1
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Tian R, Ma W, Wang L, Xie W, Wang Y, Yin Y, Weng T, He S, Fang S, Liang L, Wang L, Wang D, Bai J. The combination of DNA nanostructures and materials for highly sensitive electrochemical detection. Bioelectrochemistry 2024; 157:108651. [PMID: 38281367 DOI: 10.1016/j.bioelechem.2024.108651] [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: 11/24/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/30/2024]
Abstract
Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.
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Affiliation(s)
- Rong Tian
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Wenhao Ma
- Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Lue Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Wanyi Xie
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Yunjiao Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Yajie Yin
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Ting Weng
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Shixuan He
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Shaoxi Fang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Liyuan Liang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Liang Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Deqiang Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
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2
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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401877. [PMID: 38639403 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Li Cheng
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Mengmeng Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Suhang He
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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3
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Santermans S, Hellings G, Heyns M, Van Roy W, Martens K. Unraveling the impact of nano-scaling on silicon field-effect transistors for the detection of single-molecules. NANOSCALE 2023; 15:2354-2368. [PMID: 36644797 DOI: 10.1039/d2nr05267a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Electrolyte-gated silicon field-effect transistors (FETs) capable of detecting single molecules could enable high-throughput molecular sensing chips to advance, for example, genomics or proteomics. For solid-gated silicon FETs it is well-known that nano-scaled devices become sensitive to single elementary charges near the silicon-oxide interface. However, in electrolyte-gated FETs, electrolyte screening strongly reduces sensitivity to charges near the gate oxide. The question arises whether nano-scaling electrolyte-gated FETs can entail a sufficiently large signal-to-noise ratio (SNR) for the detection of single molecules. We enhanced a technology computer-aided design tool with electrolyte screening models to calculate the impact of the FET geometry on the single-molecule signal and FET noise. Our continuum FET model shows that a sufficiently large single-molecule SNR is only obtained when nano-scaling all FET channel dimensions. Moreover, we show that the expected scaling trend of the single-molecule SNR breaks down and no longer results in improvements for geometries approaching the decananometer size. This is the characteristic size of the FET channel region modulated by a typical molecule. For gate lengths below 50 nm, the overlap of the modulated region with the highly conductive junctions leads to saturation of the SNR. For cross-sections below 10-30 nm, SNR degrades due to the overlap of the modulated region with the convex FET corners where a larger local gate capacitance reduces charge sensitivity. In our study, assuming a commercial solid-state FET noise amplitude, we find that a suspended nanowire FET architecture with 35 nm length and 5 × 10 nm2 cross-section results in the highest SNR of about 10 for a 15-base DNA oligo in a 15 mM electrolyte. In contrast with typical silicon nanowire FET sensors which possess micron-scale gate lengths, we find it to be key that all channel dimensions are scaled down to the decananometer range.
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Affiliation(s)
- Sybren Santermans
- imec, Kapeldreef 75, 3001 Leuven, Belgium.
- Department of Materials Engineering, University of Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
| | | | - Marc Heyns
- imec, Kapeldreef 75, 3001 Leuven, Belgium.
- Department of Materials Engineering, University of Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
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4
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Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity. Proc Natl Acad Sci U S A 2022; 119:2112812119. [PMID: 35074874 PMCID: PMC8812571 DOI: 10.1073/pnas.2112812119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Detection of molecular interactions is the foundation for many important biotechnology applications in society and industry, such as drug discovery, diagnostics, and DNA sequencing. This report describes a broadly applicable platform for detecting molecular interactions at the single-molecule scale, in real-time, label-free, and potentially highly multiplexable fashion, using single-molecule sensors on a highly scalable semiconductor sensor array chip. Such chips are both practically manufacturable in the near term, and have a durable long-term scaling roadmap, thus providing an ideal way to bring the power of modern chip technology to the broad area of biosensing. This work also realizes a 50-year-old scientific vision of integrating single molecules into electronic chips to achieve the ultimate miniaturization of electronics. For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.
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5
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Xu X, Bowen BJ, Gwyther REA, Freeley M, Grigorenko B, Nemukhin AV, Eklöf‐Österberg J, Moth‐Poulsen K, Jones DD, Palma M. Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:20346-20351. [PMID: 38504924 PMCID: PMC10946871 DOI: 10.1002/ange.202104044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/24/2021] [Indexed: 11/08/2022]
Abstract
The ability to detect proteins through gating conductance by their unique surface electrostatic signature holds great potential for improving biosensing sensitivity and precision. Two challenges are: (1) defining the electrostatic surface of the incoming ligand protein presented to the conductive surface; (2) bridging the Debye gap to generate a measurable response. Herein, we report the construction of nanoscale protein-based sensing devices designed to present proteins in defined orientations; this allowed us to control the local electrostatic surface presented within the Debye length, and thus modulate the conductance gating effect upon binding incoming protein targets. Using a β-lactamase binding protein (BLIP2) as the capture protein attached to carbon nanotube field effect transistors in different defined orientations. Device conductance had influence on binding TEM-1, an important β-lactamase involved in antimicrobial resistance (AMR). Conductance increased or decreased depending on TEM-1 presenting either negative or positive local charge patches, demonstrating that local electrostatic properties, as opposed to protein net charge, act as the key driving force for electrostatic gating. This, in turn can, improve our ability to tune the gating of electrical biosensors toward optimized detection, including for AMR as outlined herein.
