1
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Duran E, Schmidt A, Welty R, Jalihal AP, Pitchiaya S, Walter NG. Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1787. [PMID: 37042458 PMCID: PMC10524090 DOI: 10.1002/wrna.1787] [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] [Received: 11/12/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Elizabeth Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameya P Jalihal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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2
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Park YS, Choi S, Jang HJ, Yoo TH. Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules. Front Bioeng Biotechnol 2023; 11:1188313. [PMID: 37456730 PMCID: PMC10343955 DOI: 10.3389/fbioe.2023.1188313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Accurate and reliable detection of biological molecules such as nucleic acids, proteins, and small molecules is essential for the diagnosis and treatment of diseases. While simple homogeneous assays have been developed and are widely used for detecting nucleic acids, non-nucleic acid molecules such as proteins and small molecules are usually analyzed using methods that require time-consuming procedures and highly trained personnel. Recently, methods using proximity-enhanced reactions (PERs) have been developed for detecting non-nucleic acids. These reactions can be conducted in a homogeneous liquid phase via a single-step procedure. Herein, we review three assays based on PERs for the detection of non-nucleic acid molecules: proximity ligation assay, proximity extension assay, and proximity proteolysis assay.
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Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Sunjoo Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hee Ju Jang
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
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3
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Li J, Wang Y, Wang B, Lou J, Ni P, Jin Y, Chen S, Duan G, Zhang R. Application of CRISPR/Cas Systems in the Nucleic Acid Detection of Infectious Diseases. Diagnostics (Basel) 2022; 12:diagnostics12102455. [PMID: 36292145 PMCID: PMC9600689 DOI: 10.3390/diagnostics12102455] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
The CRISPR/Cas system is a protective adaptive immune system against attacks from foreign mobile genetic elements. Since the discovery of the excellent target-specific sequence recognition ability of the CRISPR/Cas system, the CRISPR/Cas system has shown excellent performance in the development of pathogen nucleic-acid-detection technology. In combination with various biosensing technologies, researchers have made many rapid, convenient, and feasible innovations in pathogen nucleic-acid-detection technology. With an in-depth understanding and development of the CRISPR/Cas system, it is no longer limited to CRISPR/Cas9, CRISPR/Cas12, and other systems that had been widely used in the past; other CRISPR/Cas families are designed for nucleic acid detection. We summarized the application of CRISPR/Cas-related technology in infectious-disease detection and its development in SARS-CoV-2 detection.
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Affiliation(s)
- Junwei Li
- International School of Public Health and One Health, First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yuexia Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Juan Lou
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Peng Ni
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Rongguang Zhang
- International School of Public Health and One Health, First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Correspondence:
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4
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Sun Q, Raeeszadeh-Sarmazdeh M, Tsai SL, Chen W. Strategies for Multienzyme Assemblies. Methods Mol Biol 2022; 2487:113-131. [PMID: 35687232 DOI: 10.1007/978-1-0716-2269-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to co-localize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.
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Affiliation(s)
- Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, Taiwan
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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5
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Park HJ, Kim Y, Yoo TH. One-pot colorimetric detection of molecules based on proximity proteolysis reaction. Biosens Bioelectron 2021; 188:113349. [PMID: 34030090 DOI: 10.1016/j.bios.2021.113349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 01/06/2023]
Abstract
Various types of molecules serve as biomarkers of diseases, and numerous methods have been reported to detect and quantify them. Recently, research efforts have been made to develop point-of-care (POC) tests, which contribute to early diagnoses of diseases, particularly in resource-limited settings. An assay performed in a homogeneous phase is an obvious route to develop these methods. Here, simple homogeneous methods based on proximity proteolysis reactions (PPR) are reported to detect biological molecules. A typical PPR system has been designed such that the proteolysis reaction between protease and zymogen is enhanced in the presence of a target analyte. The activated zymogen generates a color signal by hydrolyzing a chromophore. A protease and zymogen are linked to target binders using specific hybridization between complementary single-stranded DNAs, and several molecules, including proteins, antibodies, aptamers, and small molecules, are used as target binders. The developed assay methods successfully detected several kinds of analytes at subnanomolar concentrations with the one-step procedure and color signal. The modular design of the PPR-based assay will enable the development of simple POC diagnostics for various biomarkers.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Yuseon Kim
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea.
