1
|
Babakhanova S, Jung EE, Namikawa K, Zhang H, Wang Y, Subach OM, Korzhenevskiy DA, Rakitina TV, Xiao X, Wang W, Shi J, Drobizhev M, Park D, Eisenhard L, Tang H, Köster RW, Subach FV, Boyden ES, Piatkevich KD. Rapid directed molecular evolution of fluorescent proteins in mammalian cells. Protein Sci 2022; 31:728-751. [PMID: 34913537 PMCID: PMC8862398 DOI: 10.1002/pro.4261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 12/31/2022]
Abstract
In vivo imaging of model organisms is heavily reliant on fluorescent proteins with high intracellular brightness. Here we describe a practical method for rapid optimization of fluorescent proteins via directed molecular evolution in cultured mammalian cells. Using this method, we were able to perform screening of large gene libraries containing up to 2 × 107 independent random genes of fluorescent proteins expressed in HEK cells, completing one iteration of directed evolution in a course of 8 days. We employed this approach to develop a set of green and near-infrared fluorescent proteins with enhanced intracellular brightness. The developed near-infrared fluorescent proteins demonstrated high performance for fluorescent labeling of neurons in culture and in vivo in model organisms such as Caenorhabditis elegans, Drosophila, zebrafish, and mice. Spectral properties of the optimized near-infrared fluorescent proteins enabled crosstalk-free multicolor imaging in combination with common green and red fluorescent proteins, as well as dual-color near-infrared fluorescence imaging. The described method has a great potential to be adopted by protein engineers due to its simplicity and practicality. We also believe that the new enhanced fluorescent proteins will find wide application for in vivo multicolor imaging of small model organisms.
Collapse
|
2
|
Mukherjee S, Jimenez R. Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies. J Phys Chem B 2022; 126:735-750. [DOI: 10.1021/acs.jpcb.1c05629] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| |
Collapse
|
3
|
Zhao Y, Zhang W, Zhao Y, Campbell RE, Harrison DJ. A single-phase flow microfluidic cell sorter for multiparameter screening to assist the directed evolution of Ca 2+ sensors. LAB ON A CHIP 2019; 19:3880-3887. [PMID: 31641712 DOI: 10.1039/c9lc00779b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We introduce a single-phase flow microfluidic cell sorter with a two-point detection system capable of two-parameter screening to assist with directed evolution of a fluorescent protein based Ca2+ sensor expressed in bacterial cells. The new cell sorting system utilizes two fluorescence microscopes to obtain signals at two different points along a flow path in which a change in concentration of the analyte, Ca2+, is induced. The two detectors thus determine the magnitude of fluorescence change of the sensor following the reaction, along with the overall brightness of the sensor. A design for a 3D focusing flow was configured to enhance the spatial control of cells and signal pair-matching. The cell sorter screens the sensors at a moderate throughput, 10 cells per s and 105 cells per round, enriching top variants for the subsequent manual screening with higher accuracy. Our new μFACS greatly accelerates the directed evolution of genetically encoded Ca2+ sensors compared to the previous version with single point detection for brightness-based screening. Two rounds of directed evolution led to a variant, named Y-GECO2f, which exhibits a 26% increase in brightness and a greater than 300% larger Ca2+-dependent fluorescence change in vitro relative to the variant before evolution.
