1
|
Kabtiyal P, Robbins A, Jergens E, Castro CE, Winter JO, Poirier MG, Johnston-Halperin E. Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers. NANO LETTERS 2024; 24:3097-3103. [PMID: 38417053 DOI: 10.1021/acs.nanolett.3c04848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
To date, studies on the thermodynamic and kinetic processes that underlie biological function and nanomachine actuation in biological- and biology-inspired molecular constructs have primarily focused on photothermal heating of ensemble systems, highlighting the need for probes that are localized within the molecular construct and capable of resolving single-molecule response. Here we present an experimental demonstration of wavelength-selective, localized heating at the single-molecule level using the surface plasmon resonance of a 15 nm gold nanoparticle (AuNP). Our approach is compatible with force-spectroscopy measurements and can be applied to studies of the single-molecule thermodynamic properties of DNA origami nanomachines as well as biomolecular complexes. We further demonstrate wavelength selectivity and establish the temperature dependence of the reaction coordinate for base-pair disruption in the shear-rupture geometry, demonstrating the utility and flexibility of this approach for both fundamental studies of local (nanometer-scale) temperature gradients and rapid and multiplexed nanomachine actuation.
Collapse
Affiliation(s)
- Prerna Kabtiyal
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Elizabeth Jergens
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Carlos E Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica O Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | |
Collapse
|
2
|
Cervantes-Salguero K, Freeley M, Gwyther REA, Jones DD, Chávez JL, Palma M. Single molecule DNA origami nanoarrays with controlled protein orientation. BIOPHYSICS REVIEWS 2022; 3:031401. [PMID: 38505279 PMCID: PMC10903486 DOI: 10.1063/5.0099294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/20/2022] [Indexed: 03/21/2024]
Abstract
The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.
Collapse
Affiliation(s)
- K. Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - M. Freeley
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - R. E. A. Gwyther
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - D. D. Jones
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - J. L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright Patterson Air Force Base, Dayton, Ohio 45433-7901, USA
| | - M. Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
3
|
Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
Collapse
Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| |
Collapse
|
4
|
Affiliation(s)
- Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yue-Yi Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| |
Collapse
|
5
|
Mohanta YK, Panda SK, Syed A, Ameen F, Bastia AK, Mohanta TK. Bio‐inspired synthesis of silver nanoparticles from leaf extracts of
Cleistanthus collinus
(Roxb.): its potential antibacterial and anticancer activities. IET Nanobiotechnol 2018. [DOI: 10.1049/iet-nbt.2017.0203] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Yugal Kishore Mohanta
- Biochemistry LaboratoryDepartment of BotanyNorth Orissa UniversityBaripadaOdisha 757003India
| | | | - Asad Syed
- Department of Botany and MicrobiologyCollege of ScienceKing Saud UniversityP.O. Box 2455Riyadh 11451Saudi Arabia
| | - Fuad Ameen
- Department of Botany and MicrobiologyCollege of ScienceKing Saud UniversityP.O. Box 2455Riyadh 11451Saudi Arabia
| | - Akshaya Kumar Bastia
- Biochemistry LaboratoryDepartment of BotanyNorth Orissa UniversityBaripadaOdisha 757003India
| | - Tapan Kumar Mohanta
- Department of BiotechnologyYeungnam UniversityGyeongsanGyeongbook‐do38541Korea
| |
Collapse
|
6
|
Huang D, Freeley M, Palma M. Single-Molecule Patterning via DNA Nanostructure Assembly: A Reusable Platform. Methods Mol Biol 2018; 1811:231-251. [PMID: 29926457 DOI: 10.1007/978-1-4939-8582-1_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we describe a facile strategy of general applicability for controlling the immobilization of individual nanomoieties on nanopatterned surfaces with single-molecule control. We combine the ability of DNA nanostructures as programmable platforms, with a one-step Focused Ion Beam nanopatterning, to demonstrate the controlled immobilization of DNA origami functionalized with individual quantum dots (QDs) at predesigned positions on glass coverslips and silicon substrates. Remarkably, the platform developed is reusable after a simple cleaning process, and can be designed to display different geometrical arrangements.
Collapse
Affiliation(s)
- Da Huang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Mark Freeley
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Matteo Palma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
| |
Collapse
|
7
|
Freeley M, Worthy HL, Ahmed R, Bowen B, Watkins D, Macdonald JE, Zheng M, Jones DD, Palma M. Site-Specific One-to-One Click Coupling of Single Proteins to Individual Carbon Nanotubes: A Single-Molecule Approach. J Am Chem Soc 2017; 139:17834-17840. [PMID: 29148737 DOI: 10.1021/jacs.7b07362] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the site-specific coupling of single proteins to individual carbon nanotubes (CNTs) in solution and with single-molecule control. Using an orthogonal Click reaction, Green Fluorescent Protein (GFP) was engineered to contain a genetically encoded azide group and then bound to CNT ends in different configurations: in close proximity or at longer distances from the GFP's functional center. Atomic force microscopy and fluorescence analysis in solution and on surfaces at the single-protein level confirmed the importance of bioengineering optimal protein attachment sites to achieve direct protein-nanotube communication and bridging.
Collapse
Affiliation(s)
- Mark Freeley
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| | - Harley L Worthy
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Rochelle Ahmed
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Ben Bowen
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Daniel Watkins
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - J Emyr Macdonald
- School of Physics and Astronomy, Cardiff University , Queens's Building, The Parade, Cardiff CF24 3AA, United Kingdom
| | - Ming Zheng
- Materials Science and Engineering Division, National Institute of Standards and Technology , 100 Bureau Drive, Gaithersburg, Maryland 20899-8542, United States
| | - D Dafydd Jones
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University , Cardiff, Wales CF10 3AX, United Kingdom
| | - Matteo Palma
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
| |
Collapse
|
8
|
Sato R, Kozuka J, Ueda M, Mishima R, Kumagai Y, Yoshimura A, Minoshima M, Mizukami S, Kikuchi K. Intracellular Protein-Labeling Probes for Multicolor Single-Molecule Imaging of Immune Receptor-Adaptor Molecular Dynamics. J Am Chem Soc 2017; 139:17397-17404. [PMID: 29119782 DOI: 10.1021/jacs.7b08262] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule imaging (SMI) has been widely utilized to investigate biomolecular dynamics and protein-protein interactions in living cells. However, multicolor SMI of intracellular proteins is challenging because of high background signals and other limitations of current fluorescence labeling approaches. To achieve reproducible intracellular SMI, a labeling probe ensuring both efficient membrane permeability and minimal non-specific binding to cell components is essential. We developed near-infrared fluorescent probes for protein labeling that specifically bind to a mutant β-lactamase tag. By structural fine-tuning of cell permeability and minimized non-specific binding, SiRcB4 enabled multicolor SMI in combination with a HaloTag-based red-fluorescent probe. Upon addition of both chemical probes at sub-nanomolar concentrations, single-molecule imaging revealed the dynamics of TLR4 and its adaptor protein, TIRAP, which are involved in the innate immune system. Statistical analysis of the quantitative properties and time-lapse changes in dynamics revealed a protein-protein interaction in response to ligand stimulation.