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6
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Biteghe FAN, Mungra N, Chalomie NET, Ndong JDLC, Engohang-Ndong J, Vignaux G, Padayachee E, Naran K, Barth S. Advances in epidermal growth factor receptor specific immunotherapy: lessons to be learned from armed antibodies. Oncotarget 2020; 11:3531-3557. [PMID: 33014289 PMCID: PMC7517958 DOI: 10.18632/oncotarget.27730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) has been recognized as an important therapeutic target in oncology. It is commonly overexpressed in a variety of solid tumors and is critically involved in cell survival, proliferation, metastasis, and angiogenesis. This multi-dimensional role of EGFR in the progression and aggressiveness of cancer, has evolved from conventional to more targeted therapeutic approaches. With the advent of hybridoma technology and phage display techniques, the first anti-EGFR monoclonal antibodies (mAbs) (Cetuximab and Panitumumab) were developed. Due to major limitations including host immune reactions and poor tumor penetration, these antibodies were modified and used as guiding mechanisms for the specific delivery of readily available chemotherapeutic agents or plants/bacterial toxins, giving rise to antibody-drug conjugates (ADCs) and immunotoxins (ITs), respectively. Continued refinement of ITs led to deimmunization strategies based on depletion of B and T-cell epitopes or substitution of non-human toxins leading to a growing repertoire of human enzymes capable of inducing cell death. Similarly, the modification of classical ADCs has resulted in the first, fully recombinant versions. In this review, we discuss significant advancements in EGFR-targeting immunoconjugates, including ITs and recombinant photoactivable ADCs, which serve as a blueprint for further developments in the evolving domain of cancer immunotherapy.
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Affiliation(s)
- Fleury Augustin Nsole Biteghe
- Department of Radiation Oncology and Biomedical Sciences, Cedars-Sinai Medical, Los Angeles, CA, USA.,These authors contributed equally to this work
| | - Neelakshi Mungra
- Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,These authors contributed equally to this work
| | | | - Jean De La Croix Ndong
- Department of Orthopedic Surgery, New York University School of Medicine, New York, NY, USA
| | - Jean Engohang-Ndong
- Department of Biological Sciences, Kent State University at Tuscarawas, New Philadelphia, OH, USA
| | | | - Eden Padayachee
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Krupa Naran
- Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,These authors contributed equally to this work
| | - Stefan Barth
- Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,South African Research Chair in Cancer Biotechnology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,These authors contributed equally to this work
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7
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Antibody-Based Immunotherapy: Alternative Approaches for the Treatment of Metastatic Melanoma. Biomedicines 2020; 8:biomedicines8090327. [PMID: 32899183 PMCID: PMC7555584 DOI: 10.3390/biomedicines8090327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022] Open
Abstract
Melanoma is the least common form of skin cancer and is associated with the highest mortality. Where melanoma is mostly unresponsive to conventional therapies (e.g., chemotherapy), BRAF inhibitor treatment has shown improved therapeutic outcomes. Photodynamic therapy (PDT) relies on a light-activated compound to produce death-inducing amounts of reactive oxygen species (ROS). Their capacity to selectively accumulate in tumor cells has been confirmed in melanoma treatment with some encouraging results. However, this treatment approach has not reached clinical fruition for melanoma due to major limitations associated with the development of resistance and subsequent side effects. These adverse effects might be bypassed by immunotherapy in the form of antibody–drug conjugates (ADCs) relying on the ability of monoclonal antibodies (mAbs) to target specific tumor-associated antigens (TAAs) and to be used as carriers to specifically deliver cytotoxic warheads into corresponding tumor cells. Of late, the continued refinement of ADC therapeutic efficacy has given rise to photoimmunotherapy (PIT) (a light-sensitive compound conjugated to mAbs), which by virtue of requiring light activation only exerts its toxic effect on light-irradiated cells. As such, this review aims to highlight the potential clinical benefits of various armed antibody-based immunotherapies, including PDT, as alternative approaches for the treatment of metastatic melanoma.