Collapse
Affiliation(s)
- Yufeng Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| | - Wei Zhang
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| | - Yongxin Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada. and Department of Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - D Jed Harrison
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
| |
Collapse
|
4
|
Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo MN, Palmer AE, Jimenez R. Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter. Integr Biol (Camb) 2018; 10:516-526. [PMID: 30094420 PMCID: PMC6141309 DOI: 10.1039/c8ib00103k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Green fluorescent proteins (GFP) and their blue, cyan and red counterparts offer unprecedented advantages as biological markers owing to their genetic encodability and straightforward expression in different organisms. Although significant advancements have been made towards engineering the key photo-physical properties of red fluorescent proteins (RFPs), they continue to perform sub-optimally relative to GFP variants. Advanced engineering strategies are needed for further evolution of RFPs in the pursuit of improving their photo-physics. In this report, a microfluidic sorter that discriminates members of a cell-based library based on their excited state lifetime and fluorescence intensity is used for the directed evolution of the photo-physical properties of FusionRed. In-flow measurements of the fluorescence lifetime are performed in a frequency-domain approach with sub-millisecond sampling times. Promising clones are sorted by optical force trapping with an infrared laser. Using this microfluidic sorter, mutants are generated with longer lifetimes than their precursor, FusionRed. This improvement in the excited state lifetime of the mutants leads to an increase in their fluorescence quantum yield up to 1.8-fold. In the course of evolution, we also identified one key mutation (L177M), which generated a mutant (FusionRed-M) that displayed ∼2-fold higher brightness than its precursor upon expression in mammalian (HeLa) cells. Photo-physical and mutational analyses of clones isolated at the different stages of mutagenesis reveal the photo-physical evolution towards higher in vivo brightness.
Collapse
Affiliation(s)
- Premashis Manna
- JILA, NIST and University of Colorado, Boulder, Colorado 80309, USA.
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Wiens MD, Hoffmann F, Chen Y, Campbell RE. Enhancing fluorescent protein photostability through robot-assisted photobleaching. Integr Biol (Camb) 2018; 10:419-428. [PMID: 29897363 PMCID: PMC6047911 DOI: 10.1039/c8ib00063h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Improving fluorescent proteins through the use of directed evolution requires robust techniques for screening large libraries of genetic variants. Here we describe an effective and relatively low-cost system for screening libraries of fluorescent protein variants for improved photostability in the context of colonies on a Petri dish. Application of this system to the yellow fluorescent protein mCitrine, led to the development of Citrine2 with improved photostability and similar high fluorescent brightness. The photobleaching robot was constructed using a Lego Mindstorms Ev3 set and a xenon arc lamp, which together create even and high irradiance over an entire Petri dish through patterned illumination.
Collapse
Affiliation(s)
- M D Wiens
- A Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
| | | | | | | |
Collapse
|
6
|
High-throughput, image-based screening of pooled genetic-variant libraries. Nat Methods 2017; 14:1159-1162. [PMID: 29083401 PMCID: PMC5958624 DOI: 10.1038/nmeth.4495] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022]
Abstract
We report a high-throughput screening method that allows diverse genotypes and corresponding phenotypes to be imaged in individual cells. We achieve genotyping by introducing barcoded genetic variants into cells as pooled libraries and reading the barcodes out using massively multiplexed fluorescence in situ hybridization. To demonstrate the power of image-based pooled screening, we identified brighter and more photostable variants of the fluorescent protein YFAST among 60,000 variants.
Collapse
|
7
|
Eason MG, Damry AM, Chica RA. Structure-guided rational design of red fluorescent proteins: towards designer genetically-encoded fluorophores. Curr Opin Struct Biol 2017; 45:91-99. [PMID: 28038355 DOI: 10.1016/j.sbi.2016.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 01/26/2023]
Abstract
Red fluorescent proteins (RFPs) have become an integral part of modern biological research due to their longer excitation and emission wavelengths. Protein engineering efforts have improved many key properties of RFPs for their practical use in imaging. Even so, continued engineering is required to overcome the shortcomings of the red chromophore and create RFPs with photophysical properties rivalling those of their optimized green and yellow counterparts. Here, we highlight recent examples of structure-guided rational design of RFPs to improve brightness, monomerization, maturation, and photostability, and discuss possible pathways for the future engineering of designer RFPs tailored to specific applications.
