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Han SI, Sarkes DA, Hurley MM, Renberg R, Huang C, Li Y, Jahnke JP, Sumner JJ, Stratis-Cullum DN, Han A. Identification of Microorganisms that Bind Specifically to Target Materials of Interest Using a Magnetophoretic Microfluidic Platform. ACS APPLIED MATERIALS & INTERFACES 2023; 15:11391-11402. [PMID: 36847552 PMCID: PMC10848205 DOI: 10.1021/acsami.2c15192] [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: 08/23/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Discovery of microorganisms and their relevant surface peptides that specifically bind to target materials of interest can be achieved through iterative biopanning-based screening of cellular libraries having high diversity. Recently, microfluidics-based biopanning methods have been developed and exploited to overcome the limitations of conventional methods where controlling the shear stress applied to remove cells that do not bind or only weakly bind to target surfaces is difficult and the overall experimental procedure is labor-intensive. Despite the advantages of such microfluidic methods and successful demonstration of their utility, these methods still require several rounds of iterative biopanning. In this work, a magnetophoretic microfluidic biopanning platform was developed to isolate microorganisms that bind to target materials of interest, which is gold in this case. To achieve this, gold-coated magnetic nanobeads, which only attached to microorganisms that exhibit high affinity to gold, were used. The platform was first utilized to screen a bacterial peptide display library, where only the cells with surface peptides that specifically bind to gold could be isolated by the high-gradient magnetic field generated within the microchannel, resulting in enrichment and isolation of many isolates with high affinity and high specificity toward gold even after only a single round of separation. The amino acid profile of the resulting isolates was analyzed to provide a better understanding of the distinctive attributes of peptides that contribute to their specific material-binding capabilities. Next, the microfluidic system was utilized to screen soil microbes, a rich source of extremely diverse microorganisms, successfully isolating many naturally occurring microorganisms that show strong and specific binding to gold. The results show that the developed microfluidic platform is a powerful screening tool for identifying microorganisms that specifically bind to a target material surface of interest, which can greatly accelerate the development of new peptide-driven biological materials and hybrid organic-inorganic materials.
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Affiliation(s)
- Song-I Han
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Deborah A. Sarkes
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Margaret M. Hurley
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Rebecca Renberg
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Can Huang
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Yuwen Li
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
| | - Justin P. Jahnke
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - James J. Sumner
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Dimitra N. Stratis-Cullum
- Biotechnology
Branch, U.S. Army Combat Capabilities Development Command (DEVCOM), Army Research Laboratory (ARL), Adelphi, Maryland 20783, USA
| | - Arum Han
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, USA
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, USA
- Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
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2
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Biomedical applications of solid-binding peptides and proteins. Mater Today Bio 2023; 19:100580. [PMID: 36846310 PMCID: PMC9950531 DOI: 10.1016/j.mtbio.2023.100580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Over the past decades, solid-binding peptides (SBPs) have found multiple applications in materials science. In non-covalent surface modification strategies, solid-binding peptides are a simple and versatile tool for the immobilization of biomolecules on a vast variety of solid surfaces. Especially in physiological environments, SBPs can increase the biocompatibility of hybrid materials and offer tunable properties for the display of biomolecules with minimal impact on their functionality. All these features make SBPs attractive for the manufacturing of bioinspired materials in diagnostic and therapeutic applications. In particular, biomedical applications such as drug delivery, biosensing, and regenerative therapies have benefited from the introduction of SBPs. Here, we review recent literature on the use of solid-binding peptides and solid-binding proteins in biomedical applications. We focus on applications where modulating the interactions between solid materials and biomolecules is crucial. In this review, we describe solid-binding peptides and proteins, providing background on sequence design and binding mechanism. We then discuss their application on materials relevant for biomedicine (calcium phosphates, silicates, ice crystals, metals, plastics, and graphene). Although the limited characterization of SBPs still represents a challenge for their design and widespread application, our review shows that SBP-mediated bioconjugation can be easily introduced into complex designs and on nanomaterials with very different surface chemistries.