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Affiliation(s)
- Xinzhao Xu
- Department of Chemistry and Materials Research InstituteQueen Mary University of LondonLondonE1 4NSUK
| | - Benjamin J. Bowen
- Molecular Biosciences DivisionSchool of BiosciencesSir Martin Evans BuildingCardiff UniversityCardiffCF10 3AXUK
| | - Rebecca E. A. Gwyther
- Molecular Biosciences DivisionSchool of BiosciencesSir Martin Evans BuildingCardiff UniversityCardiffCF10 3AXUK
| | - Mark Freeley
- Department of Chemistry and Materials Research InstituteQueen Mary University of LondonLondonE1 4NSUK
| | - Bella Grigorenko
- Department of ChemistryLomonosov Moscow State UniversityMoscow119991Russian Federation
- Emanuel Institute of Biochemical PhysicsRussian Academy of SciencesMoscow119991Russian Federation
| | - Alexander V. Nemukhin
- Department of ChemistryLomonosov Moscow State UniversityMoscow119991Russian Federation
- Emanuel Institute of Biochemical PhysicsRussian Academy of SciencesMoscow119991Russian Federation
| | - Johnas Eklöf‐Österberg
- Department of Chemistry and Chemical EngineeringChalmers University of Technology41296GothenburgSweden
| | - Kasper Moth‐Poulsen
- Department of Chemistry and Chemical EngineeringChalmers University of Technology41296GothenburgSweden
| | - D. Dafydd Jones
- Molecular Biosciences DivisionSchool of BiosciencesSir Martin Evans BuildingCardiff UniversityCardiffCF10 3AXUK
| | - Matteo Palma
- Department of Chemistry and Materials Research InstituteQueen Mary University of LondonLondonE1 4NSUK
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6
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Xu X, Bowen BJ, Gwyther REA, Freeley M, Grigorenko B, Nemukhin AV, Eklöf‐Österberg J, Moth‐Poulsen K, Jones DD, Palma M. Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices. Angew Chem Int Ed Engl 2021; 60:20184-20189. [PMID: 34270157 PMCID: PMC8457214 DOI: 10.1002/anie.202104044] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/24/2021] [Indexed: 11/07/2022]
Abstract
The ability to detect proteins through gating conductance by their unique surface electrostatic signature holds great potential for improving biosensing sensitivity and precision. Two challenges are: (1) defining the electrostatic surface of the incoming ligand protein presented to the conductive surface; (2) bridging the Debye gap to generate a measurable response. Herein, we report the construction of nanoscale protein-based sensing devices designed to present proteins in defined orientations; this allowed us to control the local electrostatic surface presented within the Debye length, and thus modulate the conductance gating effect upon binding incoming protein targets. Using a β-lactamase binding protein (BLIP2) as the capture protein attached to carbon nanotube field effect transistors in different defined orientations. Device conductance had influence on binding TEM-1, an important β-lactamase involved in antimicrobial resistance (AMR). Conductance increased or decreased depending on TEM-1 presenting either negative or positive local charge patches, demonstrating that local electrostatic properties, as opposed to protein net charge, act as the key driving force for electrostatic gating. This, in turn can, improve our ability to tune the gating of electrical biosensors toward optimized detection, including for AMR as outlined herein.
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Affiliation(s)
- Xinzhao Xu
- Department of Chemistry and Materials Research InstituteQueen Mary University of LondonLondonE1 4NSUK
| | - Benjamin J. Bowen
- Molecular Biosciences DivisionSchool of BiosciencesSir Martin Evans BuildingCardiff UniversityCardiffCF10 3AXUK
| | - Rebecca E. A. Gwyther
- Molecular Biosciences DivisionSchool of BiosciencesSir Martin Evans BuildingCardiff UniversityCardiffCF10 3AXUK
| | - Mark Freeley
- Department of Chemistry and Materials Research InstituteQueen Mary University of LondonLondonE1 4NSUK
| | - Bella Grigorenko
- Department of ChemistryLomonosov Moscow State UniversityMoscow119991Russian Federation
- Emanuel Institute of Biochemical PhysicsRussian Academy of SciencesMoscow119991Russian Federation
| | - Alexander V. Nemukhin
- Department of ChemistryLomonosov Moscow State UniversityMoscow119991Russian Federation
- Emanuel Institute of Biochemical PhysicsRussian Academy of SciencesMoscow119991Russian Federation
| | - Johnas Eklöf‐Österberg
- Department of Chemistry and Chemical EngineeringChalmers University of Technology41296GothenburgSweden
| | - Kasper Moth‐Poulsen
- Department of Chemistry and Chemical EngineeringChalmers University of Technology41296GothenburgSweden
| | - D. Dafydd Jones
- Molecular Biosciences DivisionSchool of BiosciencesSir Martin Evans BuildingCardiff UniversityCardiffCF10 3AXUK
| | - Matteo Palma
- Department of Chemistry and Materials Research InstituteQueen Mary University of LondonLondonE1 4NSUK
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7
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A modified approach for high-quality RNA extraction of spore-forming Bacillus subtilis at varied physiological stages. Mol Biol Rep 2021; 48:6757-6768. [PMID: 34455533 DOI: 10.1007/s11033-021-06673-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND High quality RNA is required for the molecular study. Sample preparation of the spore-forming, Gram-positive bacteria like Bacillus sp., remains challenging although several methods have been proposed. Those techniques were simply developed using cell samples at certain growth stages despite some molecular studies like transcriptomic analyses require RNA samples from different physiological stages. METHODS AND RESULTS We developed the rapid, simple yet effective cell-lysis technique with limit use of harsh reagents by modifying the kit-based protocols. Appropriate lysozyme loading (20 mg/mL), incubation time (30 min), and temperature (37 °C) enabled cell lysis and enhanced RNA extraction from both vegetative cells and endospores of Bacillus subtilis TL7-3. High RNA Integrity Numbers and ratios of A260/A280 and A260/A230 of all RNA products collected during the batch cultivation confirmed that invert mixing with absolute ethanol prevented RNA damage during protein denaturation. With the process modification of the major steps in cell lysis and RNA extraction compared with the kit-based protocols that are typically used in laboratory work, interestingly, our modified protocol, simple-yet-effective, yielded higher concentration, purity, and integrity of RNA products from all cell samples collected at different physiological stages. While the kit-based protocols either failed to provide high RNA concentration or RNA purity and integrity for all cell samples particularly during the late-log, stationary, or sporulation. CONCLUSIONS Therefore, we can claim the significance of this modified protocol to be applicable for RNA extraction to those spore-forming Gram-positive bacteria not limited to B. subtilis growing at varied physiological stages.