Collapse
Affiliation(s)
- Matthew G Eason
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - Adam M Damry
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario, K1N 6N5, Canada.
| |
Collapse
|
8
|
Fiedler BL, Van Buskirk S, Carter KP, Qin Y, Carpenter MC, Palmer AE, Jimenez R. Droplet Microfluidic Flow Cytometer For Sorting On Transient Cellular Responses Of Genetically-Encoded Sensors. Anal Chem 2017; 89:711-719. [PMID: 27959493 PMCID: PMC6019271 DOI: 10.1021/acs.analchem.6b03235] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescent biosensors are important measurement tools for in vivo quantification of pH, concentrations of metal ions and other analytes, and physical parameters such as membrane potential. Both the development of these sensors and their implementation in examining cellular heterogeneity requires technology for measuring and sorting cells based on the fluorescence levels before and after chemical or physical perturbations. We developed a droplet microfluidic platform for the screening and separation of cell populations on the basis of the in vivo response of expressed fluorescence-based biosensors after addition of an exogenous analyte. We demonstrate the capability to resolve the responses of two genetically encoded Zn2+ sensors at a range of time points spanning several seconds and subsequently sort a mixed-cell population of varying ratios with high accuracy.
Collapse
Affiliation(s)
- Brett L. Fiedler
- JILA, University of Colorado and NIST, Boulder CO 80309
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
| | | | - Kyle P. Carter
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
- BioFrontiers Institute, University of Colorado, Boulder CO 80303
| | - Yan Qin
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
- Department of Biological Sciences, University of Denver, Denver, CO 80208
| | - Margaret C. Carpenter
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
- BioFrontiers Institute, University of Colorado, Boulder CO 80303
| | - Amy E. Palmer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
- BioFrontiers Institute, University of Colorado, Boulder CO 80303
| | - Ralph Jimenez
- JILA, University of Colorado and NIST, Boulder CO 80309
- Department of Chemistry and Biochemistry, University of Colorado, Boulder CO 80309
| |
Collapse
|
9
|
Tenner B, Mehta S, Zhang J. Optical sensors to gain mechanistic insights into signaling assemblies. Curr Opin Struct Biol 2016; 41:203-210. [PMID: 27611602 PMCID: PMC5423777 DOI: 10.1016/j.sbi.2016.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/29/2016] [Indexed: 11/17/2022]
Abstract
Protein complexes play a major role in transducing information from outside the cell into instructions for growth and survival, and understanding how these complexes relay and shape intracellular signals has been a central question in signaling biology. Fluorescent proteins have proven paramount in opening windows for researchers to peer into the architecture and inner workings of signaling assemblies within the living cell and in real-time. In this review, we will provide readers with a current perspective on the development and use of genetically encoded optical probes to dissect the function of signaling complexes.
Collapse
Affiliation(s)
- Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States.
| |
Collapse
|
10
|
Lychagov VV, Shemetov AA, Jimenez R, Verkhusha VV. Microfluidic System for In-Flow Reversible Photoswitching of Near-Infrared Fluorescent Proteins. Anal Chem 2016; 88:11821-11829. [PMID: 27807973 DOI: 10.1021/acs.analchem.6b03499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have developed a microfluidic flow cytometry system to screen reversibly photoswitchable fluorescent proteins for contrast and stability of reversible photoconversion between high- and low-fluorescent states. A two-color array of 20 excitation and deactivation beams generated with diffractive optics was combined with a serpentine microfluidic channel geometry designed to provide five cycles of photoswitching with real-time calculation of photoconversion fluorescence contrast. The characteristics of photoswitching in-flow as a function of excitation and deactivation beam fluence, flow speed, and protein concentration were studied with droplets of the bacterial phytochrome from Deinococcus radiodurans (DrBphP), which is weakly fluorescent in the near-infrared (NIR) spectral range. In agreement with measurements on stationary droplets and HeLa S3 mammalian cells expressing DrBphP, optimized operation of the flow system provided up to 50% photoconversion contrast in-flow at a droplet rate of few hertz and a coefficient of variation (CV) of up to 2% over 10 000 events. The methods for calibrating the brightness and photoswitching measurements in microfluidic flow established here provide a basis for screening of cell-based libraries of reversibly switchable NIR fluorescent proteins.