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3
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Sun H, Hu N, Wang J. Application of Microfluidic Technology in Antibody Screening. Biotechnol J 2022; 17:e2100623. [PMID: 35481726 DOI: 10.1002/biot.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
Specific antibodies are widely used in the biomedical field. Current screening methods for specific antibodies mainly involve hybridoma technology and antibody engineering techniques. However, these technologies suffer from tedious screening processes, long preparation periods, high costs, low efficiency, and a degree of automation, which have become a bottleneck for the screening of specific antibodies. To overcome these difficulties, microfluidics has been developed as a promising technology for high-throughput screening and high purity of antibody. In this review, we provide an overview of the recent advances in microfluidic applications for specific antibody screening. In particular, hybridoma technology and four antibody engineering techniques (including phage display, single B cell antibody screening, antibody expression, and cell-free protein synthesis) based on microfluidics have been introduced, challenges, and the future outlook of these technologies are also discussed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
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4
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Yue H, Li Y, Yang M, Mao C. T7 Phage as an Emerging Nanobiomaterial with Genetically Tunable Target Specificity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103645. [PMID: 34914854 PMCID: PMC8811829 DOI: 10.1002/advs.202103645] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/27/2021] [Indexed: 05/05/2023]
Abstract
Bacteriophages, also known as phages, are specific antagonists against bacteria. T7 phage has drawn massive attention in precision medicine owing to its distinctive advantages, such as short replication cycle, ease in displaying peptides and proteins, high stability and cloning efficiency, facile manipulation, and convenient storage. By introducing foreign gene into phage DNA, T7 phage can present foreign peptides or proteins site-specifically on its capsid, enabling it to become a nanoparticle that can be genetically engineered to screen and display a peptide or protein capable of recognizing a specific target with high affinity. This review critically introduces the biomedical use of T7 phage, ranging from the detection of serological biomarkers and bacterial pathogens, recognition of cells or tissues with high affinity, design of gene vectors or vaccines, to targeted therapy of different challenging diseases (e.g., bacterial infection, cancer, neurodegenerative disease, inflammatory disease, and foot-mouth disease). It also discusses perspectives and challenges in exploring T7 phage, including the understanding of its interactions with human body, assembly into scaffolds for tissue regeneration, integration with genome editing, and theranostic use in clinics. As a genetically modifiable biological nanoparticle, T7 phage holds promise as biomedical imaging probes, therapeutic agents, drug and gene carriers, and detection tools.
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Affiliation(s)
- Hui Yue
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiang310027P. R. China
| | - Yan Li
- Institute of Applied Bioresource ResearchCollege of Animal ScienceZhejiang UniversityYuhangtang Road 866HangzhouZhejiang310058P. R. China
| | - Mingying Yang
- Institute of Applied Bioresource ResearchCollege of Animal ScienceZhejiang UniversityYuhangtang Road 866HangzhouZhejiang310058P. R. China
| | - Chuanbin Mao
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiang310027P. R. China
- Department of Chemistry and BiochemistryStephenson Life Science Research CenterInstitute for Biomedical Engineering, Science and TechnologyUniversity of Oklahoma101 Stephenson ParkwayNormanOklahoma73019‐5251USA
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5
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Philpott D, Gomis S, Wang H, Atwal R, Kelil A, Sack T, Morningstar B, Burnie C, Sargent EH, Angers S, Sidhu S, Kelley SO. Rapid On-Cell Selection of High-Performance Human Antibodies. ACS CENTRAL SCIENCE 2022; 8:102-109. [PMID: 35106377 PMCID: PMC8796304 DOI: 10.1021/acscentsci.1c01205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 06/14/2023]
Abstract
Phage display is a critical tool for developing antibodies. However, existing approaches require many time-consuming rounds of biopanning and screening of potential candidates due to a high rate of failure during validation. Herein, we present a rapid on-cell phage display platform which recapitulates the complex in vivo binding environment to produce high-performance human antibodies in a short amount of time. Selection is performed in a highly stringent heterogeneous mixture of cells to quickly remove nonspecific binders. A microfluidic platform then separates antigen-presenting cells with high throughput and specificity. An unsupervised machine learning algorithm analyzes sequences of phage from all pools to identify the structural trends that contribute to affinity and proposes ideal candidates for validation. In a proof-of-concept screen against human Frizzled-7, a key ligand in the Wnt signaling pathway, antibodies with picomolar affinity were discovered in two rounds of selection that outperformed current gold-standard reagents. This approach, termed μCellect, is low cost, high throughput, and compatible with a wide variety of cell types, enabling widespread adoption for antibody development.
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Affiliation(s)
- David
N. Philpott
- Edward
S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Surath Gomis
- Edward
S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Hansen Wang
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Randy Atwal
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Abdellali Kelil
- Donnelly
Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Tanja Sack
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Brandon Morningstar
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Chris Burnie
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Edward H. Sargent
- Edward
S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Stephane Angers
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Sachdev Sidhu
- Donnelly
Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Shana O. Kelley
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
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6
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Wang J, Guo J, Zhao K, Ruan W, Li L, Ling J, Peng R, Zhang H, Yang C, Zhu Z. Auto-Panning: a highly integrated and automated biopanning platform for peptide screening. LAB ON A CHIP 2021; 21:2702-2710. [PMID: 34105587 DOI: 10.1039/d1lc00129a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biopanning, a common affinity selection approach in phage display, has evolved numerous ligands for diagnosis, imaging, delivery, and therapy applications. However, traditional biopanning has suffered from time-consuming processes, highly-repetitive procedures and labor-intensive manual operation. Herein, a highly integrated and automated biopanning platform (Auto-Panning) is proposed. Based on digital microfluidics (DMF), biopanning processes are integrated on a chip with highly reproducible, precise, automated liquid manipulation. Therefore, 3 rounds of Auto-Panning can be accomplished within 16 h, instead of nearly a week of complicated manual operations. Auto-Panning has been used to evolve a specific peptide against cancer biomarker EphA2 with excellent cellular penetrating ability and significant invasion suppression biofunction, successfully demonstrating the practicality of the platform. Overall, as an automated programmable molecular screening platform, Auto-Panning will further promote the discovery and applications of novel ligands.