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8
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Woo SO, Oh M, Alhalhooly L, Farmakes J, Rajapakse AJ, Yang Z, Collins PG, Choi Y. Different Single-Enzyme Conformational Dynamics upon Binding Hydrolyzable or Nonhydrolyzable Ligands. J Phys Chem B 2021; 125:5750-5756. [PMID: 34038124 DOI: 10.1021/acs.jpcb.1c01589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule measurements of protein dynamics help unveil the complex conformational changes and transitions that occur during ligand binding and catalytic processes. Using high-resolution single-molecule nanocircuit techniques, we have investigated differences in the conformational dynamics and transitions of lysozyme interacting with three ligands: peptidoglycan substrate, substrate-based chitin analogue, and indole derivative inhibitors. While processing peptidoglycan, lysozyme followed one of the two mechanistic pathways for the hydrolysis of the glycosidic bonds: a concerted mechanism inducing direct conformational changes from open to fully closed conformations or a nonconcerted mechanism involving transient pauses in intermediate conformations between the open and closed conformations. In the presence of either chitin or an indole inhibitor, lysozyme was unable to access the fully closed conformation where catalysis occurs. Instead, lysozymes' conformational closures terminated at slightly closed, "excited" conformations that were approximately one-quarter of the full hinge-bending range. With the indole inhibitor, lysozyme reached this excited conformation in a single step without any evidence of rate-liming intermediates, but the same conformational motions with chitin involved three hidden, intermediate processes and features similar to the nonconcerted peptidoglycan mechanism. The similarities suggest that these hidden processes involve attempts to accommodate imperfectly aligned polysaccharides in the active site. The results provide a detailed glimpse of the enzyme-ligand interplay at the crux of molecular recognition, enzyme specificity, and catalysis.
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Affiliation(s)
- Sung Oh Woo
- Department of Physics, North Dakota State University, Fargo, North Dakota 5810, United States
| | - Myungkeun Oh
- Materials and Nanotechnology Program, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Lina Alhalhooly
- Department of Physics, North Dakota State University, Fargo, North Dakota 5810, United States
| | - Jasmin Farmakes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Arith J Rajapakse
- Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Philip G Collins
- Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, North Dakota 5810, United States.,Materials and Nanotechnology Program, North Dakota State University, Fargo, North Dakota 58108, United States
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9
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Wang L, Zhang J, Han M, Zhang L, Chen C, Huang A, Xie R, Wang G, Zhu J, Wang Y, Liu X, Zhuang W, Li Y, Wang J. A Genetically Encoded Two‐Dimensional Infrared Probe for Enzyme Active‐Site Dynamics. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Li Wang
- School of Life Sciences University of Chinese Academy of Sciences Yuquan Road, Shijingshan District Beijing 100049 China
- Institute of Biophysics Chinese Academy of Sciences Datun Road, Chaoyang District Beijing 100101 China
| | - Jia Zhang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Ming‐Jie Han
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center Futian District Shenzhen 518052 China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou 350002 China
| | - Chao Chen
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Ruipei Xie
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Guosheng Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
| | - Jiangrui Zhu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Yuchuan Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center Futian District Shenzhen 518052 China
| | - Xiaohong Liu
- Institute of Biophysics Chinese Academy of Sciences Datun Road, Chaoyang District Beijing 100101 China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou 350002 China
- Institute of urban environment Chinese Academy of Sciences Xiamen Fujian 361021 China
| | - Yunliang Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100190 China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China
- Songshan Lake Materials Laboratory Dongguan Guangdong 523808 China
| | - Jiangyun Wang
- Institute of Biophysics Chinese Academy of Sciences Datun Road, Chaoyang District Beijing 100101 China
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center Futian District Shenzhen 518052 China
- School of Life Sciences University of Chinese Academy of Sciences Yuquan Road, Shijingshan District Beijing 100049 China
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10
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Wang L, Zhang J, Han MJ, Zhang L, Chen C, Huang A, Xie R, Wang G, Zhu J, Wang Y, Liu X, Zhuang W, Li Y, Wang J. A Genetically Encoded Two-Dimensional Infrared Probe for Enzyme Active-Site Dynamics. Angew Chem Int Ed Engl 2021; 60:11143-11147. [PMID: 33644946 DOI: 10.1002/anie.202016880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/10/2021] [Indexed: 11/08/2022]
Abstract
While two-dimensional infrared (2D-IR) spectroscopy is uniquely suitable for monitoring femtosecond (fs) to picosecond (ps) water dynamics around static protein structures, its utility for probing enzyme active-site dynamics is limited due to the lack of site-specific 2D-IR probes. We demonstrate the genetic incorporation of a novel 2D-IR probe, m-azido-L-tyrosine (N3Y) in the active-site of DddK, an iron-dependent enzyme that catalyzes the conversion of dimethylsulfoniopropionate to dimethylsulphide. Our results show that both the oxidation of active-site iron to FeIII , and the addition of denaturation reagents, result in significant decrease in enzyme activity and active-site water motion confinement. As tyrosine residues play important roles, including as general acids and bases, and electron transfer agents in many key enzymes, the genetically encoded 2D-IR probe N3Y should be broadly applicable to investigate how the enzyme active-site motions at the fs-ps time scale direct reaction pathways to facilitating specific chemical reactions.