Collapse
Affiliation(s)
| | | | | | - Vladislav V Verkhusha
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki , Helsinki 00029, Finland
| |
Collapse
|
11
|
Dean KM, Davis LM, Lubbeck JL, Manna P, Friis P, Palmer AE, Jimenez R. High-speed multiparameter photophysical analyses of fluorophore libraries. Anal Chem 2015; 87:5026-30. [PMID: 25898152 DOI: 10.1021/acs.analchem.5b00607] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is a critical need for high-speed multiparameter photophysical measurements of large libraries of fluorescent probe variants for imaging and biosensor development. We present a microfluidic flow cytometer that rapidly assays 10(4)-10(5) member cell-based fluorophore libraries, simultaneously measuring fluorescence lifetime and photobleaching. Together, these photophysical characteristics determine imaging performance. We demonstrate the ability to resolve the diverse photophysical characteristics of different library types and the ability to identify rare populations.
Collapse
Affiliation(s)
- Kevin M Dean
- †BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, United States.,‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Lloyd M Davis
- §Department of Physics, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States.,∥Center for Laser Applications, University of Tennessee Space Institute, Tullahoma, Tennessee 37388, United States
| | - Jennifer L Lubbeck
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States.,⊥JILA, NIST, and University of Colorado, Boulder, Colorado 80309, United States
| | - Premashis Manna
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States.,⊥JILA, NIST, and University of Colorado, Boulder, Colorado 80309, United States
| | - Pia Friis
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States.,⊥JILA, NIST, and University of Colorado, Boulder, Colorado 80309, United States
| | - Amy E Palmer
- †BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, United States.,‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States.,⊥JILA, NIST, and University of Colorado, Boulder, Colorado 80309, United States
| |
Collapse
|
12
|
Manna P, Jimenez R. Time and frequency-domain measurement of ground-state recovery times in red fluorescent proteins. J Phys Chem B 2015; 119:4944-54. [PMID: 25781915 DOI: 10.1021/acs.jpcb.5b00950] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The field of bioimaging and biosensors has been revolutionized by the discovery of fluorescent proteins (FPs) and their use in live cells. FPs are characterized with rich photodynamics due to the presence of nonfluorescent or dark states which are responsible for fluorescence intermittency or "blinking", which has been exploited in several localization-based super-resolution techniques that surpass the diffraction-limited resolution of conventional microscopy. Molecules that convert to these dark states recover to the ground states either spontaneously or upon absorption of another photon, depending on the particular FP and the structural transition that is involved. In this work, we demonstrate time- and frequency-domain methods for the measurement of the ground-state recovery (GSR) times of FPs both in live cells and in solutions. In the time-domain method, we excited the sample with millisecond pulses at varying dark times to obtain percent-recovery. In the frequency-domain method, dark-state hysteresis was employed to obtain the positive phase shift or "phase advance". We extracted the GSR time constants from our measurements using calculations and simulations based on a three-state model system. The GSR time constants of the red FPs studied in these experiments fall in the range from μs to msec time-scales. We find that the time- and frequency-domain techniques are complementary to each other. While accurate GSR times can be extracted from the time-domain technique, frequency-domain measurements are primarily sensitive to the rates of dark-state conversion (DSC) processes. A correlation between GSR times, DSC, and photobleaching rates for the red FPs mCherry, TagRFP-T, and Kriek were observed. These time- and frequency-domain methods can be used in high-throughput screening and sorting of FPs clones based on GSR time constant and photostability and will therefore be valuable for the development of new photoswitchable or photoactivatable FPs.