Collapse
Affiliation(s)
- Ryota Sato
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Jun Kozuka
- RIKEN Quantitative Biology , Suita, Osaka 565-0874, Japan
| | - Masahiro Ueda
- RIKEN Quantitative Biology , Suita, Osaka 565-0874, Japan
| | - Reiko Mishima
- Quantitative Immunology Research Unit, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| | - Yutaro Kumagai
- Quantitative Immunology Research Unit, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| | - Akimasa Yoshimura
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Masafumi Minoshima
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University , Sendai, Miyagi, 980-8577, Japan
| | - Kazuya Kikuchi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan.,Chemical Imaging Techniques, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| |
Collapse
|
9
|
Pattanayak S, Mollick MMR, Maity D, Chakraborty S, Dash SK, Chattopadhyay S, Roy S, Chattopadhyay D, Chakraborty M. Butea monosperma bark extract mediated green synthesis of silver nanoparticles: Characterization and biomedical applications. JOURNAL OF SAUDI CHEMICAL SOCIETY 2017. [DOI: 10.1016/j.jscs.2015.11.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
10
|
Usui D, Inaba S, Sekiguchi H, Sasaki YC, Tanaka T, Oda M. First observation of metal ion-induced structural fluctuations of α-helical peptides by using diffracted X-ray tracking. Biophys Chem 2017; 228:81-86. [DOI: 10.1016/j.bpc.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/12/2017] [Accepted: 07/12/2017] [Indexed: 10/19/2022]
|
11
|
Gooding JJ, Gaus K. Single‐Molecule Sensors: Challenges and Opportunities for Quantitative Analysis. Angew Chem Int Ed Engl 2016; 55:11354-66. [DOI: 10.1002/anie.201600495] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/17/2016] [Indexed: 11/09/2022]
Affiliation(s)
- J. Justin Gooding
- The University of New South Wales School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, UNSW Sydney 2052 Australia
| | - Katharina Gaus
- The University of New South Wales EMBL Australia Node in Single Molecule Science ARC Centre of Excellence in Advanced Molecular Imaging Sydney 2052 Australia
| |
Collapse
|
12
|
Gooding JJ, Gaus K. Einzelmolekül‐Sensoren: Herausforderungen und Möglichkeiten für die quantitative Analyse. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- J. Justin Gooding
- The University of New South Wales School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, UNSW Sydney 2052 Australien
| | - Katharina Gaus
- The University of New South Wales EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging,UNSW Sydney 2052 Australien
| |
Collapse
|
13
|
Chang JB, Kim YH, Thompson E, No YH, Kim NH, Arrieta J, Manfrinato VR, Keating AE, Berggren KK. The Orientations of Large Aspect-Ratio Coiled-Coil Proteins Attached to Gold Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:1498-1505. [PMID: 26799936 DOI: 10.1002/smll.201502419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/30/2015] [Indexed: 06/05/2023]
Abstract
Methods for patterning biomolecules on a substrate at the single molecule level have been studied as a route to sensors with single-molecular sensitivity or as a way to probe biological phenomena at the single-molecule level. However, the arrangement and orientation of single biomolecules on substrates has been less investigated. Here, the arrangement and orientation of two rod-like coiled-coil proteins, cortexillin and tropomyosin, around patterned gold nanostructures is examined. The high aspect ratio of the coiled coils makes it possible to study their orientations and to pursue a strategy of protein orientation via two-point attachment. The proteins are anchored to the surfaces using thiol groups, and the number of cysteine residues in tropomyosin is varied to test how this variation affects the structure and arrangement of the surface-attached proteins. Molecular dynamics studies are used to interpret the observed positional distributions. Based on initial studies of protein attachment to gold post structures, two 31-nm-long tropomyosin molecules are aligned between the two sidewalls of a trench with a width of 68 nm. Because the approach presented in this study uses one of twenty natural amino acids, this method provides a convenient way to pattern biomolecules on substrates using standard chemistry.
Collapse
Affiliation(s)
- Jae-Byum Chang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yong Ho Kim
- Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 440-746, South Korea
- Department of Chemistry, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Evan Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Young Hyun No
- Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Nam Hyeong Kim
- Department of Chemistry, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Jose Arrieta
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vitor R Manfrinato
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Karl K Berggren
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| |
Collapse
|
14
|
Abstract
Photomigration in azo polymers is an area of research that witnessed intensive studies owing to its potential in optical manipulation, e.g., optical tweezing, the physical mechanism of which remains unsolved since its discovery about two decades ago. In this paper, a detailed theoretical study that reproduces the phenomena associated with photomigration is presented, including the physical models and the associated master equations. Polarization effects are discussed and analytical solutions are given to describe the steady-state and the dynamics of photomigration. Such a theory leads to new theoretical experiments relating material properties to light action. A photoisomerization force which is described by a spring-type model is introduced. This force is derived from a harmonic light potential that moves the azo polymer. This force is parenting to optical tweezers, but it is quite different in the sense that it requires photoisomerization to occur. The azo polymer's motion is governed by four competing forces: the photoisomerization force, and the restoring optical gradient and elastic forces, as well as the random forces due to spontaneous diffusion.