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Affiliation(s)
- Junxia Wang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Jingjing Guo
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Kaifeng Zhao
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China. and Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Weidong Ruan
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Liang Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Jiajun Ling
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Ruixiao Peng
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Huimin Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China. and Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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7
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Evenson WE, Lin WZS, Pang K, Czaja AT, Jalali-Yazdi F, Takahashi TT, Malmstadt N, Roberts RW. Enabling Flow-Based Kinetic Off-Rate Selections Using a Microfluidic Enrichment Device. Anal Chem 2020; 92:10218-10222. [PMID: 32633489 PMCID: PMC10368462 DOI: 10.1021/acs.analchem.0c01867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modern genomic sequencing efforts are identifying potential diagnostic and therapeutic targets more rapidly than existing methods can generate the peptide- and protein-based ligands required to study them. To address this problem, we have developed a microfluidic enrichment device (MFED) enabling kinetic off-rate selection without the use of exogenous competitor. We tuned the conditions of the device (bed volume, flow rate, immobilized target) such that modest, readily achievable changes in flow rates favor formation or dissociation of target-ligand complexes based on affinity. Simple kinetic equations can be used to describe the behavior of ligand binding in the MFED and the kinetic rate constants observed agree with independent measurements. We demonstrate the utility of the MFED by showing a 4-fold improvement in enrichment compared to standard selection. The MFED described here provides a route to simultaneously bias pools toward high-affinity ligands while reducing the demand for target-protein to less than a nanomole per selection.
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Affiliation(s)
- William E Evenson
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089, United States
| | - Wan-Zhen Sophie Lin
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States
| | - Kenmond Pang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States
| | - Alexander T Czaja
- Department of Biomedical Engineering, University of Southern California, 1042 Downey Way, Denney Research Center (DRB) 140, Los Angeles, California 90089, United States
| | - Farzad Jalali-Yazdi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States
| | - Terry T Takahashi
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089, United States
| | - Noah Malmstadt
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089, United States.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States.,Department of Biomedical Engineering, University of Southern California, 1042 Downey Way, Denney Research Center (DRB) 140, Los Angeles, California 90089, United States.,USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, California 90033, United States
| | - Richard W Roberts
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089, United States.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, 925 Bloom Walk, HED 216, Los Angeles, California 90089, United States.,Department of Biomedical Engineering, University of Southern California, 1042 Downey Way, Denney Research Center (DRB) 140, Los Angeles, California 90089, United States.,USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, California 90033, United States.,Department of Molecular and Computational Biology, University of Southern California, 1050 Child Way, RRI 201, Los Angeles, California 90089, United States
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8
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Kim WG, Zueger C, Kim C, Wong W, Devaraj V, Yoo HW, Hwang S, Oh JW, Lee SW. Experimental and numerical evaluation of a genetically engineered M13 bacteriophage with high sensitivity and selectivity for 2,4,6-trinitrotoluene. Org Biomol Chem 2020; 17:5666-5670. [PMID: 30973549 DOI: 10.1039/c8ob03075h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Selective and sensitive detection of desired targets is very critical in sensor design. Here, we report a genetically engineered M13 bacteriophage-based sensor system evaluated by quantum mechanics (QM) calculations. Phage display is a facile way to develop the desired peptide sequences, but the resulting sequences can be imperfect peptides for binding of target molecules. A TNT binding peptide (WHW) carrying phage was self-assembled to fabricate thin films and tested for the sensitive and selective surface plasmon resonance-based detection of TNT molecules at the 500 femtomole level. SPR studies performed with the WHW peptide and control peptides (WAW, WHA, AHW) were well-matched with those of the QM calculations. Our combined method between phage engineering and QM calculation will significantly enhance our ability to design selective and sensitive sensors.
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Affiliation(s)
- Won-Geun Kim
- Department of Nano Fusion Technology, Pusan National University, Busan, 609-735, South Korea.
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9
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Raftery LJ, Howard CB, Grewal YS, Vaidyanathan R, Jones ML, Anderson W, Korbie D, Duarte T, Cao MD, Nguyen SH, Coin LJM, Mahler SM, Trau M. Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing. LAB ON A CHIP 2019; 19:4083-4092. [PMID: 31712799 DOI: 10.1039/c9lc00978g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phage display methodologies offer a versatile platform for the isolation of single-chain Fv (scFv) molecules which may be rebuilt into monoclonal antibodies. Herein, we report on a complete workflow termed PhageXpress, for rapid selection of single-chain Fv sequences by leveraging electrohydrodynamic-manipulation of a solution containing phage library particles to enhance target binding whilst minimizing non-specific interactions. Our PhageXpress technique is combined with Oxford Nanopore Technologies' MinION sequencer and custom bioinformatics to achieve high-throughput screening of phage libraries. We performed 4 rounds of biopanning against Dengue virus (DENV) non-structural protein 1 (NS1) using traditional methods (4 week turnaround), which resulted in the isolation of 19 unique scFv clones. We validated the feasibility and efficiency of the PhageXpress method utilizing the same phage library and antigen target. Notably, we successfully mapped 14 of the 19 anti-NS1 scFv sequences (∼74%) with our new method, despite using ∼30-fold less particles during screening and conducting only a single round of biopanning. We believe this approach supersedes traditional methods for the discovery of bio-recognition molecules such as antibodies by speeding up the process for the development of therapeutic and diagnostic biologics.
