dsDNA can directly distinguish guanine-to-inosine substitutions at the single-molecule level with ∼99% accuracy. The slow dsDNA threading and translocation processes indicate this wild-type γ-HL channel has potential to detect other base modifications in dsDNA.

Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA

In DNA, guanine oxidation yields diastereomers of 5-guanidinohydantoin (Gh) as one of the major products. In nucleosides and single-stranded DNA, Gh is in a pH-dependent equilibrium with its constitutional isomer iminoallantoin (Ia). Herein, the isomerization reaction between Gh and Ia was monitored in duplex DNA using a protein nanopore by measuring the ionic current when duplex DNA interacts with the pore under an electrophoretic force. Monitoring current levels in this single-molecule method proved to be superior for analysis of population distributions in an equilibrating mixture of four isomers in duplex DNA as a function of pH. The results identified Gh as a major isomer observed when base paired with A, C, or G at pH 6.4-8.4, and Ia was a minor isomer of the reaction mixture that was only observed when the pH was >7.4 in the duplex DNA context. The present results suggest that Gh will be the dominant isomer in duplex DNA under physiological conditions regardless of the base-pairing partner in the duplex.

Processes at nanopores and bio-nanointerfaces: general discussion

Hassan Alzahrani, Christophe Antoine, Lane Baker, Sebastien Balme, Gourav Bhattacharya, Paul W. Bohn, Qiong Cai, Chrys Chikere, Richard M. Crooks, Naren Das, Martin Edwards, Cyril Ehi-Eromosele, Niklas Ermann, Lei Jiang, Frederic Kanoufi, Christine Kranz, Yitao Long, Julie MacPherson, Kim McKelvey, Michael Mirkin, Richard Nichols, Wojciech Nogala, Juan Pelta, Hang Ren, Jennifer Rudd, Wolfgang Schuhmann, Zuzanna Siwy, Zhongqun Tian, Patrick Unwin, Liping Wen, Henry White, Katherine Willets, Yanfang Wu and Yilun Ying