Collapse
|
15
|
Ahmad N, Bhatnagar S, Ali SS, Dutta R. Phytofabrication of bioinduced silver nanoparticles for biomedical applications. Int J Nanomedicine 2015; 10:7019-30. [PMID: 26648715 PMCID: PMC4648599 DOI: 10.2147/ijn.s94479] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Synthesis of nanomaterials holds infinite possibilities as nanotechnology is revolutionizing the field of medicine by its myriad applications. Green synthesis of nanoparticles has become the need of the hour because of its eco-friendly, nontoxic, and economic nature. In this study, leaf extract of Rosa damascena was used as a bioreductant to reduce silver nitrate, leading to synthesis of silver nanoparticles (AgNPs) in a single step, without the use of any additional reducing or capping agents. The synthesized nanoparticles were characterized by the use of UV-visible spectroscopy, fourier transform infrared spectroscopy, dynamic light scattering, transmission electron microscopy, and field emission scanning electron microscopy. Time-dependent synthesis of AgNPs was studied spectrophotometrically. Synthesized AgNPs were found to possess flower-like spherical structure where individual nanoparticles were of 16 nm in diameter, whereas the agglomerated AgNPs were in the range of 60–80 nm. These biologically synthesized AgNPs exhibited significant antibacterial activity against Gram-negative bacterial species but not against Gram-positive ones (Escherichia coli and Bacillus cereus). Anti-inflammatory and analgesic activities were studied on a Wistar rat model to gauge the impact of AgNPs for a probable role in these applications. AgNPs tested positive for both these activities, although the potency was less as compared to the standard drugs.
Collapse
Affiliation(s)
- Nabeel Ahmad
- School of Biotechnology, IFTM University, Lodhipur Rajput, Moradabad, Uttar Pradesh, India
| | - Sharad Bhatnagar
- School of Biotechnology, IFTM University, Lodhipur Rajput, Moradabad, Uttar Pradesh, India
| | - Syed Salman Ali
- School of Pharmaceutical Sciences, IFTM University, Lodhipur Rajput, Moradabad, Uttar Pradesh, India
| | - Rajiv Dutta
- Institute of Bio-Science and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, India
| |
Collapse
|
16
|
Yamamura H, Suzuki Y, Imaizumi Y. New light on ion channel imaging by total internal reflection fluorescence (TIRF) microscopy. J Pharmacol Sci 2015; 128:1-7. [PMID: 26002253 DOI: 10.1016/j.jphs.2015.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 03/30/2015] [Accepted: 04/06/2015] [Indexed: 11/28/2022] Open
Abstract
Ion channels play pivotal roles in a wide variety of cellular functions; therefore, their physiological characteristics, pharmacological responses, and molecular structures have been extensively investigated. However, the mobility of an ion channel itself in the cell membrane has not been examined in as much detail. A total internal reflection fluorescence (TIRF) microscope allows fluorophores to be imaged in a restricted region within an evanescent field of less than 200 nm from the interface of the coverslip and plasma membrane in living cells. Thus the TIRF microscope is useful for selectively visualizing the plasmalemmal surface and subplasmalemmal zone. In this review, we focused on a single-molecule analysis of the dynamic movement of ion channels in the plasma membrane using TIRF microscopy. We also described two single-molecule imaging techniques under TIRF microscopy: fluorescence resonance energy transfer (FRET) for the identification of molecules that interact with ion channels, and subunit counting for the determination of subunit stoichiometry in a functional channel. TIRF imaging can also be used to analyze spatiotemporal Ca(2+) events in the subplasmalemma. Single-molecule analyses of ion channels and localized Ca(2+) signals based on TIRF imaging provide beneficial pharmacological and physiological information concerning the functions of ion channels.
Collapse
Affiliation(s)
- Hisao Yamamura
- Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan.
| | - Yoshiaki Suzuki
- Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Yuji Imaizumi
- Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| |
Collapse
|
17
|
Wang Z, Lu HP. Probing Single-Molecule Protein Spontaneous Folding–Unfolding Conformational Fluctuation Dynamics: The Multiple-State and Multiple-Pathway Energy Landscape. J Phys Chem B 2015; 119:6366-78. [DOI: 10.1021/acs.jpcb.5b00735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Zijian Wang
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| |
Collapse
|
18
|
Pi J, Jin H, Yang F, Chen ZW, Cai J. In situ single molecule imaging of cell membranes: linking basic nanotechniques to cell biology, immunology and medicine. NANOSCALE 2014; 6:12229-12249. [PMID: 25227707 DOI: 10.1039/c4nr04195j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The cell membrane, which consists of a viscous phospholipid bilayer, different kinds of proteins and various nano/micrometer-sized domains, plays a very important role in ensuring the stability of the intracellular environment and the order of cellular signal transductions. Exploring the precise cell membrane structure and detailed functions of the biomolecules in a cell membrane would be helpful to understand the underlying mechanisms involved in cell membrane signal transductions, which could further benefit research into cell biology, immunology and medicine. The detection of membrane biomolecules at the single molecule level can provide some subtle information about the molecular structure and the functions of the cell membrane. In particular, information obtained about the molecular mechanisms and other information at the single molecule level are significantly different from that detected from a large amount of biomolecules at the large-scale through traditional techniques, and can thus provide a novel perspective for the study of cell membrane structures and functions. However, the precise investigations of membrane biomolecules prompts researchers to explore cell membranes at the single molecule level by the use of in situ imaging methods, as the exact conformation and functions of biomolecules are highly controlled by the native cellular environment. Recently, the in situ single molecule imaging of cell membranes has attracted increasing attention from cell biologists and immunologists. The size of biomolecules and their clusters on the cell surface are set at the nanoscale, which makes it mandatory to use high- and super-resolution imaging techniques to realize the in situ single molecule imaging of cell membranes. In the past few decades, some amazing imaging techniques and instruments with super resolution have been widely developed for molecule imaging, which can also be further employed for the in situ single molecule imaging of cell membranes. In this review, we attempt to summarize the characteristics of these advanced techniques for use in the in situ single molecule imaging of cell membranes. We believe that this work will help to promote the technological and methodological developments of super-resolution techniques for the single molecule imaging of cell membranes and help researchers better understand which technique is most suitable for their future exploring of membrane biomolecules; ultimately promoting further developments in cell biology, immunology and medicine.