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Affiliation(s)
- Li Wang
- School of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing, 100049, China.,Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jia Zhang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming-Jie Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Futian District, Shenzhen, 518052, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China
| | - Chao Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Ruipei Xie
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guosheng Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiangrui Zhu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuchuan Wang
- Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Futian District, Shenzhen, 518052, China
| | - Xiaohong Liu
- Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China.,Institute of urban environment, Chinese Academy of Sciences, Xiamen, Fujian, 361021, China
| | - Yunliang Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China.,Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Futian District, Shenzhen, 518052, China.,School of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing, 100049, China
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11
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Huang Q, Li N, Zhang H, Che C, Sun F, Xiong Y, Canady TD, Cunningham BT. Critical Review: digital resolution biomolecular sensing for diagnostics and life science research. LAB ON A CHIP 2020; 20:2816-2840. [PMID: 32700698 PMCID: PMC7485136 DOI: 10.1039/d0lc00506a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.
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Affiliation(s)
- Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Hanyuan Zhang
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Congnyu Che
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fu Sun
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Taylor D. Canady
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Illinois Cancer Center, University of Illinois at Urbana-Champaign Urbana, IL 61801
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12
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Woo SO, Froberg J, Pan Y, Tani S, Goldsmith BR, Yang Z, Choi Y. Protein Detection using Quadratic Fit Analysis Near Dirac Point of Graphene Field Effect Biosensors. ACS APPLIED ELECTRONIC MATERIALS 2020; 2:913-919. [PMID: 32550598 PMCID: PMC7299209 DOI: 10.1021/acsaelm.9b00840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Although graphene-based biosensors provid extreme sensitivity for the detection of atoms, gases, and biomolecules, the specificity of graphene biosensors to the target molecules requires surface decoration of graphene with bifunctional linkers such pyrene derivatives. Here, we demonstrate that the pyrene functionalization influences graphene's electrical properties by yielding partial formation of bilayer graphene which was confirmed by Raman 2D spectrum. Based on this observation, we introduce quadratic fit analysis of the nonlinear electrical behavior of pyrene-functionalized graphene near the Dirac point. Compared to the conventional linear fit analysis of the transconductance at a distance from the Dirac point, the quadratic fit analysis of the nonlinear transconductance near the Dirac point increased the overall protein detection sensitivity by a factor of 5. Furthermore, we show that both pyrene linkers and gating voltage near the Dirac point play critical roles in sensitive and reliable detection of proteins' biological activities with the graphene biosensors.
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Affiliation(s)
- Sung Oh Woo
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
| | - James Froberg
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Sakurako Tani
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Brett R. Goldsmith
- Cardea Bio Inc., 9649 Towne Centre Dr. Suite 100, San Diego, California 92121, USA
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA
- Materials and Nanotechnology Program, North Dakota State University, Fargo, North Dakota 58108, USA
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13
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Tuovinen R, Sentef MA, Gomes da Rocha C, Ferreira MS. Time-resolved impurity-invisibility in graphene nanoribbons. NANOSCALE 2019; 11:12296-12304. [PMID: 31211315 DOI: 10.1039/c9nr02738f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigate time-resolved charge transport through graphene nanoribbons supplemented with adsorbed impurity atoms. Depending on the location of the impurities with respect to the hexagonal carbon lattice, the transport properties of the system may become invisible to the impurity due to the symmetry properties of the binding mechanism. This motivates a chemical sensing device since dopants affecting the underlying sublattice symmetry of the pristine graphene nanoribbon introduce scattering. Using the time-dependent Landauer-Büttiker formalism, we extend the stationary current-voltage picture to the transient regime, where we observe how the impurity invisibility takes place at sub-picosecond time scales further motivating ultrafast sensor technology. We further characterize time-dependent local charge and current profiles within the nanoribbons, and we identify rearrangements of the current pathways through the nanoribbons due to the impurities. We finally study the behavior of the transients with ac driving which provides another way of identifying the lattice-symmetry breaking caused by the impurities.
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Affiliation(s)
- Riku Tuovinen
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany.
| | - Michael A Sentef
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany.
| | - Claudia Gomes da Rocha
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mauro S Ferreira
- School of Physics, Trinity College Dublin, Dublin 2, Ireland and Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN) and Advanced Materials and Bioengineering Research (AMBER) Centre, Trinity College Dublin, Dublin 2, Ireland
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14
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You S, Froberg J, Yu J, Haldar M, Sedigh A, Mallik S, Srivastava DK, Choi Y. Real-time monitoring of conformational transitions of single-molecule histone deacetylase 8 with nanocircuits. Chem Commun (Camb) 2018; 53:3307-3310. [PMID: 28261707 DOI: 10.1039/c6cc09949a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using single-molecule approaches, we directly observed the dynamic interaction between HDAC8 and various ligands as well as conformational interconversions during the catalytic reaction. Statistical analysis identified key kinetic parameters, demonstrating that the enzymatic activity is highly sensitive to both minor variations in the ligand structures and small synthetic molecules.