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Affiliation(s)
- Lyndon J Raftery
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia.
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia. and Centre for Personalised Nanomedicine, AIBN, University of Queensland, Brisbane, Australia and ARC Training Centre for Biopharmaceutical Innovation, AIBN, University of Queensland, Brisbane, Australia
| | - Yadveer S Grewal
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia. and Centre for Personalised Nanomedicine, AIBN, University of Queensland, Brisbane, Australia
| | - Ramanathan Vaidyanathan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia. and Centre for Personalised Nanomedicine, AIBN, University of Queensland, Brisbane, Australia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia. and ARC Training Centre for Biopharmaceutical Innovation, AIBN, University of Queensland, Brisbane, Australia
| | - Will Anderson
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia. and Centre for Personalised Nanomedicine, AIBN, University of Queensland, Brisbane, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia. and Centre for Personalised Nanomedicine, AIBN, University of Queensland, Brisbane, Australia
| | - Tania Duarte
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Minh Duc Cao
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Son Hoang Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia. and ARC Training Centre for Biopharmaceutical Innovation, AIBN, University of Queensland, Brisbane, Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia. and Centre for Personalised Nanomedicine, AIBN, University of Queensland, Brisbane, Australia and School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, Australia
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10
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Lee DJ, Park HS, Koo K, Lee JY, Nam YS, Lee W, Yang MY. Gold Binding Peptide Identified from Microfluidic Biopanning: An Experimental and Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:522-528. [PMID: 30592604 DOI: 10.1021/acs.langmuir.8b02563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biopanning refers to the processes of screening peptides with a high affinity to a target material. Microfluidic biopanning has advantages compared to conventional biopanning which requires large amounts of the target material and involves inefficient multiple pipetting steps to remove nonspecific or low-affinity peptides. Here, we fabricate a microfluidic biopanning system to identify a new gold-binding peptide (GBP). A polydimethylsiloxane microfluidic device is fabricated and bonded to a glass slide with a gold pattern that is deposited by electron-beam evaporation. The microfluidic biopanning system can provide high adjustability in the washing step during the biopanning process because the liquid flow rate and the resulting shear stress can be precisely controlled. The surface plasmon resonance analysis shows that the binding affinity of the identified GBP is comparable to previously reported GBPs. Moreover, molecular dynamics simulations are performed to understand its binding affinity against the gold surface in detail. Theoretical calculations suggest that the association and dissociation rates of the GBPs depend on their sequence-dependent conformations and interactions with the gold surface. These findings provide insight into designing efficient biopanning tools and peptides with a high affinity for various target materials.
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Affiliation(s)
| | | | - Kunmo Koo
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Republic of Korea
| | - Jeong Yong Lee
- Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , 291 Daehak-ro, Yuseong-gu , Daejeon 34141 , Republic of Korea
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11
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Using phage display technology to obtain Crybodies active against non-target insects. Sci Rep 2017; 7:14922. [PMID: 29097681 PMCID: PMC5668233 DOI: 10.1038/s41598-017-09384-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/26/2017] [Indexed: 11/09/2022] Open
Abstract
The insecticidal Cry toxins produced by Bacillus thuringiensis (Bt) are increasingly important in the biological control of insect pests and vectors of human disease. Markets for Bt products and transgenic plants expressing their toxins are driven by their specificity, safety and the move away from chemical control agents. However, the high specificity of Cry toxins can also prove to be a limitation when there is no known Cry toxin active against a particular target. Novel activities can be discovered by screening natural Bt isolates or through modifications of the Cry proteins. Here we demonstrate the use of λ-phage displaying Cry1Aa13 toxin variants modified in domain II loop 2 (Crybodies) to select retargeted toxins. Through biopanning using gut tissue from larvae of the non-target insect Aedes aegypti, we isolated a number of phage for further testing. Two of the overexpressed Cry toxin variants showed significant activity against A. aegypti larvae while another induced mortality at the pupal stage. We present the first report of the use of phage display to identify novel activities toward insects from distant taxonomic Orders and establish this technology based on the use of Crybodies as a powerful tool for developing tailor-made insecticides against new target insects.