Collapse
Affiliation(s)
- Premashis Manna
- †Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
- ‡JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- †Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
- ‡JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| |
Collapse
|
13
|
Dean KM, Lubbeck JL, Davis LM, Regmi CK, Chapagain PP, Gerstman BS, Jimenez R, Palmer AE. Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching. Integr Biol (Camb) 2015; 7:263-73. [PMID: 25477249 PMCID: PMC4323946 DOI: 10.1039/c4ib00251b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fluorescent proteins offer exceptional labeling specificity in living cells and organisms. Unfortunately, their photophysical properties remain far from ideal for long-term imaging of low-abundance cellular constituents, in large part because of their poor photostability. Despite widespread engineering efforts, improving the photostability of fluorescent proteins remains challenging due to lack of appropriate high-throughput selection methods. Here, we use molecular dynamics guided mutagenesis in conjunction with a recently developed microfluidic-based platform, which sorts cells based on their fluorescence photostability, to identify red fluorescent proteins with decreased photobleaching from a HeLa cell-based library. The identified mutant, named Kriek, has 2.5- and 4-fold higher photostability than its progenitor, mCherry, under widefield and confocal illumination, respectively. Furthermore, the results provide insight into mechanisms for enhancing photostability and their connections with other photophysical processes, thereby providing direction for ongoing development of fluorescent proteins with improved single-molecule and low-copy imaging capabilities.
Collapse
Affiliation(s)
- Kevin M. Dean
- BioFrontiers Institute, University of Colorado, Boulder, CO, U.S.A
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, U.S.A
| | - Jennifer L. Lubbeck
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, U.S.A
- JILA, NIST, and University of Colorado, Boulder, CO, U.S.A
| | - Lloyd M. Davis
- Center for Laser Applications, University of Tennessee Space Institute, Tullahoma, TN, U.S.A
- Department of Physics, University of Tennessee Knoxville, Knoxville, TN, U.S.A
| | - Chola K. Regmi
- Department of Physics, Florida International University, Miami, FL, U.S.A
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL, U.S.A
| | | | - Ralph Jimenez
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, U.S.A
- JILA, NIST, and University of Colorado, Boulder, CO, U.S.A
| | - Amy E. Palmer
- BioFrontiers Institute, University of Colorado, Boulder, CO, U.S.A
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, U.S.A
| |
Collapse
|
14
|
Hu C, Yue W, Yang M. Nanoparticle-based signal generation and amplification in microfluidic devices for bioanalysis. Analyst 2014; 138:6709-20. [PMID: 24067742 DOI: 10.1039/c3an01321a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Signal generation and amplification based on nanomaterials and microfluidic techniques have both attracted considerable attention separately due to the demands for ultrasensitive and high-throughput detection of biomolecules. This article reviews the latest development of signal amplification strategies based on nanoparticles for bioanalysis and their integration and applications in microfluidic systems. The applications of nanoparticles in bioanalysis were categorized based on the different approaches of signal amplification, and the microfluidic techniques were summarized based on cell analysis and biomolecule detection with a focus on the integration of nanoparticle-based amplification in microfluidic devices for ultrasensitive bioanalysis. The advantages and limitations of the combination of nanoparticles-based amplification with microfluidic techniques were evaluated, and the possible developments for future research were discussed.
Collapse
Affiliation(s)
- Chong Hu
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, People's Republic of China.
| | | | | |
Collapse
|
15
|
Advances in fluorescence labeling strategies for dynamic cellular imaging. Nat Chem Biol 2014; 10:512-23. [PMID: 24937069 DOI: 10.1038/nchembio.1556] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/16/2014] [Indexed: 12/23/2022]
Abstract
Synergistic advances in optical physics, probe design, molecular biology, labeling techniques and computational analysis have propelled fluorescence imaging into new realms of spatiotemporal resolution and sensitivity. This review aims to discuss advances in fluorescent probes and live-cell labeling strategies, two areas that remain pivotal for future advances in imaging technology. Fluorescent protein- and bio-orthogonal-based methods for protein and RNA imaging are discussed as well as emerging bioengineering techniques that enable their expression at specific genomic loci (for example, CRISPR and TALENs). Important attributes that contribute to the success of each technique are emphasized, providing a guideline for future advances in dynamic live-cell imaging.