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Affiliation(s)
- Seungyong You
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA.
| | - James Froberg
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA.
| | - Junru Yu
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Manas Haldar
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Abbas Sedigh
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Sanku Mallik
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58108, USA
| | - D K Srivastava
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, USA
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, USA.
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15
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Lakshminarayanan A, Richard M, Davis BG. Studying glycobiology at the single-molecule level. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0019-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Villa-Rodríguez E, Ibarra-Gámez C, de Los Santos-Villalobos S. Extraction of high-quality RNA from Bacillus subtilis with a lysozyme pre-treatment followed by the Trizol method. J Microbiol Methods 2018; 147:14-16. [PMID: 29474841 DOI: 10.1016/j.mimet.2018.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 02/17/2018] [Accepted: 02/17/2018] [Indexed: 11/16/2022]
Abstract
A suitable technique (lysozyme combined with Trizol reagent) was developed to improve the RNA yield, purity and integrity from Bacillus subtilis, under different bacterial growth stages. The obtained RNA was intact, having the required characteristics for downstream applications.
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Affiliation(s)
- Eber Villa-Rodríguez
- Instituto Tecnológico de Sonora, 5 de Febrero 818 Sur, C.P.85000, Col. Centro, Ciudad Obregón, Sonora, Mexico
| | - Cuauhtemoc Ibarra-Gámez
- Instituto Tecnológico de Sonora, 5 de Febrero 818 Sur, C.P.85000, Col. Centro, Ciudad Obregón, Sonora, Mexico
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17
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Lu M, Lu HP. Revealing Multiple Pathways in T4 Lysozyme Substep Conformational Motions by Single-Molecule Enzymology and Modeling. J Phys Chem B 2017; 121:5017-5024. [DOI: 10.1021/acs.jpcb.7b03039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maolin Lu
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
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18
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Sheu SY, Yang DY. Mechanically Controlled Electron Transfer in a Single-Polypeptide Transistor. Sci Rep 2017; 7:39792. [PMID: 28051140 PMCID: PMC5209712 DOI: 10.1038/srep39792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/28/2016] [Indexed: 02/03/2023] Open
Abstract
Proteins are of interest in nano-bio electronic devices due to their versatile structures, exquisite functionality and specificity. However, quantum transport measurements produce conflicting results due to technical limitations whereby it is difficult to precisely determine molecular orientation, the nature of the moieties, the presence of the surroundings and the temperature; in such circumstances a better understanding of the protein electron transfer (ET) pathway and the mechanism remains a considerable challenge. Here, we report an approach to mechanically drive polypeptide flip-flop motion to achieve a logic gate with ON and OFF states during protein ET. We have calculated the transmission spectra of the peptide-based molecular junctions and observed the hallmarks of electrical current and conductance. The results indicate that peptide ET follows an NC asymmetric process and depends on the amino acid chirality and α-helical handedness. Electron transmission decreases as the number of water molecules increases, and the ET efficiency and its pathway depend on the type of water-bridged H-bonds. Our results provide a rational mechanism for peptide ET and new perspectives on polypeptides as potential candidates in logic nano devices.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences, Institute of Genome Sciences and Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
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19
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Gül OT, Pugliese KM, Choi Y, Sims PC, Pan D, Rajapakse AJ, Weiss GA, Collins PG. Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths. BIOSENSORS-BASEL 2016; 6:bios6030029. [PMID: 27348011 PMCID: PMC5039648 DOI: 10.3390/bios6030029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 01/17/2023]
Abstract
As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein’s activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF’s base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures.
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Affiliation(s)
- O Tolga Gül
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
- Department of Physics, Polatlı Faculty of Science and Arts, Gazi University, Polatlı 06900, Turkey
| | - Kaitlin M Pugliese
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697, USA
| | - Yongki Choi
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Patrick C Sims
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Deng Pan
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Arith J Rajapakse
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA
| | - Gregory A Weiss
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697, USA.
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697, USA.
| | - Philip G Collins
- Department of Physics and Astronomy, University of California at Irvine, Irvine, CA 92697, USA.
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20
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Xiang D, Wang X, Jia C, Lee T, Guo X. Molecular-Scale Electronics: From Concept to Function. Chem Rev 2016; 116:4318-440. [DOI: 10.1021/acs.chemrev.5b00680] [Citation(s) in RCA: 816] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Dong Xiang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Key
Laboratory of Optical Information Science and Technology, Institute
of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chuancheng Jia
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Takhee Lee
- Department
of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea
| | - Xuefeng Guo
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Department
of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China
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21
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Pugliese KM, Gul OT, Choi Y, Olsen TJ, Sims PC, Collins PG, Weiss GA. Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits. J Am Chem Soc 2015; 137:9587-94. [PMID: 26147714 DOI: 10.1021/jacs.5b02074] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA polymerases exhibit a surprising tolerance for analogs of deoxyribonucleoside triphosphates (dNTPs), despite the enzymes' highly evolved mechanisms for the specific recognition and discrimination of native dNTPs. Here, individual DNA polymerase I Klenow fragment (KF) molecules were tethered to a single-walled carbon nanotube field-effect transistor (SWCNT-FET) to investigate accommodation of dNTP analogs with single-molecule resolution. Each base incorporation accompanied a change in current with its duration defined by τclosed. Under Vmax conditions, the average time of τclosed was similar for all analog and native dNTPs (0.2 to 0.4 ms), indicating no kinetic impact on this step due to analog structure. Accordingly, the average rates of dNTP analog incorporation were largely determined by durations with no change in current defined by τopen, which includes molecular recognition of the incoming dNTP. All α-thio-dNTPs were incorporated more slowly, at 40 to 65% of the rate for the corresponding native dNTPs. During polymerization with 6-Cl-2APTP, 2-thio-dTTP, or 2-thio-dCTP, the nanocircuit uncovered an alternative conformation represented by positive current excursions that does not occur with native dNTPs. A model consistent with these results invokes rotations by the enzyme's O-helix; this motion can test the stability of nascent base pairs using nonhydrophilic interactions and is allosterically coupled to charged residues near the site of SWCNT attachment. This model with two opposing O-helix motions differs from the previous report in which all current excursions were solely attributed to global enzyme closure and covalent-bond formation. The results suggest the enzyme applies a dynamic stability-checking mechanism for each nascent base pair.