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8
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Hill BD, Prabhu P, Rizvi SM, Wen F. Yeast Intracellular Staining (yICS): Enabling High-Throughput, Quantitative Detection of Intracellular Proteins via Flow Cytometry for Pathway Engineering. ACS Synth Biol 2020; 9:2119-2131. [PMID: 32603587 DOI: 10.1021/acssynbio.0c00199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complexities of pathway engineering necessitate screening libraries to discover phenotypes of interest. However, this approach is challenging when desirable phenotypes cannot be directly linked to growth advantages or fluorescence. In these cases, the ability to rapidly quantify intracellular proteins in the pathway of interest is critical to expedite the clonal selection process. While Saccharomyces cerevisiae remains a common host for pathway engineering, current approaches for intracellular protein detection in yeast either have low throughput, can interfere with protein function, or lack the ability to detect multiple proteins simultaneously. To fill this need, we developed yeast intracellular staining (yICS) that enables fluorescent antibodies to access intracellular compartments of yeast cells while maintaining their cellular integrity for analysis by flow cytometry. Using the housekeeping proteins β actin and glyceraldehyde 3-phophate dehydrogenase (GAPDH) as targets for yICS, we demonstrated for the first time successful antibody-based flow cytometric detection of yeast intracellular proteins with no modification. Further, yICS characterization of a recombinant d-xylose assimilation pathway showed 3-plexed, quantitative detection of the xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulokinase (XK) enzymes each fused with a small (6-10 amino acids) tag, revealing distinct enzyme expression profiles between plasmid-based and genome-integrated expression approaches. As a result of its high-throughput and quantitative capability, yICS enabled rapid screening of a library created from CRISPR-mediated XDH integration into the yeast δ site, identifying rare (1%) clones that led to an 8.4-fold increase in XDH activity. These results demonstrate the utility of yICS for greatly accelerating pathway engineering efforts, as well as any application where the high-throughput and quantitative detection of intracellular proteins is desired.
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Affiliation(s)
- Brett D. Hill
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ponnandy Prabhu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Syed M. Rizvi
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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9
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Chang D, Kim KT, Lindberg E, Winssinger N. Smartphone DNA or RNA Sensing Using Semisynthetic Luciferase-Based Logic Device. ACS Sens 2020; 5:807-813. [PMID: 32124606 DOI: 10.1021/acssensors.9b02454] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Detection of specific oligonucleotide sequences is central to numerous applications, and technologies amenable to point-of-care diagnostics or end users are needed. Here, we report a technology making use of a bioluminescent readout and smartphone quantification. The sensor is a semisynthetic luciferase (H-Luc-PNA conjugate) that is turned on by a strand-displacement reaction. We demonstrated sensing of three different microRNAs (miRs), as representative cancer biomarkers, and demonstrate the possibility to integrate an AND gate to sense two sequences simultaneously.
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Affiliation(s)
- Dalu Chang
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
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10
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Berckman EA, Hartzell EJ, Mitkas AA, Sun Q, Chen W. Biological Assembly of Modular Protein Building Blocks as Sensing, Delivery, and Therapeutic Agents. Annu Rev Chem Biomol Eng 2020; 11:35-62. [PMID: 32155350 DOI: 10.1146/annurev-chembioeng-101519-121526] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nature has evolved a wide range of strategies to create self-assembled protein nanostructures with structurally defined architectures that serve a myriad of highly specialized biological functions. With the advent of biological tools for site-specific protein modifications and de novo protein design, a wide range of customized protein nanocarriers have been created using both natural and synthetic biological building blocks to mimic these native designs for targeted biomedical applications. In this review, different design frameworks and synthetic decoration strategies for achieving these functional protein nanostructures are summarized. Key attributes of these designer protein nanostructures, their unique functions, and their impact on biosensing and therapeutic applications are discussed.
