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Pim S, Bourgès AC, Wu D, Durán-Sampedro G, Garre M, O'Shea DF. Observing bioorthogonal macrocyclizations in the nuclear envelope of live cells using on/on fluorescence lifetime microscopy. Chem Sci 2024:d4sc03489a. [PMID: 39184298 PMCID: PMC11343072 DOI: 10.1039/d4sc03489a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024] Open
Abstract
The reactive partnership between azides and strained alkynes is at the forefront of bioorthogonal reactions, with their in situ cellular studies often achieved through the use of off to on fluorophores with fluorescence microscopy. In this work, the first demonstration of a bioorthogonal, macrocycle-forming reaction occurring within the nuclear envelope of live cells has been accomplished, utilising on/on fluorescence lifetime imaging microscopy for real-time continuous observation of the transformation. The fluorescent, macrocyclic BF2 azadipyrromethene was accessible through a double 1,3-dipolar cycloaddition within minutes, between a precursor bis-azido substituted fluorophore and Sondheimer diyne in water or organic solvents. Photophysical properties of both the starting bis-azide BF2 azadipyrromethene and the fluorescent macrocyclic products were obtained, with near identical emission wavelengths and intensities, but different lifetimes. In a novel approach, the progress of the live-cell bioorthogonal macrocyclization was successfully tracked through a fluorescence lifetime change of 0.6 ns from starting material to products, with reaction completion achieved within 45 min. The continuous monitoring and imaging of this bioorthogonal transformation in the nuclear membrane and invaginations, of two different cancer cell lines, has been demonstrated using a combination of fluorescence intensity and lifetime imaging with phasor plot analysis. As there is a discernible difference in fluorescence lifetimes between starting material and products, this approach removes the necessity for off-to-on fluorogenic probes when preparing for bioorthogonal cell-imaging and microscopy.
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Affiliation(s)
| | | | - Dan Wu
- Department of Chemistry, RCSI Dublin 2 Ireland
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2
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He Z, Wang Z, Lu L, Wang X, Guo G. Enhanced recognition of G-quadruplex DNA oxidative damage based on DNA-mediated charge transfer. Bioelectrochemistry 2024; 158:108714. [PMID: 38653106 DOI: 10.1016/j.bioelechem.2024.108714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 04/25/2024]
Abstract
G-quadruplex (G4) DNA is present in human telomere oligonucleotide sequences. Oxidative damage to telomeric DNA accelerates telomere shortening, which is strongly associated with aging and cancer. Most of the current analyses on oxidative DNA damage are based on ds-DNA. Here, we developed a electrochemiluminescence (ECL) probe for enhanced recognition of oxidative damage in G4-DNA based on DNA-mediated charge transfer (CT), which could specifically recognize damaged sites depending on the position of 8-oxoguanine (8-oxoG). First, a uniform G4-DNA monolayer interface was fabricated; the G4-DNA mediated CT properties were examined using an iridium(III) complex [Ir(ppy)2(pip)]PF6 stacked with G4-DNA as an indicator. The results showed that G4-DNA with 8-oxoG attenuated DNA CT. The topological effects of oxidative damage at different sites of G4-DNA and their effects on DNA CT were revealed. The sensing platform was also used for the sensitive and quantitative detection of 8-oxoG in G4-DNA, with a detection limit of 28.9 fmol. Overall, these findings present a sensitive platform to study G4-DNA structural and stability changes caused by oxidative damage as well as the specific and quantitative detection of oxidation sites. The different damage sites in the G-quadruplex could provide detailed clues for understanding the function of G4-associated telomere functional enzymes.
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Affiliation(s)
- Zhangjin He
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China
| | - Ziqi Wang
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China
| | - Liping Lu
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China; Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China.
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China
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3
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Single-molecule junction spontaneously restored by DNA zipper. Nat Commun 2021; 12:5762. [PMID: 34599166 PMCID: PMC8486845 DOI: 10.1038/s41467-021-25943-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
The electrical properties of DNA have been extensively investigated within the field of molecular electronics. Previous studies on this topic primarily focused on the transport phenomena in the static structure at thermodynamic equilibria. Consequently, the properties of higher-order structures of DNA and their structural changes associated with the design of single-molecule electronic devices have not been fully studied so far. This stems from the limitation that only extremely short DNA is available for electrical measurements, since the single-molecule conductance decreases sharply with the increase in the molecular length. Here, we report a DNA zipper configuration to form a single-molecule junction. The duplex is accommodated in a nanogap between metal electrodes in a configuration where the duplex is perpendicular to the nanogap axis. Electrical measurements reveal that the single-molecule junction of the 90-mer DNA zipper exhibits high conductance due to the delocalized π system. Moreover, we find an attractive self-restoring capability that the single-molecule junction can be repeatedly formed without full structural breakdown even after electrical failure. The DNA zipping strategy presented here provides a basis for novel designs of single-molecule junctions. The versatility of DNA has inspired many single-molecule investigations utilizing nanotechnology. Harashima et al. have a somewhat different take on the subject and study a zipper configuration bridging electrodes that resembles an active electro-mechanical component instead.