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Affiliation(s)
- Kaitlin M Pugliese
- Departments of †Chemistry, §Physics and Astronomy, and ⊥Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - O Tolga Gul
- Departments of †Chemistry, §Physics and Astronomy, and ⊥Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Yongki Choi
- Departments of †Chemistry, §Physics and Astronomy, and ⊥Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Tivoli J Olsen
- Departments of †Chemistry, §Physics and Astronomy, and ⊥Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Patrick C Sims
- Departments of †Chemistry, §Physics and Astronomy, and ⊥Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Philip G Collins
- Departments of †Chemistry, §Physics and Astronomy, and ⊥Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Gregory A Weiss
- Departments of †Chemistry, §Physics and Astronomy, and ⊥Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
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22
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Akhterov MV, Choi Y, Olsen TJ, Sims PC, Iftikhar M, Gul OT, Corso BL, Weiss GA, Collins PG. Observing lysozyme's closing and opening motions by high-resolution single-molecule enzymology. ACS Chem Biol 2015; 10:1495-501. [PMID: 25763461 DOI: 10.1021/cb500750v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Single-molecule techniques can monitor the kinetics of transitions between enzyme open and closed conformations, but such methods usually lack the resolution to observe the underlying transition pathway or intermediate conformational dynamics. We have used a 1 MHz bandwidth carbon nanotube transistor to electronically monitor single molecules of the enzyme T4 lysozyme as it processes substrate. An experimental resolution of 2 μs allowed the direct recording of lysozyme's opening and closing transitions. Unexpectedly, both motions required 37 μs, on average. The distribution of transition durations was also independent of the enzyme's state: either catalytic or nonproductive. The observation of smooth, continuous transitions suggests a concerted mechanism for glycoside hydrolysis with lysozyme's two domains closing upon the polysaccharide substrate in its active site. We distinguish these smooth motions from a nonconcerted mechanism, observed in approximately 10% of lysozyme openings and closings, in which the enzyme pauses for an additional 40-140 μs in an intermediate, partially closed conformation. During intermediate forming events, the number of rate-limiting steps observed increases to four, consistent with four steps required in the stepwise, arrow-pushing mechanism. The formation of such intermediate conformations was again independent of the enzyme's state. Taken together, the results suggest lysozyme operates as a Brownian motor. In this model, the enzyme traces a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity. The observed symmetry in enzyme opening and closing thus suggests that substrate translocation occurs while the enzyme is closed.
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Affiliation(s)
- Maxim V. Akhterov
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Yongki Choi
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Tivoli J. Olsen
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Patrick C. Sims
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Mariam Iftikhar
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - O. Tolga Gul
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Brad L. Corso
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Gregory A. Weiss
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
| | - Philip G. Collins
- Departments of †Physics and Astronomy, ‡Molecular Biology and Biochemistry, and §Chemistry, University of California, Irvine, California 92697, United States
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23
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Bavishi K, Hatzakis NS. Shedding light on protein folding, structural and functional dynamics by single molecule studies. Molecules 2014; 19:19407-34. [PMID: 25429564 PMCID: PMC6272019 DOI: 10.3390/molecules191219407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 11/16/2022] Open
Abstract
The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.
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Affiliation(s)
- Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Center for Synthetic Biology "bioSYNergy", Villum Research Center "Plant Plasticity", University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark.
| | - Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark.
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24
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Hatzakis NS. Single molecule insights on conformational selection and induced fit mechanism. Biophys Chem 2014; 186:46-54. [DOI: 10.1016/j.bpc.2013.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 11/01/2013] [Accepted: 11/01/2013] [Indexed: 01/24/2023]
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25
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JØRGENSEN SUNEK, HATZAKIS NIKOSS. INSIGHTS IN ENZYME FUNCTIONAL DYNAMICS AND ACTIVITY REGULATION BY SINGLE MOLECULE STUDIES. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013300028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The advent of advanced single molecule measurements heralded the arrival of a wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways not deducible by conventional bulk assays. They offered the direct observation and quantification of the abundance and life time of multiple states and transient intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements, thus providing unprecedented insights into complex biological processes. Here we survey the current state of the art in single-molecule fluorescence microscopy methodology for studying the mechanism of enzymatic activity and the insights on protein functional dynamics. We will initially discuss the strategies employed to date, their limitations and possible ways to overcome them, and finally how single enzyme kinetics can advance our understanding on mechanisms underlying function and regulation of proteins. [Formula: see text]Special Issue Comment: This review focuses on functional dynamics of individual enzymes and is related to the review on ion channels by Lu,44 the reviews on mathematical treatment of Flomenbom45 and Sach et al.,46 and review on FRET by Ruedas-Rama et al.41
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Affiliation(s)
- SUNE K. JØRGENSEN
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center, Biomembranes in Nanomedicine University of Copenhagen, 2100 Copenhagen, Denmark
| | - NIKOS S. HATZAKIS
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center, Biomembranes in Nanomedicine University of Copenhagen, 2100 Copenhagen, Denmark
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Guo Q, He Y, Lu HP. Manipulating and probing enzymatic conformational fluctuations and enzyme–substrate interactions by single-molecule FRET-magnetic tweezers microscopy. Phys Chem Chem Phys 2014; 16:13052-8. [DOI: 10.1039/c4cp01454e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To investigate the critical role of the enzyme–substrate interactions in enzymatic reactions, the enzymatic conformation and enzyme–substrate interaction at a single-molecule level are manipulated by magnetic tweezers, and the impact of the manipulation on enzyme–substrate interactions are simultaneously probed by single-molecule FRET spectroscopy.