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Affiliation(s)
- Emily A Berckman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA; .,Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Emily J Hartzell
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA;
| | - Alexander A Mitkas
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA;
| | - Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA;
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11
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Abstract
Nucleic acid analysis plays an important role in diagnosing diseases as well as understanding biology. Despite advances in technology, there is still a need to develop a rapid and simple method to detect specific nucleic acids, especially in remote locations and low-resource cases. Here, we proposed a proximity proteolysis reaction in which the reaction between protease and zymogen is enhanced in the presence of a target molecule. The pair of proteins was site-specifically modified with oligonucleotides, and the conjugates were used to develop a method of detecting nucleic acids. Target DNA and RNA could be detected in less than 1 h at sub-nanomolar concentrations based on an absorbance signal. The assay method was resistant to interference by biological matrixes, and its sensitivity could be improved when combined with an isothermal nucleic acid amplification method. The results demonstrated the feasibility of this proximity proteolysis reaction as a new platform technology for detecting specific nucleic acid sequences.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yengtong-gu, Suwon 16499, Korea
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12
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de Marco A. Nanomaterial bio-activation and macromolecules functionalization: The search for reliable protocols. Protein Expr Purif 2018; 147:49-54. [DOI: 10.1016/j.pep.2018.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 02/24/2018] [Indexed: 02/08/2023]
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13
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Manzoor O, Soleja N, Mohsin M. Nanoscale gizmos - the novel fluorescent probes for monitoring protein activity. Biochem Eng J 2018; 133:83-95. [PMID: 32518506 PMCID: PMC7270366 DOI: 10.1016/j.bej.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/27/2017] [Accepted: 02/06/2018] [Indexed: 11/15/2022]
Abstract
Genetically-encoded FRET, organic dye, QD based sensors. Real-time monitoring of the respective metabolite level at sub cellular level. Spatio temporal resolution of the fluorophores by low intensity light. Monitoring of various metabolite levels in any cell type prokaryotic and eukaryotic as well. Functional analysis of the role of proteases in several diseases.
Nanobiotechnology has emerged inherently as an interdisciplinary field, with collaborations from researchers belonging to diverse backgrounds like molecular biology, materials science and organic chemistry. Till the current times, researchers have been able to design numerous types of nanoscale fluorescent tool kits for monitoring protein–protein interactions through real time cellular imagery in a fluorescence microscope. It is apparent that supplementing any protein of interest with a fluorescence habit traces its function and regulation within a cell. Our review therefore highlights the application of several fluorescent probes such as molecular organic dyes, quantum dots (QD) and fluorescent proteins (FPs) to determine activity state, expression and localization of proteins in live and fixed cells. The focus is on Fluorescence Resonance Energy Transfer (FRET) based nanosensors that have been developed by researchers to visualize and monitor protein dynamics and quantify metabolites of diverse nature. FRET based toolkits permit the resolution of ambiguities that arise due to the rotation of sensor molecules and flexibility of the probe. Achievements of live cell imaging and efficient spatiotemporal resolution however have been possible only with the advent of fluorescence microscopic technology, equipped with precisely sensitive automated softwares.
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14
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Chen RP, Blackstock D, Sun Q, Chen W. Dynamic protein assembly by programmable DNA strand displacement. Nat Chem 2018. [DOI: 10.1038/s41557-018-0016-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Chen Q, Yu S, Myung N, Chen W. DNA-guided assembly of a five-component enzyme cascade for enhanced conversion of cellulose to gluconic acid and H 2 O 2. J Biotechnol 2017; 263:30-35. [DOI: 10.1016/j.jbiotec.2017.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/25/2017] [Accepted: 10/09/2017] [Indexed: 01/17/2023]
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16
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Zhang Y, Qian L, Wei W, Wang Y, Wang B, Lin P, Liu W, Xu L, Li X, Liu D, Cheng S, Li J, Ye Y, Li H, Zhang X, Dong Y, Zhao X, Liu C, Zhang HM, Ouyang Q, Lou C. Paired Design of dCas9 as a Systematic Platform for the Detection of Featured Nucleic Acid Sequences in Pathogenic Strains. ACS Synth Biol 2017; 6:211-216. [PMID: 27718551 DOI: 10.1021/acssynbio.6b00215] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We developed an in vitro DNA detection system using a pair of dCas9 proteins linked to split halves of luciferase. Luminescence was induced upon colocalization of the reporter pair to a ∼44 bp target sequence defined by sgRNAs. We used the system to detect Mycobacterium tuberculosis DNA with high specificity and sensitivity. The reprogrammability of dCas9 was further leveraged in an array design that accesses sequence information across the entire genome.