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Akhtar A, Rashid U, Seth C, Kumar S, Broekmann P, Kaliginedi V. Modulating the charge transport in metal│molecule│metal junctions via electrochemical gating. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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HARASHIMA T, HASEGAWA Y, KIGUCHI M, NISHINO T. Evaluation of the Kinetic Property of Single-Molecule Junctions by Tunneling Current Measurements. ANAL SCI 2018; 34:639-641. [DOI: 10.2116/analsci.18c011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Takanori HARASHIMA
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Yusuke HASEGAWA
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Manabu KIGUCHI
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Tomoaki NISHINO
- Department of Chemistry, School of Science, Tokyo Institute of Technology
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KOZAKAI T, HARASHIMA T, KIGUCHI M, NISHINO T. Measurement of Electron Transfer within a Single Supramolecular Assembly Containing a Biological Molecule. ANAL SCI 2018; 34:521-523. [DOI: 10.2116/analsci.18c010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Takafumi KOZAKAI
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Takanori HARASHIMA
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Manabu KIGUCHI
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Tomoaki NISHINO
- Department of Chemistry, School of Science, Tokyo Institute of Technology
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Nishino T, Shiigi H, Kiguchi M, Nagaoka T. Specific single-molecule detection of glucose in a supramolecularly designed tunnel junction. Chem Commun (Camb) 2018; 53:5212-5215. [PMID: 28443849 DOI: 10.1039/c6cc09932g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Scanning tunneling microscopy tips were functionalized with a boronic acid derivative. In combination with a similarly modified substrate, the molecular tip forms a supramolecular complex selectively with a glucose molecule. The conductance of the resulting single complex allows one to achieve the specific single-molecule detection of glucose.
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Affiliation(s)
- Tomoaki Nishino
- Department of Chemistry, School of Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
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Li X, Hu D, Tan Z, Bai J, Xiao Z, Yang Y, Shi J, Hong W. Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions. Top Curr Chem (Cham) 2017; 375:42. [PMID: 28337670 DOI: 10.1007/s41061-017-0123-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/18/2017] [Indexed: 11/26/2022]
Abstract
The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.
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Affiliation(s)
- Xiaohui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Duan Hu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Zhibing Tan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Jie Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Zongyuan Xiao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China.
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China.
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China.
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Li Y, Kaneko S, Fujii S, Nishino T, Kiguchi M. Atomic structure of water/Au, Ag, Cu and Pt atomic junctions. Phys Chem Chem Phys 2017; 19:4673-4677. [PMID: 28125112 DOI: 10.1039/c6cp07549e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Much progress has been made in understanding the transport properties of atomic-scale conductors. We prepared atomic-scale metal contacts of Cu, Ag, Au and Pt using a mechanically controllable break junction method at 10 K in a cryogenic vacuum. Water molecules were exposed to the metal atomic contacts and the effect of molecular adsorption was investigated by electronic conductance measurements. Statistical analysis of the electronic conductance showed that the water molecule(s) interacted with the surface of the inert Au contact and the reactive Cu ant Pt contacts, where molecular adsorption decreased the electronic conductance. A clear conductance signature of water adsorption was not apparent at the Ag contact. Detailed analysis of the conductance behaviour during a contact-stretching process indicated that metal atomic wires were formed for the Au and Pt contacts. The formation of an Au atomic wire consisting of low coordination number atoms leads to increased reactivity of the inert Au surface towards the adsorption of water.
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Affiliation(s)
- Yu Li
- Department of Chemistry, Graduate School of Science and Engineering, Institute of Technology, 2-12-1 W4-10 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
| | - Satoshi Kaneko
- Department of Chemistry, Graduate School of Science and Engineering, Institute of Technology, 2-12-1 W4-10 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
| | - Shintaro Fujii
- Department of Chemistry, Graduate School of Science and Engineering, Institute of Technology, 2-12-1 W4-10 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
| | - Tomoaki Nishino
- Department of Chemistry, Graduate School of Science and Engineering, Institute of Technology, 2-12-1 W4-10 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
| | - Manabu Kiguchi
- Department of Chemistry, Graduate School of Science and Engineering, Institute of Technology, 2-12-1 W4-10 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
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11
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Harashima T, Kojima C, Fujii S, Kiguchi M, Nishino T. Single-molecule conductance of DNA gated and ungated by DNA-binding molecules. Chem Commun (Camb) 2017; 53:10378-10381. [DOI: 10.1039/c7cc02911j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Single-molecule conductance can be controllably modulated by DNA-binding molecules.
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Affiliation(s)
- Takanori Harashima
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Meguro-ku
- Japan
| | - Chie Kojima
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka Prefecture University
- Sakai
- Japan
| | - Shintaro Fujii
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Meguro-ku
- Japan
| | - Manabu Kiguchi
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Meguro-ku
- Japan
| | - Tomoaki Nishino
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Meguro-ku
- Japan
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12
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Qi J, Govind N, Anantram MP. The role of cytosine methylation on charge transport through a DNA strand. J Chem Phys 2015; 143:094306. [DOI: 10.1063/1.4929909] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jianqing Qi
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500, USA
| | - Niranjan Govind
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M. P. Anantram
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500, USA
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