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Domke KF, Aragonès AC. Playing catch and release with single molecules: mechanistic insights into plasmon-controlled nanogaps. NANOSCALE 2023; 15:497-506. [PMID: 36394540 DOI: 10.1039/d2nr05448e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Single-molecule (SM) detection is essential for investigating processes at the molecular level. Nanogap-based detection approaches have proven to be highly accurate SM capture and detection platforms in the last decade. Unfortunately, these approaches face several inherent drawbacks, such as short detection times and the effects of Brownian motion, that can hinder molecular capture. Nanogap-based SM detection approaches have been successfully coupled to optical-based setups to exploit nearfield-assisted trapping to overcome these drawbacks and thus improve SM capture and detection. Here we present the first mechanistic study of nearfield effects on SM capture and release in nanogaps, using unsupervised machine learning methods based on hidden Markov models. We show that the nearfield strength can manipulate the kinetics of the SM capture and release processes. With increasing field strength, the rate constant of the capture kinetics increase while the release kinetics decrease, favouring the former over the latter. As a result, the SM capture state is more likely and more stable than the release state above a specific threshold nearfild strength. We have also estimated the decrease in the capture free-energy profile and the increase in the release profiles to be around 5 kJ mol-1 for the laser powers employed, ranging from laser-OFF conditions to 11 mW μm-2. We envisage that our findings can be combined with the electrocatalytic capabilities of the (nearfield) nanogap to develop next-generation molecular nanoreactors. This approach will open the door to highly efficient SM catalysis with precise extended monitoring timescales facilitated through the longer residence times of the reactant trapped inside the nanogap.
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Affiliation(s)
- Katrin F Domke
- University of Duisburg-Essen, Faculty of Chemistry, Universitätsstr. 5, 45141 Essen, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Albert C Aragonès
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Marti i Franquès 1, 08028, Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC), Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Spain.
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Harashima T, Egami Y, Homma K, Jono Y, Kaneko S, Fujii S, Ono T, Nishino T. Unique Electrical Signature of Phosphate for Specific Single-Molecule Detection of Peptide Phosphorylation. J Am Chem Soc 2022; 144:17449-17456. [DOI: 10.1021/jacs.2c05787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takanori Harashima
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 W4-11 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yoshiyuki Egami
- Division of Applied Physics, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Kanji Homma
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 W4-11 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yuki Jono
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 W4-11 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Satoshi Kaneko
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 W4-11 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Shintaro Fujii
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 W4-11 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tomoya Ono
- Department of Electrical and Electronic Engineering, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Tomoaki Nishino
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 W4-11 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
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Zhang L, Kaneko S, Fujii S, Kiguchi M, Nishino T. Single-molecule determination of chemical equilibrium of DNA intercalation by electrical conductance. Chem Commun (Camb) 2021; 57:4380-4383. [PMID: 33949386 DOI: 10.1039/d0cc08348h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated a single-molecule reaction of DNA intercalation as an example of a bimolecular association reaction. Single-molecule conductance values of the product and reactant molecules adsorbed on an Au surface were measured to identify and quantify these molecules. The binding isotherm was constructed, and the association constant of the reaction was determined on a single-molecule basis.
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Affiliation(s)
- Lu Zhang
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
| | - Satoshi Kaneko
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
| | - Shintaro Fujii
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
| | - Manabu Kiguchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
| | - Tomoaki Nishino
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
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Harashima T, Hasegawa Y, Kaneko S, Jono Y, Fujii S, Kiguchi M, Nishino T. Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance. Chem Sci 2020; 12:2217-2224. [PMID: 34163987 PMCID: PMC8179252 DOI: 10.1039/d0sc04449k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Direct monitoring of single-molecule reactions has recently become a promising means of mechanistic investigation. However, the resolution of reaction pathways from single-molecule experiments remains elusive, primarily because of interference from extraneous processes such as bulk diffusion. Herein, we report a single-molecule kinetic investigation of DNA hybridization on a metal surface, as an example of a bimolecular association reaction. The tip of the scanning tunneling microscope (STM) was functionalized with single-stranded DNA (ssDNA), and hybridization with its complementary strand on an Au(111) surface was detected by the increase in the electrical conductance associated with the electron transport through the resulting DNA duplex. Kinetic analyses of the conductance changes successfully resolved the elementary processes, which involve not only the ssDNA strands and their duplex but also partially hybridized intermediate strands, and we found an increase in the hybridization efficiency with increasing the concentration of DNA in contrast to the knowledge obtained previously by conventional ensemble measurements. The rate constants derived from our single-molecule studies provide a rational explanation of these findings, such as the suppression of DNA melting on surfaces with higher DNA coverage. The present methodology, which relies on intermolecular conductance measurements, can be extended to a range of single-molecule reactions and to the exploration of novel chemical syntheses. Hybridization of a single DNA molecule on a surface was investigated by electrical conductance measurements. The hybridization efficiency increases with increasing the DNA concentration, in contrast to preceding studies with ensemble studies.![]()
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Affiliation(s)
- Takanori Harashima
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Yusuke Hasegawa
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Satoshi Kaneko
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Yuki Jono
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Shintaro Fujii
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Manabu Kiguchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
| | - Tomoaki Nishino
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 W4-11 Ookayama Meguro-ku Tokyo 152-8551 Japan
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Hasegawa Y, Harashima T, Jono Y, Seki T, Kiguchi M, Nishino T. Kinetic investigation of a chemical process in single-molecule junction. Chem Commun (Camb) 2020; 56:309-312. [DOI: 10.1039/c9cc08383a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report on the kinetic investigation for the breakdown of single-molecule junctions.
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Affiliation(s)
- Yusuke Hasegawa
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Takanori Harashima
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Yuki Jono
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Takumi Seki
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Manabu Kiguchi
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Tomoaki Nishino
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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