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Affiliation(s)
- Yihao Zhang
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
- Center
for Quantitative Biology and Peking-Tsinghua Joint Center for Life
Sciences, Peking University, Beijing, 100871, China
| | - Long Qian
- Department
of Biology and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, New York 10003, United States
| | - Weijia Wei
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
- CAS Key Laboratory of Microbial Physiological
and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Science, Beijing, 100149, China
| | - Yu Wang
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Beining Wang
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Pingping Lin
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Wenchao Liu
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Luze Xu
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Xiang Li
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Dongming Liu
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Sida Cheng
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Jiaofeng Li
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Yixuan Ye
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Hang Li
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Xiaohan Zhang
- Peking University Team for the International Genetically Engineered Machine Competition (iGEM), Beijing, 100871, China
| | - Yiming Dong
- Center
for Quantitative Biology and Peking-Tsinghua Joint Center for Life
Sciences, Peking University, Beijing, 100871, China
| | - Xuejin Zhao
- CAS Key Laboratory of Microbial Physiological
and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cuihua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology,
Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haoqian M. Zhang
- Center
for Quantitative Biology and Peking-Tsinghua Joint Center for Life
Sciences, Peking University, Beijing, 100871, China
| | - Qi Ouyang
- Center
for Quantitative Biology and Peking-Tsinghua Joint Center for Life
Sciences, Peking University, Beijing, 100871, China
- The State Key Laboratory
for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Chunbo Lou
- CAS Key Laboratory of Microbial Physiological
and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Science, Beijing, 100149, China
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17
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Shigeto H, Nakatsuka K, Ikeda T, Hirota R, Kuroda A, Funabashi H. Continuous Monitoring of Specific mRNA Expression Responses with a Fluorescence Resonance Energy Transfer-Based DNA Nano-tweezer Technique That Does Not Require Gene Recombination. Anal Chem 2016; 88:7894-8. [DOI: 10.1021/acs.analchem.6b02710] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hajime Shigeto
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Keisuke Nakatsuka
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
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18
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pMINERVA: A donor-acceptor system for the in vivo recombineering of scFv into IgG molecules. J Immunol Methods 2016; 431:22-30. [PMID: 26851519 DOI: 10.1016/j.jim.2016.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/12/2016] [Accepted: 02/01/2016] [Indexed: 11/22/2022]
Abstract
Phage display is the most widely used method for selecting binding molecules from recombinant antibody libraries. However, validation of the phage antibodies often requires early production of the cognate full-length immunoglobulin G (IgG). The conversion of phage library outputs to a full immunoglobulin via standard subcloning is time-consuming and limits the number of clones that can be evaluated. We have developed a novel system to convert scFvs from a phage display vector directly into IgGs without any in vitro subcloning steps. This new vector system, named pMINERVA, makes clever use of site-specific bacteriophage integrases that are expressed in Escherichia coli and intron splicing that occurs within mammalian cells. Using this system, a phage display vector contains both bacterial and mammalian regulatory regions that support antibody expression in E. coli and mammalian cells. A single-chain variable fragment (scFv) antibody is expressed on the surface of bacteriophage M13 as a genetic fusion to the gpIII coat protein. The scFv is converted to an IgG that can be expressed in mammalian cells by transducing a second E. coli strain. In that strain, the phiC31 recombinase fuses the heavy chain constant domain from an acceptor plasmid to the heavy chain variable domain and introduces controlling elements upstream of the light chain variable domain. Splicing in mammalian cells removes a synthetic intron containing the M13 gpIII gene to produce the fusion of the light chain variable domain to the constant domain. We show that phage displaying a scFv and recombinant IgGs generated using this system are expressed at wild-type levels and retain normal function. Use of the pMINERVA completely eliminates the labor-intensive subcloning and DNA sequence confirmation steps currently needed to convert a scFv into a functional IgG Ab.
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19
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Sun Q, Chen W. HaloTag mediated artificial cellulosome assembly on a rolling circle amplification DNA template for efficient cellulose hydrolysis. Chem Commun (Camb) 2016; 52:6701-4. [DOI: 10.1039/c6cc02035f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report here the generation of artificial cellulosomes onto a DNA scaffold using the self-labeling HaloTag for DNA conjugation. Rolling circle amplification multiplexing templates were used to increase the complexity of this system with higher efficiency observed.
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Affiliation(s)
- Qing Sun
- Department of Chemical and Biomolecular Engineering
- University of Delaware
- Newark
- USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering
- University of Delaware
- Newark
- USA
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20
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Funabashi H, Shigeto H, Nakatsuka K, Kuroda A. A FRET-based DNA nano-tweezer technique for the imaging analysis of specific mRNA. Analyst 2015; 140:999-1003. [PMID: 25529369 DOI: 10.1039/c4an02064b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A DNA nano-tweezer (DNA-NT) structure-based target mRNA detection probe, which uses fluorescence resonance energy transfer (FRET) as a detection signal and works as a single molecule, has been developed. This FRET-paired fluorescent dye-modified DNA-NT, self-assembled from three single-stranded DNAs, alters its structure from open to closed states and produces a FRET signal in response to in vitro transcripts of Hes-1 mRNA. Our results showed that the FRET-based DNA-NT detected both GLUT1 mRNA as a pre-fixed target mRNA model and Hes-1 mRNA as a model expressed inside a living cell. These results confirm the feasibility of using the FRET-based DNA-NT for imaging analysis of target mRNA.