Collapse
Affiliation(s)
- Jiang Pi
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technique, Macau, China.
| | | | | | | | | |
Collapse
|
19
|
Howorka S, Hesse J. Microarrays and single molecules: an exciting combination. SOFT MATTER 2014; 10:931-41. [PMID: 24651891 DOI: 10.1039/c3sm52561a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Biomolecules positioned at interfaces have spawned many applications in bioanalysis, biophysics, and cell biology. This Highlight describes recent developments in the research areas of protein and DNA arrays, and single-molecule sensing. We cover the ultrasensitive scanning of conventional microarrays as well as the generation of arrays composed of individual molecules. The combination of these tools has improved the detection limits and the dynamic range of microarray analysis, helped develop powerful single-molecule sequencing approaches, and offered biophysical examination with high throughput and molecular detail. The topic of this Highlight integrates several disciplines and is written for interested chemists, biophysicists and nanotechnologists.
Collapse
Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London WC1H 0AJ, UK.
| | | |
Collapse
|
20
|
Lente G. Stochastic mapping of first order reaction networks: a systematic comparison of the stochastic and deterministic kinetic approaches. J Chem Phys 2012; 137:164101. [PMID: 23126689 DOI: 10.1063/1.4758458] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Stochastic maps are developed and used for first order reaction networks to decide whether the deterministic kinetic approach is appropriate for a certain evaluation problem or the use of the computationally more demanding stochastic approach is inevitable. On these maps, the decision between the two approaches is based on the standard deviation of the expectation of detected variables: when the relative standard deviation is larger than 1%, the use of the stochastic method is necessary. Four different systems are considered as examples: the irreversible first order reaction, the reversible first order reaction, two consecutive irreversible first order reactions, and the unidirectional triangle reaction. Experimental examples are used to illustrate the practical use of the theoretical results. It is shown that the maps do not only depend on particle numbers, but the influence of parameters such as time, rate constants, and the identity of the detected target variable is also an important factor.
Collapse
Affiliation(s)
- Gábor Lente
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen, Hungary.
| |
Collapse
|
21
|
Quantification of amino acids in a single cell by microchip electrophoresis with chemiluminescence detection. Methods Mol Biol 2012; 828:351-8. [PMID: 22125158 DOI: 10.1007/978-1-61779-445-2_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Analyzing individual cells allows detecting a minor group of abnormal cells present in a large population of normal cells. This ability can be essential to understanding diseases, such as cancer and diabetes. Microchip electrophoresis (MCE) is the technique of choice for single-cell analysis. However, since the channels in microfluidic devices are very small, achieving the desired assay sensitivity on a microfluidic platform remains a challenge. Here, we describe an MCE method with highly sensitive chemiluminescence detection for simultaneous determination of multiple amino acids present in single cells.
Collapse
|
22
|
Dóka É, Lente G. Stochastic mapping of the Michaelis-Menten mechanism. J Chem Phys 2012; 136:054111. [DOI: 10.1063/1.3681942] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
23
|
Abstract
Regenerative medicine is an emerging field aiming to the development of new reparative strategies to treat degenerative diseases, injury, and trauma through developmental pathways in order to rebuild the architecture of the original injured organ and take over its functionality. Most of the processes and interactions involved in the regenerative process take place at subcellular scale. Nanotechnology provides the tools and technology not only to detect, to measure, or to image the interactions between the different biomolecules and biological entities, but also to control and guide the regenerative process. The relevance of nanotechnology for the development of regenerative medicine as well as an overview of the different tools that contribute to unravel and engineer biological systems are presented in this chapter. In addition, general data about the social impact and global investment in nanotechnology are provided.
Collapse
Affiliation(s)
- Melba Navarro
- Institute for Bioengineering of Catalonia, Barcelona, Spain.
| | | |
Collapse
|
24
|
Single-molecule protein arrays enabled by scanning probe block copolymer lithography. Proc Natl Acad Sci U S A 2011; 108:19521-5. [PMID: 22106270 DOI: 10.1073/pnas.1116099108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to control the placement of individual protein molecules on surfaces could enable advances in a wide range of areas, from the development of nanoscale biomolecular devices to fundamental studies in cell biology. Such control, however, remains a challenge in nanobiotechnology due to the limitations of current lithographic techniques. Herein we report an approach that combines scanning probe block copolymer lithography with site-selective immobilization strategies to create arrays of proteins down to the single-molecule level with arbitrary pattern control. Scanning probe block copolymer lithography was used to synthesize individual sub-10-nm single crystal gold nanoparticles that can act as scaffolds for the adsorption of functionalized alkylthiol monolayers, which facilitate the immobilization of specific proteins. The number of protein molecules that adsorb onto the nanoparticles is dependent upon particle size; when the particle size approaches the dimensions of a protein molecule, each particle can support a single protein. This was demonstrated with both gold nanoparticle and quantum dot labeling coupled with transmission electron microscopy imaging experiments. The immobilized proteins remain bioactive, as evidenced by enzymatic assays and antigen-antibody binding experiments. Importantly, this approach to generate single-biomolecule arrays is, in principle, applicable to many parallelized cantilever and cantilever-free scanning probe molecular printing methods.