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12
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Abstract
Novel affinity agents with high specificity are needed to make progress in disease diagnosis and therapy. Over the last several years, peptides have been considered to have fundamental benefits over other affinity agents, such as antibodies, due to their fast blood clearance, low immunogenicity, rapid tissue penetration, and reproducible chemical synthesis. These features make peptides ideal affinity agents for applications in disease diagnostics and therapeutics for a wide variety of afflictions. Virus-derived peptide techniques provide a rapid, robust, and high-throughput way to identify organism-targeting peptides with high affinity and selectivity. Here, we will review viral peptide display techniques, how these techniques have been utilized to select new organism-targeting peptides, and their numerous biomedical applications with an emphasis on targeted imaging, diagnosis, and therapeutic techniques. In the future, these virus-derived peptides may be used as common diagnosis and therapeutics tools in local clinics.
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Affiliation(s)
- Mingying Yang
- Institute of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Kegan Sunderland
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
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13
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Hsiao YH, Huang CY, Hu CY, Wu YY, Wu CH, Hsu CH, Chen C. Continuous microfluidic assortment of interactive ligands (CMAIL). Sci Rep 2016; 6:32454. [PMID: 27578501 PMCID: PMC5006012 DOI: 10.1038/srep32454] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/09/2016] [Indexed: 01/15/2023] Open
Abstract
Finding an interactive ligand-receptor pair is crucial to many applications, including the development of monoclonal antibodies. Biopanning, a commonly used technique for affinity screening, involves a series of washing steps and is lengthy and tedious. Here we present an approach termed continuous microfluidic assortment of interactive ligands, or CMAIL, for the screening and sorting of antigen-binding single-chain variable antibody fragments (scFv) displayed on bacteriophages (phages). Phages carrying native negative charges on their coat proteins were electrophoresed through a hydrogel matrix functionalized with target antigens under two alternating orthogonal electric fields. During the weak horizontal electric field phase, phages were differentially swept laterally depending on their affinity for the antigen, and all phages were electrophoresed down to be collected during the strong vertical electric field phase. Phages of different affinity were spatially separated, allowing the continuous operation. More than 105 CFU (colony forming unit) antigen-interacting phages were isolated with ~100% specificity from a phage library containing 3 × 109 individual members within 40 minutes of sorting using CMAIL. CMAIL is rapid, sensitive, specific, and does not employ washing, elution or magnetic beads. In conclusion, we have developed an efficient and cost-effective method for isolating and sorting affinity reagents involving phage display.
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Affiliation(s)
- Yi-Hsing Hsiao
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Chao-Yang Huang
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chih-Yung Hu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Yen-Yu Wu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chung-Hsiun Wu
- Development Center for Biotechnology, New Taipei City 22180, Taiwan
| | - Chia-Hsien Hsu
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Chihchen Chen
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.,Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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14
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Hung LY, Wang CH, Fu CY, Gopinathan P, Lee GB. Microfluidics in the selection of affinity reagents for the detection of cancer: paving a way towards future diagnostics. LAB ON A CHIP 2016; 16:2759-74. [PMID: 27381813 DOI: 10.1039/c6lc00662k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Microfluidic technologies have miniaturized a variety of biomedical applications, and these chip-based systems have several significant advantages over their large-scale counterparts. Recently, this technology has been used for automating labor-intensive and time-consuming screening processes, whereby affinity reagents, including aptamers, peptides, antibodies, polysaccharides, glycoproteins, and a variety of small molecules, are used to probe for molecular biomarkers. When compared to conventional methods, the microfluidic approaches are faster, more compact, require considerably smaller quantities of samples and reagents, and can be automated. Furthermore, they allow for more precise control of reaction conditions (e.g., pH, temperature, and shearing forces) such that more efficient screening can be performed. A variety of affinity reagents for targeting cancer cells or cancer biomarkers are now available and will likely replace conventional antibodies. In this review article, the selection of affinity reagents for cancer cells or cancer biomarkers on microfluidic platforms is reviewed with the aim of highlighting the utility of such approaches in cancer diagnostics.