Collapse
|
16
|
Zhao Y, Abdelfattah AS, Zhao Y, Ruangkittisakul A, Ballanyi K, Campbell RE, Harrison DJ. Microfluidic cell sorter-aided directed evolution of a protein-based calcium ion indicator with an inverted fluorescent response. Integr Biol (Camb) 2014; 6:714-25. [PMID: 24840546 DOI: 10.1039/c4ib00039k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We demonstrate a simple, low cost and disposable microfluidic fluorescence activated cell sorting system (μFACS) for directed evolution of fluorescent proteins (FP) and FP-based calcium ion (Ca(2+)) indicators. The system was employed to pre-screen libraries of up to 10(6) variants of a yellow FP-based Ca(2+) indicator (Y-GECO) with throughput up to 300 cells per s. Compared to traditional manual screening of FP libraries, this system accelerated the discovery of improved variants and saved considerable time and effort during the directed evolution of Y-GECO. Y-GECO1, the final product of the μFACS-aided directed evolution, has a unique fluorescence hue that places it in the middle of the spectral gap that separates the currently available green and orange FP-based Ca(2+) indicators, exhibits bright fluorescence in the resting (Ca(2+) free) state, and gives a large response to intracellular Ca(2+) fluctuations in live cells.
Collapse
Affiliation(s)
- Yongxin Zhao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada.
| | | | | | | | | | | | | |
Collapse
|
17
|
Chen Y, Li P, Huang PH, Xie Y, Mai JD, Wang L, Nguyen NT, Huang TJ. Rare cell isolation and analysis in microfluidics. LAB ON A CHIP 2014; 14:626-45. [PMID: 24406985 PMCID: PMC3991782 DOI: 10.1039/c3lc90136j] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Rare cells are low-abundance cells in a much larger population of background cells. Conventional benchtop techniques have limited capabilities to isolate and analyze rare cells because of their generally low selectivity and significant sample loss. Recent rapid advances in microfluidics have been providing robust solutions to the challenges in the isolation and analysis of rare cells. In addition to the apparent performance enhancements resulting in higher efficiencies and sensitivity levels, microfluidics provides other advanced features such as simpler handling of small sample volumes and multiplexing capabilities for high-throughput processing. All of these advantages make microfluidics an excellent platform to deal with the transport, isolation, and analysis of rare cells. Various cellular biomarkers, including physical properties, dielectric properties, as well as immunoaffinities, have been explored for isolating rare cells. In this Focus article, we discuss the design considerations of representative microfluidic devices for rare cell isolation and analysis. Examples from recently published works are discussed to highlight the advantages and limitations of the different techniques. Various applications of these techniques are then introduced. Finally, a perspective on the development trends and promising research directions in this field are proposed.
Collapse
Affiliation(s)
- Yuchao Chen
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peng Li
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Po-Hsun Huang
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yuliang Xie
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - John D. Mai
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, PR China
| | - Lin Wang
- Ascent Bio-Nano Technologies Inc., State College, PA 16801, USA
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Brisbane 4111, Australia
| | - Tony Jun Huang
- Fax: 814-865-9974; Tel: 814-863-4209; Fax: 61-(0)7-3735-8021; Tel: 61-(0)7-3735-3921;
| |
Collapse
|
18
|
Cabrera FC, de Souza JCP, Job AE, Crespilho FN. Natural-rubber-based flexible microfluidic device. RSC Adv 2014. [DOI: 10.1039/c4ra07458k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This paper reports a new method developed to fabricate natural-rubber-based microfluidic devices (NRMDs) for optical and electrochemical applications.
Collapse
Affiliation(s)
- Flávio C. Cabrera
- A Faculdade de Ciências e Tecnologia FCT/UNESP
- Departamento de Física
- Presidente Prudente, Brasil
| | | | - Aldo E. Job
- A Faculdade de Ciências e Tecnologia FCT/UNESP
- Departamento de Física
- Presidente Prudente, Brasil
| | | |
Collapse
|