Collapse
|
25
|
Mi HW, Lee MC, Chiang YC, Chow LP, Lin CP. Single-Molecule Imaging of Bmp4 Dimerization on Human Periodontal Ligament Cells. J Dent Res 2011; 90:1318-24. [DOI: 10.1177/0022034511418340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We expressed bone morphogenetic protein 4 (BMP4) fused with enhanced green fluorescent protein (BMP4-EGFP) in the secretory pathways of producer cells. Fluorescent EGFP was acquired only after we interrupted the transport of BMP4-EGFP by culturing cells at a lower temperature (20°C), and the dynamics of BMP4-EGFP could be monitored by single-molecule microscopy. Western blotting analysis confirmed that exposure to low temperature helped the integrated formation of BMP4-EGFP fusion proteins. In this study, for the first time, we could image the fluorescently labeled BMP4 molecules localized on the plasma membrane of living hPDL cells. The one-step photobleaching with EGFP and the “blinking” behavior of quantum dots suggest that the fluorescent spots represent the events of single BMP4 molecules. Single-molecule tracking showed that the BMP receptors (BMPR) dimerize after BMP4 stimulation, or that a complex of one BMP4 molecule and a pre-formed BMPR dimer develops first, followed by the binding of the second BMP4 molecule. Furthermore, BMP4-EGFP enhanced the osteogenic differentiation of hPDL cells via signal transduction involving BMP receptors. This single-molecule imaging technique might be a valuable tool for the future development of BMP4 gene therapy and regenerative medicine mediated by hPDLs. Abbreviations: BMP4, bone morphogenetic protein 4; BMPR, BMP receptor; EGFP, enhanced green fluorescent protein; hPDL cells, human periodontal ligament cells; QDs, quantum dots; TIRFM, total internal reflection fluorescence microscopy; 293 cells, human embryonic kidney cells; oDM, osteogenic differentiation medium; HcoI, type I collagen; ALP, alkaline phosphatase; BSP, bone sialoprotein; GAPDH, glyceraldehyde-3-phosphate dehydrogenase.
Collapse
Affiliation(s)
- H.-W. Mi
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University and National Taiwan University Hospital, No.1, Changde St., Jhongjheng District, Taipei 100, Taiwan, ROC
| | - M.-C. Lee
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Y.-C. Chiang
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University and National Taiwan University Hospital, No.1, Changde St., Jhongjheng District, Taipei 100, Taiwan, ROC
| | - L.-P. Chow
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - C.-P. Lin
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University and National Taiwan University Hospital, No.1, Changde St., Jhongjheng District, Taipei 100, Taiwan, ROC
| |
Collapse
|
26
|
MubarakAli D, Thajuddin N, Jeganathan K, Gunasekaran M. Plant extract mediated synthesis of silver and gold nanoparticles and its antibacterial activity against clinically isolated pathogens. Colloids Surf B Biointerfaces 2011; 85:360-5. [DOI: 10.1016/j.colsurfb.2011.03.009] [Citation(s) in RCA: 470] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/09/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
|
27
|
Palma M, Abramson JJ, Gorodetsky AA, Penzo E, Gonzalez RL, Sheetz MP, Nuckolls C, Hone J, Wind SJ. Selective biomolecular nanoarrays for parallel single-molecule investigations. J Am Chem Soc 2011; 133:7656-9. [PMID: 21528859 DOI: 10.1021/ja201031g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The ability to direct the self-assembly of biomolecules on surfaces with true nanoscale control is key for the creation of functional substrates. Herein we report the fabrication of nanoscale biomolecular arrays via selective self-assembly on nanopatterned surfaces and minimized nonspecific adsorption. We demonstrate that the platform developed allows for the simultaneous screening of specific protein-DNA binding events at the single-molecule level. The strategy presented here is generally applicable and enables high-throughput monitoring of biological activity in real time and with single-molecule resolution.
Collapse
Affiliation(s)
- Matteo Palma
- Department of Applied Physics & Applied Mathematics, Columbia University, New York, New York 10027, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Collier C, Esplandiu M, Bittner V, Shapiro I. Nanowiring Enzymes to Carbon Nanotube Probes. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-823-w8.7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe observation of spectroscopic signals in response to mechanically induced changes in biological macromolecules can be enabled at an unprecedented level of resolution by coupling single-molecule manipulation/sensing using carbon nanotubes with single-molecule fluorescence imaging. Proteins, DNA and other biomolecules can be attached to nanotubes to give highly specific single-molecule probes for the investigation of intermolecular dynamics, the assembly of hybrid biological and nanoscale materials and the development of molecular electronics. Recent advances in nanotube fabrication and Atomic Force Microscope (AFM) imaging with nanotube tips have demonstrated the potential of these tools to achieve high-resolution images of single molecules. In addition, proof-of-principle demonstrations of nanotube functionalization and attachment of single molecules to these probes have been successfully made.Improved techniques for the growth and attachment of single wall carbon nanotubes as robust and well-characterized tools for AFM imaging are being developed. This work serves as a foundation toward development of single-molecule sensors and manipulators on nanotube AFM tips for a hybrid atomic force microscope that also has single-molecule fluorescence imaging capability. An individual single wall carbon nanotube (SWNT) attached to an AFM tip can function as a structural scaffold for nanoscale device fabrication on a scanning probe. Such a probe can have a novel role, to trigger specific biochemical reactions or conformational changes in a biological system with nanometer precision. The consequences of these perturbations can be read out in real time by single-molecule fluorescence and/or AFM sensing. For example, electrical wiring of single redox enzymes to carbon nanotube scanning probes will allow for observation and electrochemical control of single enzymatic reactions, by monitoring fluorescence from a redox-active cofactor or the formation of fluorescent products. Enzymes “nanowired” to carbon nanotube tips may enable extremely sensitive probing of biological stimulus-response with high spatial resolution, including product-induced signal transduction.
Collapse
|
29
|
Iancu C, Ilie IR, Georgescu CE, Ilie R, Biris AR, Mocan T, Mocan LC, Zaharie F, Todea-Iancu D, Susman S, Ciuca DR, Biris AS. Applications of Nanomaterials in Cell Stem Therapies and the Onset of Nanomedicine. PARTICULATE SCIENCE AND TECHNOLOGY 2009. [DOI: 10.1080/02726350903328985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
30
|
Zhao S, Huang Y, Liu YM. Microchip electrophoresis with chemiluminescence detection for assaying ascorbic acid and amino acids in single cells. J Chromatogr A 2009; 1216:6746-51. [PMID: 19691964 PMCID: PMC2758624 DOI: 10.1016/j.chroma.2009.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Revised: 08/03/2009] [Accepted: 08/05/2009] [Indexed: 02/07/2023]
Abstract
A method based on microchip electrophoresis (MCE) with chemiluminescence (CL) detection was developed for the determination of ascorbic acid (AA) and amino acids including tryptophan (Trp), glycine (Gly) and alanine (Ala) present in single cells. Cell injection, loading, lysing, electrophoretic separation and CL detection were integrated onto a simple cross microfluidic chip. A single cell was loaded in the cross intersection by electrophoretic means through applying a set of potentials at the reservoirs. The docked cell was lysed rapidly under a direct electric field. The intracellular contents were MCE separated within 130 s. CL detection was based on the enhancing effects of AA and amino acids on the CL reaction of luminol with K(3)[Fe(CN)(6)]. Rat hepatocytes were prepared and analyzed as the test cellular model. The average intracellular contents of AA, Trp, Gly and Ala in single rat hepatocytes were found to be 38.3, 5.15, 3.78 and 3.84 fmol (n=12), respectively.