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MESH Headings
- Animals
- Antibodies, Immobilized/chemistry
- Antibodies, Immobilized/metabolism
- Antibodies, Neoplasm/chemistry
- Antibodies, Neoplasm/metabolism
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cells, Cultured
- Coculture Techniques
- Humans
- Immobilized Nucleic Acids/chemistry
- Immobilized Nucleic Acids/metabolism
- Immobilized Proteins/metabolism
- Lab-On-A-Chip Devices/trends
- Leukocytes/cytology
- Leukocytes/metabolism
- Ligands
- Mice
- Neoplasms/blood
- Neoplasms/diagnosis
- Neoplasms/metabolism
- Neoplasms/pathology
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Single-Chain Antibodies/chemistry
- Single-Chain Antibodies/metabolism
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Affiliation(s)
- Lien-Yu Hung
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
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15
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Huang R, Kiss MM, Batonick M, Weiner MP, Kay BK. Generating Recombinant Antibodies to Membrane Proteins through Phage Display. Antibodies (Basel) 2016; 5:antib5020011. [PMID: 31557992 PMCID: PMC6698964 DOI: 10.3390/antib5020011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 01/03/2023] Open
Abstract
One of the most important classes of proteins in terms of drug targets is cell surface membrane proteins, and yet it is a challenging set of proteins for generating high-quality affinity reagents. In this review, we focus on the use of phage libraries, which display antibody fragments, for generating recombinant antibodies to membrane proteins. Such affinity reagents generally have high specificity and affinity for their targets. They have been used for cell staining, for promoting protein crystallization to solve three-dimensional structures, for diagnostics, and for treating diseases as therapeutics. We cover publications on this topic from the past 10 years, with a focus on the various formats of membrane proteins for affinity selection and the diverse affinity selection strategies used. Lastly, we discuss the challenges faced in this field and provide possible directions for future efforts.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
| | - Margaret M Kiss
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Melissa Batonick
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Michael P Weiner
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
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16
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Tan Y, Tian T, Liu W, Zhu Z, J Yang C. Advance in phage display technology for bioanalysis. Biotechnol J 2016; 11:732-45. [PMID: 27061133 DOI: 10.1002/biot.201500458] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/30/2016] [Accepted: 03/15/2016] [Indexed: 11/06/2022]
Abstract
Phage display technology has emerged as a powerful tool for target gene expression and target-specific ligand selection. It is widely used to screen peptides, proteins and antibodies with the advantages of simplicity, high efficiency and low cost. A variety of targets, including ions, small molecules, inorganic materials, natural and biological polymers, nanostructures, cells, bacteria, and even tissues, have been demonstrated to generate specific binding ligands by phage display. Phages and target-specific ligands screened by phage display have been widely used as affinity reagents in therapeutics, diagnostics and biosensors. In this review, comparisons of different types of phage display systems are first presented. Particularly, microfluidic-based phage display, which enables screening with high throughput, high efficiency and integration, is highlighted. More importantly, we emphasize the advances in biosensors based on phages or phage-derived probes, including nonlytic phages, lytic phages, peptides or proteins screened by phage display, phage assemblies and phage-nanomaterial complexes. However, more efficient and higher throughput phage display methods are still needed to meet an explosion in demand for bioanalysis. Furthermore, screening of cyclic peptides and functional peptides will be the hotspot in bioanalysis.
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Affiliation(s)
- Yuyu Tan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Tian Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Wenli Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Zhi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
| | - Chaoyong J Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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17
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Park HS, Lee W, Nam YS. Elution dynamics of M13 bacteriophage bound to streptavidin immobilized in a microfluidic channel. BIOCHIP JOURNAL 2015. [DOI: 10.1007/s13206-016-0107-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Cusano AM, Causa F, Moglie RD, Falco N, Scognamiglio PL, Aliberti A, Vecchione R, Battista E, Marasco D, Savarese M, Raucci U, Rega N, Netti PA. Integration of binding peptide selection and multifunctional particles as tool-box for capture of soluble proteins in serum. J R Soc Interface 2015; 11:rsif.2014.0718. [PMID: 25100324 DOI: 10.1098/rsif.2014.0718] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this paper, we report on a general approach for the detection of a specific tumoural biomarker directly in serum. Such detection is made possible using a protein-binding peptide selected through an improved phage display technique and then conjugated to engineered microparticles (MPs). Protein biomarkers represent an unlimited source of information for non-invasive diagnostic and prognostic tests; MP-based assays are becoming largely used in manipulation of soluble biomarkers, but their direct use in serum is hampered by the complex biomolecular environment. Our technique overcomes the current limitations as it produces a selective MP--engineered with an antifouling layer--that 'captures' the relevant protein staying impervious to the background. Our system succeeds in fishing-out the human tumour necrosis factor alpha directly in serum with a high selectivity degree. Our method could have great impact in soluble protein manipulation and detection for a wide variety of diagnostic applications.