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Affiliation(s)
- Hisakage Funabashi
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan.
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21
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Sun Q, Chen Q, Blackstock D, Chen W. Post-Translational Modification of Bionanoparticles as a Modular Platform for Biosensor Assembly. ACS NANO 2015; 9:8554-8561. [PMID: 26235232 DOI: 10.1021/acsnano.5b03688] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Context driven biosensor assembly with modular targeting and detection moieties is gaining significant attentions. Although protein-based nanoparticles have emerged as an excellent platform for biosensor assembly, current strategies of decorating bionanoparticles with targeting and detection moieties often suffer from unfavorable spacing and orientation as well as bionanoparticle aggregation. Herein, we report a highly modular post-translational modification approach for biosensor assembly based on sortase A-mediated ligation. This approach enables the simultaneous modifications of the Bacillus stearothermophilus E2 nanoparticles with different functional moieties for antibody, enzyme, DNA aptamer, and dye decoration. The resulting easy-purification platform offers a high degree of targeting and detection modularity with signal amplification. This flexibility is demonstrated for the detection of both immobilized antigens and cancer cells.
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Affiliation(s)
- Qing Sun
- Department of Chemical and Biomolecular Engineering, University of Delaware , Newark, Delaware 19716, United States
| | - Qi Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware , Newark, Delaware 19716, United States
| | - Daniel Blackstock
- Department of Chemical and Biomolecular Engineering, University of Delaware , Newark, Delaware 19716, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware , Newark, Delaware 19716, United States
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22
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Chang X, Yu C, Wang G, Fan J, Zhang J, Qi Y, Liu K, Fang Y. Constitutional Dynamic Chemistry-based New Concept of Molecular Beacons for High Efficient Development of Fluorescent Probes. J Phys Chem B 2015; 119:6721-9. [PMID: 25985384 DOI: 10.1021/acs.jpcb.5b02664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Inspired by the concept of constitutional dynamic chemistry, we propose a new and well-adaptable strategy for developing molecular beacon (MB)-like fluorescent probes. To demonstrate the strategy, we synthesized and used an amino group containing pyrenyl derivative of cholesterol (CP) for the construction of new fluorescent probes with EDTA and sulfuric acid. The probes as created were successfully used for n-hexane purity checking and Ba(2+)and Pb(2+)sensing, respectively.
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Affiliation(s)
- Xingmao Chang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Chunmeng Yu
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Gang Wang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Jiayun Fan
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Jianyun Zhang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Yanyu Qi
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Kaiqiang Liu
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Yu Fang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
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23
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Abstract
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Exploration of protein function and
interaction is critical for
discovering links among genomics, proteomics, and disease state; yet,
the immense complexity of proteomics found in biological systems currently
limits our investigational capacity. Although affinity and autofluorescent
tags are widely employed for protein analysis, these methods have
been met with limited success because they lack specificity and require
multiple fusion tags and genetic constructs. As an alternative approach,
the innovative HaloTag protein fusion platform allows protein function
and interaction to be comprehensively analyzed using a single genetic
construct with multiple capabilities. This is accomplished using a
simplified process, in which a variable HaloTag ligand binds rapidly
to the HaloTag protein (usually linked to the protein of interest)
with high affinity and specificity. In this review, we examine all
current applications of the HaloTag technology platform for biomedical
applications, such as the study of protein isolation and purification,
protein function, protein–protein and protein–DNA interactions,
biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the
HaloTag platform are briefly discussed along with potential future
applications.
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Affiliation(s)
- Christopher G England
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Haiming Luo
- ‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weibo Cai
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,§University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53705, United States
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24
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Sun AL, Zhang YF, Wang XN. Sensitive voltammetric determination of DNA via a target-induced strand-displacement reaction using quantum dot-labeled probe DNA. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1467-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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