Collapse
Affiliation(s)
- Shulin Zhao
- College of Chemistry and Chemical Engineering, Guangxi Normal University, Guilin 51004, China
| | | | | |
Collapse
|
31
|
|
32
|
Zhao S, Li X, Liu YM. Integrated microfluidic system with chemiluminescence detection for single cell analysis after intracellular labeling. Anal Chem 2009; 81:3873-8. [PMID: 19382810 PMCID: PMC2718560 DOI: 10.1021/ac900391u] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work describes the first application of microchip electrophoresis with chemiluminescence detection (MCE-CL) in single cell analysis. Human red blood cells were assayed to determine intracellular content of glutathione (GSH). Intracellular GSH was first labeled by incubating cells with diazo-luminol, and then individual cells were injected, in-line lysed, and MCE separated. CL detection was based on the oxidation reaction of luminol-labeled GSH with NaBrO. The MCE-CL assay had a linear calibration curve over a range from 0.2-90 amol GSH injected with a correlation coefficient of 0.9991 and a detection limit of 50 zmol or 3.6 x 10(-9) M (S/N = 3). The average content of GSH in individual human red blood cells was found 64.9 amol (n = 17). Compared with the MCE methods with laser induced fluorescence detection (LIF) reported so far for single cell analysis, the present MCE-CL assay of GSH is simple and about 100 times more sensitive.
Collapse
Affiliation(s)
- Shulin Zhao
- College of Chemistry and Chemical Engineering, Guangxi Normal University, Guilin, 541004, China
| | | | | |
Collapse
|
33
|
Jonás A, Zemánek P. Light at work: the use of optical forces for particle manipulation, sorting, and analysis. Electrophoresis 2009; 29:4813-51. [PMID: 19130566 DOI: 10.1002/elps.200800484] [Citation(s) in RCA: 257] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We review the combinations of optical micro-manipulation with other techniques and their classical and emerging applications to non-contact optical separation and sorting of micro- and nanoparticle suspensions, compositional and structural analysis of specimens, and quantification of force interactions at the microscopic scale. The review aims at inspiring researchers, especially those working outside the optical micro-manipulation field, to find new and interesting applications of these methods.
Collapse
Affiliation(s)
- Alexandr Jonás
- Institute of Scientific Instruments of the AS CR, vvi, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | | |
Collapse
|
34
|
Fluctuation as a tool of biological molecular machines. Biosystems 2008; 93:3-7. [DOI: 10.1016/j.biosystems.2008.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 04/21/2008] [Accepted: 04/21/2008] [Indexed: 11/22/2022]
|
35
|
Miyake T, Tanii T, Sonobe H, Akahori R, Shimamoto N, Ueno T, Funatsu T, Ohdomari I. Real-Time Imaging of Single-Molecule Fluorescence with a Zero-Mode Waveguide for the Analysis of Protein−Protein Interaction. Anal Chem 2008; 80:6018-22. [DOI: 10.1021/ac800726g] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takeo Miyake
- Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan, Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Nanotechnology Research Laboratory, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Kagami Memorial Laboratory
| | - Takashi Tanii
- Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan, Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Nanotechnology Research Laboratory, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Kagami Memorial Laboratory
| | - Hironori Sonobe
- Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan, Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Nanotechnology Research Laboratory, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Kagami Memorial Laboratory
| | - Rena Akahori
- Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan, Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Nanotechnology Research Laboratory, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Kagami Memorial Laboratory
| | - Naonobu Shimamoto
- Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan, Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Nanotechnology Research Laboratory, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Kagami Memorial Laboratory
| | - Taro Ueno
- Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan, Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Nanotechnology Research Laboratory, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Kagami Memorial Laboratory
| | - Takashi Funatsu
- Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan, Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Nanotechnology Research Laboratory, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Kagami Memorial Laboratory
| | - Iwao Ohdomari
- Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku, Tokyo 169-8555, Japan, Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Nanotechnology Research Laboratory, Waseda University, 513 Waseda, Tsurumakicho, Shinjuku, Tokyo 162-0041, Japan, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan, and Kagami Memorial Laboratory
| |
Collapse
|
36
|
Melin J, Jarvius J, Larsson C, Söderberg O, Landegren U, Nilsson M. Ligation-based molecular tools for lab-on-a-chip devices. N Biotechnol 2008; 25:42-8. [DOI: 10.1016/j.nbt.2008.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 01/17/2008] [Accepted: 02/07/2008] [Indexed: 10/22/2022]
|
37
|
Shibata T, Ueda M. Noise generation, amplification and propagation in chemotactic signaling systems of living cells. Biosystems 2008; 93:126-32. [PMID: 18501501 DOI: 10.1016/j.biosystems.2008.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 04/11/2008] [Accepted: 04/15/2008] [Indexed: 12/29/2022]
Abstract
Theoretical considerations of stochastic signal transduction in living cells have revealed the gain-fluctuation relation, which provides a theoretical framework to describe quantitatively how noise is generated, amplified and propagated along a signaling cascade in living cells. We chose the chemotactic signaling of bacteria and eukaryotic cells as a typical example of noisy signal transduction and applied the gain-fluctuation relation to these signaling systems in order to analyze the effects of noise on signal transduction. Comparing our theoretical analysis with the experimental results of chemotaxis in bacteria Escherichia coli and eukaryote Dictyostelium discoideum revealed that noise in signal transduction systems limits the cells' chemotactic ability and contributes to their behavioral variability. Based on the kinetic properties of signaling molecules in living cells, the gain-fluctuation relation can quantitatively explain stochastic cellular behaviors.