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Affiliation(s)
- Angela Maria Cusano
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy
| | - Filippo Causa
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples 'Federico II', Naples, Italy Department of Chemical and Materials Engineering and Industrial Production, University of Naples 'Federico II', Naples, Italy
| | - Raffaella Della Moglie
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy
| | - Nunzia Falco
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy
| | | | - Anna Aliberti
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy
| | - Raffaele Vecchione
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy
| | - Edmondo Battista
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples 'Federico II', DFM-Scarl, Naples, Italy
| | - Marika Savarese
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy Department of Chemical Science, University of Naples 'Federico II', Naples, Italy
| | - Umberto Raucci
- Department of Chemical Science, University of Naples 'Federico II', Naples, Italy
| | - Nadia Rega
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples 'Federico II', Naples, Italy Department of Chemical Science, University of Naples 'Federico II', Naples, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia, Naples, Italy Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples 'Federico II', Naples, Italy Department of Chemical and Materials Engineering and Industrial Production, University of Naples 'Federico II', Naples, Italy
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19
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Che YJ, Wu HW, Hung LY, Liu CA, Chang HY, Wang K, Lee GB. An integrated microfluidic system for screening of phage-displayed peptides specific to colon cancer cells and colon cancer stem cells. BIOMICROFLUIDICS 2015; 9:054121. [PMID: 26543513 PMCID: PMC4608964 DOI: 10.1063/1.4933067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 09/30/2015] [Indexed: 05/15/2023]
Abstract
Affinity reagents recognizing biomarkers specifically are essential components of clinical diagnostics and target therapeutics. However, conventional methods for screening of these reagents often have drawbacks such as large reagent consumption, the labor-intensive or time-consuming procedures, and the involvement of bulky or expensive equipment. Alternatively, microfluidic platforms could potentially automate the screening process within a shorter period of time and reduce reagent and sample consumption dramatically. It has been demonstrated recently that a subpopulation of tumor cells known as cancer stem cells possess high drug resistance and proliferation potential and are regarded as the main cause of metastasis. Therefore, a peptide that recognizes cancer stem cells and differentiates them from other cancer cells will be extremely useful in early diagnosis and target therapy. This study utilized M13 phage display technology to identify peptides that bind, respectively, to colon cancer cells and colon cancer stem cells using an integrated microfluidic system. In addition to positive selection, a negative selection process was integrated on the chip to achieve the selection of peptides of high affinity and specificity. We successfully screened three peptides specific to colon cancer cells and colon cancer stem cells, namely, HOLC-1, HOLC-2, and COLC-1, respectively, and their specificity was measured by the capture rate between target, control, and other cell lines. The capture rates are 43.40 ± 7.23%, 45.16 ± 7.12%, and 49.79 ± 5.34% for colon cancer cells and colon cancer stem cells, respectively, showing a higher specificity on target cells than on control and other cell lines. The developed technique may be promising for early diagnosis of cancer cells and target therapeutics.
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Affiliation(s)
- Yu-Jui Che
- Department of Power Mechanical Engineering, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Huei-Wen Wu
- Department of Power Mechanical Engineering, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Lien-Yu Hung
- Department of Power Mechanical Engineering, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Ching-Ann Liu
- Nanomedicine Program and Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Hwan-You Chang
- Institute of Molecular Medicine, National Tsing Hua University , Hsinchu 30013, Taiwan
| | - Kuan Wang
- Nanomedicine Program and Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
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20
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Selection strategies for anticancer antibody discovery: searching off the beaten path. Trends Biotechnol 2015; 33:292-301. [PMID: 25819764 DOI: 10.1016/j.tibtech.2015.02.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 01/13/2023]
Abstract
Antibody-based drugs represent one of the most successful and promising therapeutic approaches in oncology. Large combinatorial phage antibody libraries are available for the identification of therapeutic antibodies and various technologies exist for their further conversion into multivalent and multispecific formats optimized for the desired pharmacokinetics and the pathological context. However, there is no technology for antigen profiling of intact tumors to identify tumor markers targetable with antibodies. Such constraints have led to a relative paucity of tumor-associated antigens for antibody targeting in oncology. Here we review novel approaches aimed at the identification of antibody-targetable, accessible antigens in intact tumors. We hope that such advanced selection approaches will be useful in the development of next-generation antibody therapies for cancer.
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21
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Wang CH, Weng CH, Che YJ, Wang K, Lee GB. Cancer cell-specific oligopeptides selected by an integrated microfluidic system from a phage display library for ovarian cancer diagnosis. Theranostics 2015; 5:431-42. [PMID: 25699101 PMCID: PMC4329505 DOI: 10.7150/thno.10891] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/07/2015] [Indexed: 12/03/2022] Open
Abstract
Ovarian cancer is one of the leading causes of female mortality worldwide. Unfortunately, there are currently few high-specificity candidate oligopeptide targeting agents that can be used for early diagnosis of this cancer. It has been suggested that cancer-specific oligopeptides could be screened from a phage display library. However, conventional methods are tedious, labor-intensive, and time consuming. Therefore, a novel, integrated microfluidic system was developed to automate the entire screening process for ovarian cancer cell-specific oligopeptides. An oligopeptide screened with microfluidic chip-based technique was demonstrated to have high affinity to ovarian cancer cells and demonstrated relatively low binding to other cancer cells, indicating a high specificity. Furthermore, the developed method consumed relatively low volumes of samples and reagents; only 70 μL of reactant was used within the whole experimental process. Each panning process was also significantly shortened to only 7.5 hours. Therefore, the screened oligopeptide could be used to isolate ovarian cancer cells in a rapid manner, thus greatly expediting the diagnosis and its application as oligopeptide targeting agent for theranostics of this cancer.