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Affiliation(s)
- Qing Guo
- Bowling Green State University
- Center for Photochemical Sciences
- Department of Chemistry
- Bowling Green, USA
| | - Yufan He
- Bowling Green State University
- Center for Photochemical Sciences
- Department of Chemistry
- Bowling Green, USA
| | - H. Peter Lu
- Bowling Green State University
- Center for Photochemical Sciences
- Department of Chemistry
- Bowling Green, USA
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Matsumoto A, Miyahara Y. Current and emerging challenges of field effect transistor based bio-sensing. NANOSCALE 2013; 5:10702-10718. [PMID: 24064964 DOI: 10.1039/c3nr02703a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Field-effect-transistor (FET) based electrical signal transduction is an increasingly prevalent strategy for bio-sensing. This technique, often termed "Bio-FETs", provides an essentially label-free and real-time based bio-sensing platform effective for a variety of targets. This review highlights recent progress and challenges in the field. A special focus is on the comprehension of emerging nanotechnology-based approaches to facilitate signal-transduction and amplification. Some new targets of Bio-FETs and the future perspectives are also discussed.
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Affiliation(s)
- Akira Matsumoto
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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Sensitive Single Particle Method for Characterizing Rapid Rotational and Translational Diffusion and Aspect Ratio of Anisotropic Nanoparticles and Its Application in Immunoassays. Anal Chem 2013; 85:9433-8. [DOI: 10.1021/ac4023956] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Abstract
Single molecule bioelectronic circuits provide an opportunity to study chemical kinetics and kinetic variability with bond-by-bond resolution. To demonstrate this approach, we examined the catalytic activity of T4 lysozyme processing peptidoglycan substrates. Monitoring a single lysozyme molecule through changes in a circuit's conductance helped elucidate unexplored and previously invisible aspects of lysozyme's catalytic mechanism and demonstrated lysozyme to be a processive enzyme governed by 9 independent time constants. The variation of each time constant with pH or substrate crosslinking provided different insights into catalytic activity and dynamic disorder. Overall, ten lysozyme variants were synthesized and tested in single molecule circuits to dissect the transduction of chemical activity into electronic signals. Measurements show that a single amino acid with the appropriate properties is sufficient for good signal generation, proving that the single molecule circuit technique can be easily extended to other proteins.
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Affiliation(s)
- Yongki Choi
- Department of Physics and Astronomy, University of California at Irvine, Irvine, California 92697, United States
| | - Gregory A. Weiss
- Departments of Chemistry and Molecular Biology and Biochemistry, University of California at Irvine, Irvine, California 92697, United States
| | - Philip G. Collins
- Department of Physics and Astronomy, University of California at Irvine, Irvine, California 92697, United States
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Guo X. Single-molecule electrical biosensors based on single-walled carbon nanotubes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:3397-408. [PMID: 23696446 DOI: 10.1002/adma.201301219] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Indexed: 05/21/2023]
Abstract
Interactions between biological molecules are fundamental to biology. Probing the complex behaviors of biological systems at the molecular level provides new opportunities to uncover the wealth of molecular information that is usually hidden in conventional ensemble experiments and address the "unanswerable" questions in the physical, chemical and biological sciences. Nanometer-scale materials are particularly well matched with biomolecular interactions due to their biocompatibility, size comparability, and remarkable electrical properties, thus setting the basis for biological sensing with ultrahigh sensitivity. This brief review aims to highlight the recent progress of the burgeoning field of single-molecule electrical biosensors based on nanomaterials, with a particular focus on single-walled carbon nanotubes (SWNTs), for better understanding of the molecular structure, interacting dynamics, and molecular functions. The perspectives and key issues that will be critical to the success of next-generation single-molecule biosensors toward practical applications are also discussed, such as the device reproducibility, system integration, and theoretical simulation.
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Affiliation(s)
- Xuefeng Guo
- Center for Nanochemistry, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China.
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Olsen TJ, Choi Y, Sims PC, Gul OT, Corso BL, Dong C, Brown WA, Collins PG, Weiss GA. Electronic measurements of single-molecule processing by DNA polymerase I (Klenow fragment). J Am Chem Soc 2013; 135:7855-60. [PMID: 23631761 DOI: 10.1021/ja311603r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bioconjugating single molecules of the Klenow fragment of DNA polymerase I into electronic nanocircuits allowed electrical recordings of enzymatic function and dynamic variability with the resolution of individual nucleotide incorporation events. Continuous recordings of DNA polymerase processing multiple homopolymeric DNA templates extended over 600 s and through >10,000 bond-forming events. An enzymatic processivity of 42 nucleotides for a template of the same length was directly observed. Statistical analysis determined key kinetic parameters for the enzyme's open and closed conformations. Consistent with these nanocircuit-based observations, the enzyme's closed complex forms a phosphodiester bond in a highly efficient process >99.8% of the time, with a mean duration of only 0.3 ms for all four dNTPs. The rate-limiting step for catalysis occurs during the enzyme's open state, but with a nearly 2-fold longer duration for dATP or dTTP incorporation than for dCTP or dGTP into complementary, homopolymeric DNA templates. Taken together, the results provide a wealth of new information complementing prior work on the mechanism and dynamics of DNA polymerase I.