Collapse
Affiliation(s)
- Tatsuo Shibata
- Department of Mathematical and Life Sciences, University of Hiroshima, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | | |
Collapse
|
38
|
Arata HF, Kumemura M, Sakaki N, Fujita H. Towards single biomolecule handling and characterization by MEMS. Anal Bioanal Chem 2008; 391:2385-93. [PMID: 18363049 PMCID: PMC3715683 DOI: 10.1007/s00216-008-1853-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 12/25/2007] [Accepted: 01/08/2008] [Indexed: 11/28/2022]
Abstract
Applications of microelectromechanical systems (MEMS) technology are widespread in both industrial and research fields providing miniaturized smart tools. In this review, we focus on MEMS applications aiming at manipulations and characterization of biomaterials at the single molecule level. Four topics are discussed in detail to show the advantages and impact of MEMS tools for biomolecular manipulations. They include the microthermodevice for rapid temperature alternation in real-time microscopic observation, a microchannel with microelectrodes for isolating and immobilizing a DNA molecule, and microtweezers to manipulate a bundle of DNA molecules directly for analyzing its conductivity. The feasibilities of each device have been shown by conducting specific biological experiments. Therefore, the development of MEMS devices for single molecule analysis holds promise to overcome the disadvantages of the conventional technique for biological experiments and acts as a powerful strategy in molecular biology. Towards single bio molecular handling and characterization by MEMS ![]()
Collapse
Affiliation(s)
- Hideyuki F Arata
- Institute of Industrial Science (IIS), The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
| | | | | | | |
Collapse
|
39
|
|
40
|
Jesorka A, Orwar O. Liposomes: technologies and analytical applications. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:801-32. [PMID: 20636098 DOI: 10.1146/annurev.anchem.1.031207.112747] [Citation(s) in RCA: 335] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Liposomes are structurally and functionally some of the most versatile supramolecular assemblies in existence. Since the beginning of active research on lipid vesicles in 1965, the field has progressed enormously and applications are well established in several areas, such as drug and gene delivery. In the analytical sciences, liposomes serve a dual purpose: Either they are analytes, typically in quality-assessment procedures of liposome preparations, or they are functional components in a variety of new analytical systems. Liposome immunoassays, for example, benefit greatly from the amplification provided by encapsulated markers, and nanotube-interconnected liposome networks have emerged as ultrasmall-scale analytical devices. This review provides information about new developments in some of the most actively researched liposome-related topics.
Collapse
Affiliation(s)
- Aldo Jesorka
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
| | | |
Collapse
|
41
|
Smirnov AY, Mourokh LG, Nori F. Förster mechanism of electron-driven proton pumps. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:011919. [PMID: 18351888 DOI: 10.1103/physreve.77.011919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Indexed: 05/26/2023]
Abstract
We examine a simple model of proton pumping through the inner membrane of mitochondria in the living cell. We demonstrate that the pumping process can be described using approaches of condensed matter physics. In the framework of this model, we show that the resonant Förster-type energy exchange due to electron-proton Coulomb interaction can provide a unidirectional flow of protons against an electrochemical proton gradient, thereby accomplishing proton pumping. The dependence of this effect on temperature as well as electron and proton voltage buildups are obtained taking into account electrostatic forces and noise in the environment. We find that the proton pump works with maximum efficiency in the range of temperatures and transmembrane electrochemical potentials which correspond to the parameters of living cells.
Collapse
Affiliation(s)
- Anatoly Yu Smirnov
- Frontier Research System, The Institute of Physical and Chemical Research (RIKEN), Wako-shi, Saitama 351-0198, Japan
| | | | | |
Collapse
|
42
|
Abstract
We have developed a new method to intelligently sample analytes and introduce the analytes to sensors. The method automatically adjusts sampling duration according to the sensors' response to the analytes and converts the amplitude of the sensor output to a frequency output, giving us another opportunity to reduce noise in the signal. It also addresses some of the common sensor issues such as response time, saturation, chemical dynamic range, and sensor protection, saving precious detection time, protecting sensors, and enabling sensitive sensors built for low-concentration detection to be used for high-concentration detection as well. We have put together a system using a tuning fork chemical sensor as a sample sensor to demonstrate the feasibility and benefits of the new sensing technique.
Collapse
Affiliation(s)
- Francis Tsow
- Department of Electrical Engineering Arizona State University, Tempe, Arizona 85287, USA
| | | | | |
Collapse
|
43
|
Junier I, Ritort F. Unstructured intermediate states in single protein force experiments. Proteins 2007; 71:1145-55. [DOI: 10.1002/prot.21802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
44
|
Liu X, Wu Z, Nie H, Liu Z, He Y, Yeung E. Single DNA molecules as probes for interrogating silica surfaces after various chemical treatments. Anal Chim Acta 2007; 602:229-35. [DOI: 10.1016/j.aca.2007.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 08/31/2007] [Accepted: 09/08/2007] [Indexed: 10/22/2022]
|
45
|
Melin J, Jarvius J, Göransson J, Nilsson M. Homogeneous amplified single-molecule detection: Characterization of key parameters. Anal Biochem 2007; 368:230-8. [PMID: 17572370 DOI: 10.1016/j.ab.2007.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 05/02/2007] [Accepted: 05/03/2007] [Indexed: 11/16/2022]
Abstract
We recently presented a method that enables single-molecule enumeration by transforming specific molecular recognition events at nanometer dimensions to micrometer-sized DNA macromolecules. This transformation process is mediated by target-specific padlock probe ligation, followed by rolling circle amplification (RCA), resulting in the creation of one rolling circle product (RCP) for each recognized target. The transformation makes optical detection and quantification possible using standard fluorescence microscopy by counting the number of generated RCPs in a sample pumped through a microfluidic channel. In this study, we demonstrate that confocal volume definition is crucial to achieve high-precision measurements in the microfluidic quantification (coefficient of variance typically 3%). We further demonstrate that complementary sequence motifs between RCPs is only a weak inducer of aggregates and that all detection sites of the RCPs are occupied at detection oligonucleotide concentrations greater than 5 nM if hybridized in the proper buffer conditions. Therefore, the signal/noise ratio is limited by the number of detection sites. By increasing the density of detection sites in the RCP by a factor of 1.9, we show that the optical signal/noise level can be increased from 42 to 75.