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Affiliation(s)
- Tivoli J Olsen
- Department of Chemistry, University of California, Irvine, California 92697, USA
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Sims PC, Moody IS, Choi Y, Dong C, Iftikhar M, Corso BL, Gul OT, Collins PG, Weiss GA. Electronic measurements of single-molecule catalysis by cAMP-dependent protein kinase A. J Am Chem Soc 2013; 135:7861-8. [PMID: 23631749 DOI: 10.1021/ja311604j] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-molecule studies of enzymes open a window into their dynamics and kinetics. A single molecule of the catalytic domain of cAMP-dependent protein kinase A (PKA) was attached to a single-walled carbon nanotube device for long-duration monitoring. The electronic recording clearly resolves substrate binding, ATP binding, and cooperative formation of PKA's catalytically functional, ternary complex. Using recordings of a single PKA molecule extending over 10 min and tens of thousands of binding events, we determine the full transition probability matrix and conversion rates governing formation of the apo, intermediate, and closed enzyme configurations. We also observe kinetic rates varying over 2 orders of magnitude from one second to another. Anti-correlation of the on and off rates for PKA binding to the peptide substrate, but not ATP, demonstrates that regulation of enzyme activity results from altering the stability of the PKA-substrate complex, not its binding to ATP. The results depict a highly dynamic enzyme offering dramatic possibilities for regulated activity, an attribute useful for an enzyme with crucial roles in cell signaling.
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Affiliation(s)
- Patrick C Sims
- Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
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Choi Y, Olsen TJ, Sims PC, Moody IS, Corso BL, Dang MN, Weiss GA, Collins PG. Dissecting single-molecule signal transduction in carbon nanotube circuits with protein engineering. NANO LETTERS 2013; 13:625-31. [PMID: 23323846 PMCID: PMC3575522 DOI: 10.1021/nl304209p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, nonfluorescent single-molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems.
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Affiliation(s)
- Yongki Choi
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, United States
| | - Tivoli J. Olsen
- Department of Chemistry, University of California, Irvine, CA 92697, United States
| | - Patrick C. Sims
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, United States
| | - Issa S. Moody
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States
| | - Brad L. Corso
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, United States
| | - Mytrang N. Dang
- Department of Chemistry, University of California, Irvine, CA 92697, United States
| | - Gregory A. Weiss
- Department of Chemistry, University of California, Irvine, CA 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States
- Corresponding Author: G.A.W. () or P.G.C. ()
| | - Philip G. Collins
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, United States
- Corresponding Author: G.A.W. () or P.G.C. ()
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Yuan TZ, Overstreet CM, Moody IS, Weiss GA. Protein engineering with biosynthesized libraries from Bordetella bronchiseptica bacteriophage. PLoS One 2013; 8:e55617. [PMID: 23409008 PMCID: PMC3567102 DOI: 10.1371/journal.pone.0055617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/03/2013] [Indexed: 12/21/2022] Open
Abstract
Phage display offers a powerful approach to engineer protein affinity. A naturally occurring analog to phage display, the Bordetella bronchiseptica bacteriophage (BP) employs a highly variable protein termed the major tropism determinant (Mtd) to recognize its dynamic host. Propagation of BP provides a self-made phage library (SMPL) with vast numbers of phage particles, each displaying a single Mtd variant. We report applying the diversity of the BP-SMPL to access a tyrosine-rich library of Mtd variants. Expression of the SMPL-engineered Mtd variant as a GST-bound fusion protein demonstrated specific binding to the target T4 lysozyme with dissociation constants in the sub-micromolar range. The results guide future experiments with SMPLs applied to protein engineering.
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Affiliation(s)
- Tom Z. Yuan
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Cathie M. Overstreet
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Issa S. Moody
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Gregory A. Weiss
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
- Department Chemistry, University of California Irvine, Irvine, California, United States of America
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Sharf T, Kevek JW, Deborde T, Wardini JL, Minot ED. Origins of charge noise in carbon nanotube field-effect transistor biosensors. NANO LETTERS 2012; 12:6380-6384. [PMID: 23171196 DOI: 10.1021/nl303651t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Determining the major noise sources in nanoscale field-effect transistor (nanoFET) biosensors is critical for improving bioelectronic interfaces. We use the carbon nanotube (CNT) FET biosensor platform to examine the noise generated by substrate interactions and surface adsorbates, both of which are present in current nanoFET biosensors. The charge noise model is used as a quantitative framework to show that insulating substrates and surface adsorbates are both significant contributors to the noise floor of CNT FET biosensors. Removing substrate interactions and surface adsorbates reduces the power spectral density of background voltage fluctuations by 19-fold.
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Affiliation(s)
- Tal Sharf
- Department of Physics, Oregon State University, Corvallis, Oregon 97331-6507, United States
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38
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Kaganman I. Single-molecule circuits. Nat Methods 2012. [DOI: 10.1038/nmeth.1920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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