Collapse
Affiliation(s)
- Jonas Melin
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, S-751 85 Uppsala, Sweden
| | | | | | | |
Collapse
|
46
|
Nir E, Michalet X, Hamadani KM, Laurence TA, Neuhauser D, Kovchegov Y, Weiss S. Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments. J Phys Chem B 2007; 110:22103-24. [PMID: 17078646 PMCID: PMC3085016 DOI: 10.1021/jp063483n] [Citation(s) in RCA: 233] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a simple approach and present a straightforward numerical algorithm to compute the best fit shot-noise limited proximity ratio histogram (PRH) in single-molecule fluorescence resonant energy transfer diffusion experiments. The key ingredient is the use of the experimental burst size distribution, as obtained after burst search through the photon data streams. We show how the use of an alternated laser excitation scheme and a correspondingly optimized burst search algorithm eliminates several potential artifacts affecting the calculation of the best fit shot-noise limited PRH. This algorithm is tested extensively on simulations and simple experimental systems. We find that dsDNA data exhibit a wider PRH than expected from shot noise only and hypothetically account for it by assuming a small Gaussian distribution of distances with an average standard deviation of 1.6 A. Finally, we briefly mention the results of a future publication and illustrate them with a simple two-state model system (DNA hairpin), for which the kinetic transition rates between the open and closed conformations are extracted.
Collapse
Affiliation(s)
- Eyal Nir
- Department of Chemistry and Biochemistry, and California NanoScience Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Mukhopadhyay S, Deniz AA. Fluorescence from diffusing single molecules illuminates biomolecular structure and dynamics. J Fluoresc 2007; 17:775-83. [PMID: 17641956 DOI: 10.1007/s10895-007-0214-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2007] [Accepted: 05/30/2007] [Indexed: 10/23/2022]
Abstract
This review provides an account of single-molecule fluorescence methodologies for freely diffusing molecules applied to a diverse array of biological problems pertaining to biomolecular folding and assembly. We describe the principles of confocal fluorescence microscopy to detect and analyze fluorescence bursts from diffusing single molecules. These methods including single-molecule fluorescence resonance energy transfer, coincidence, correlations and polarization offer a powerful means to uncover hidden information about conformational sub-populations and interconversion dynamics of biomolecular systems in a wide range of timescales. We offer several key examples to illustrate how these methodologies have been extremely useful in teasing out structural and dynamical aspects of many important biomolecular systems.
Collapse
Affiliation(s)
- Samrat Mukhopadhyay
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | |
Collapse
|
48
|
Vanzi F, Sacconi L, Pavone FS. Analysis of kinetics in noisy systems: application to single molecule tethered particle motion. Biophys J 2007; 93:21-36. [PMID: 17434935 PMCID: PMC1914433 DOI: 10.1529/biophysj.106.094151] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 02/15/2007] [Indexed: 11/18/2022] Open
Abstract
In the tethered particle motion method the length of a DNA molecule is monitored by measuring the range of diffusion of a microsphere tethered to the surface of a microscope coverslip through the DNA molecule itself. Looping of DNA (induced by binding of a specific protein) can be detected with this method and the kinetics of the looping/unlooping processes can be measured at the single molecule level. The microsphere's position variance represents the experimental variable reporting on the polymer length. Therefore, data windowing is required to obtain position variance from raw position data. Due to the characteristic diffusion time of the microsphere, the low-pass filtering required to attain a good signal/noise ratio (S/N) in the discrimination of looped versus unlooped state impacts significantly the measurement's time resolution. Here we present a method for measuring lifetimes based on half-amplitude thresholding and then correcting the kinetic measurements, taking into account low S/N (leading to false events) and limited time resolution (leading to missed events). This method allows an accurate and unbiased estimation of the kinetic parameters under investigation, independently of the choice of the window used for variance calculation, with potential applications to other single molecule measurements with low S/N.
Collapse
Affiliation(s)
- F Vanzi
- LENS-European Laboratory for Nonlinear Spectroscopy, Sesto Fiorentino, Italy.
| | | | | |
Collapse
|
49
|
Hong F, Root DD. Downscaling functional bioassays by single-molecule techniques. Drug Discov Today 2007; 11:640-5. [PMID: 16793533 DOI: 10.1016/j.drudis.2006.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 04/07/2006] [Accepted: 05/11/2006] [Indexed: 11/17/2022]
Abstract
In this short review we examine the potential of single-molecule assays in drug development and in basic research to provide new types of information at the smallest assay scales. A key advantage of many single-molecule assays is the requirement for conservative amounts of precious sample compared to conventional assays. In addition, they measure processes that are not observed directly in molecular ensembles. These advantages are balanced currently by difficulties in assay setup, preparation and equipment expense. However, future developments will ameliorate these drawbacks with the production of simpler, less expensive experimental systems for single-molecule assays.
Collapse
Affiliation(s)
- Feng Hong
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, University of North Texas, Denton, TX 76203-5220, USA
| | | |
Collapse
|
50
|
Gai H, Griess GA, Demeler B, Weintraub ST, Serwer P. Routine fluorescence microscopy of single untethered protein molecules confined to a planar zone. J Microsc 2007; 226:256-62. [PMID: 17535264 DOI: 10.1111/j.1365-2818.2007.01776.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To bypass limitations of ensemble averaging biochemical analysis, microscopy-based detection and tracking are needed for single protein molecules that are diffusing in aqueous solution. Confining the molecules to a planar zone dramatically assists tracking. Procedures of microscopy should be routine enough so that effort is focused on the biochemistry. Fluorescence microscopy and partial planar confinement of single, untethered, aqueous protein molecules have been achieved here by use of a routine procedure. With this procedure, multiple thermally diffusing Alexa 488-stained bovine serum albumin molecules were observed during partial confinement to a thin aqueous zone next to a cover slip. The procedure produces confinement by partial re-swelling of a previously dried agarose gel on the microscope slide. Confinement was confirmed through analysis that revealed thermal motion lower in the third dimension than it was in the plane of observation.
Collapse
Affiliation(s)
- Hongwei Gai
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA
| | | | | | | | | |
Collapse
|