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22
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Cho M, Oh SS, Nie J, Stewart R, Radeke MJ, Eisenstein M, Coffey PJ, Thomson JA, Soh HT. Array-based discovery of aptamer pairs. Anal Chem 2014; 87:821-8. [PMID: 25495696 PMCID: PMC4287840 DOI: 10.1021/ac504076k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Affinity
reagent pairs that recognize distinct epitopes on a target
protein can greatly improve the sensitivity and specificity of molecular
detection. Importantly, such pairs can be conjugated to generate reagents
that achieve two-site “bidentate” target recognition,
with affinities greatly exceeding either monovalent component. DNA
aptamers are especially well-suited for such constructs, because they
can be linked via standard synthesis techniques without requiring
chemical conjugation. Unfortunately, aptamer pairs are difficult to
generate, primarily because conventional selection methods preferentially
yield aptamers that recognize a dominant “hot spot”
epitope. Our array-based discovery platform for multivalent aptamers
(AD-MAP) overcomes this problem to achieve efficient discovery of
aptamer pairs. We use microfluidic selection and high-throughput sequencing
to obtain an enriched pool of aptamer sequences. Next, we synthesize
a custom array based on these sequences, and perform parallel affinity
measurements to identify the highest-affinity aptamer for the target
protein. We use this aptamer to form complexes that block the primary
binding site on the target, and then screen the same array with these
complexes to identify aptamers that bind secondary epitopes. We used
AD-MAP to discover DNA aptamer pairs that bind distinct sites on human
angiopoietin-2 with high affinities, even in undiluted serum. To the
best of our knowledge, this is the first work to discover new aptamer
pairs using arrays. We subsequently conjugated these aptamers with
a flexible linker to construct ultra-high-affinity bidentate reagents,
with equilibrium dissociation constants as low as 97 pM: >200-fold
better than either component aptamer. Functional studies confirm that
both aptamers critically contribute to this ultrahigh affinity, highlighting
the promise of such reagents for research and clinical use.
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Affiliation(s)
- Minseon Cho
- Department of Mechanical Engineering, University of California-Santa Barbara , Santa Barbara, California 93106, United States
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23
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Tokel O, Inci F, Demirci U. Advances in plasmonic technologies for point of care applications. Chem Rev 2014; 114:5728-52. [PMID: 24745365 PMCID: PMC4086846 DOI: 10.1021/cr4000623] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Onur Tokel
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
| | - Fatih Inci
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford
for Cancer Early Detection, Palo
Alto, California 94304, United States
| | - Utkan Demirci
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
- Division of Infectious Diseases, Brigham
and Women’s Hospital, Harvard Medical
School, Boston, Massachusetts 02115, United States
- Harvard-MIT
Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford
for Cancer Early Detection, Palo
Alto, California 94304, United States
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24
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Houlihan G, Gatti-Lafranconi P, Kaltenbach M, Lowe D, Hollfelder F. An experimental framework for improved selection of binding proteins using SNAP display. J Immunol Methods 2014; 405:47-56. [DOI: 10.1016/j.jim.2014.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/15/2013] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
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25
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Maaß A, Heiseler T, Maaß F, Fritz J, Hofmeyer T, Glotzbach B, Becker S, Kolmar H. A general strategy for antibody library screening via conversion of transient target binding into permanent reporter deposition. Protein Eng Des Sel 2014; 27:41-7. [PMID: 24402333 DOI: 10.1093/protein/gzt060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report here a generally applicable method for the selective covalent attachment of a reporter molecule to a replicating entity that allows one to obtain specific binders from a single round of library screening. We show that selective biotinylation of phage particles displaying a binder to any given target can be achieved by application of a coupled enzyme reaction on the surface of the target-binding phage particles that includes a peroxidase, an oxidase and a catalase. Due to the covalent linkage of biotin together with the tight and stable interaction of biotin with streptavidin, very stringent wash conditions for removal of nonspecific binders can be applied. The method termed (3)CARD (triple catalytic reporter deposition) was successfully applied to single-round screening of a phage display library of camelid single-domain antibodies against three different target proteins.
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Affiliation(s)
- Alexander Maaß
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
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26
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Close DW, Ferrara F, Dichosa AEK, Kumar S, Daughton AR, Daligault HE, Reitenga KG, Velappan N, Sanchez TC, Iyer S, Kiss C, Han CS, Bradbury ARM. Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. BMC Microbiol 2013; 13:270. [PMID: 24279426 PMCID: PMC3907030 DOI: 10.1186/1471-2180-13-270] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/21/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Single cell genomics has revolutionized microbial sequencing, but complete coverage of genomes in complex microbiomes is imperfect due to enormous variation in organismal abundance and amplification bias. Empirical methods that complement rapidly improving bioinformatic tools will improve characterization of microbiomes and facilitate better genome coverage for low abundance microbes. METHODS We describe a new approach to sequencing individual species from microbiomes that combines antibody phage display against intact bacteria with fluorescence activated cell sorting (FACS). Single chain (scFv) antibodies are selected using phage display against a bacteria or microbial community, resulting in species-specific antibodies that can be used in FACS for relative quantification of an organism in a community, as well as enrichment or depletion prior to genome sequencing. RESULTS We selected antibodies against Lactobacillus acidophilus and demonstrate a FACS-based approach for identification and enrichment of the organism from both laboratory-cultured and commercially derived bacterial mixtures. The ability to selectively enrich for L. acidophilus when it is present at a very low abundance (<0.2%) leads to complete (>99.8%) de novo genome coverage whereas the standard single-cell sequencing approach is incomplete (<68%). We show that specific antibodies can be selected against L. acidophilus when the monoculture is used as antigen as well as when a community of 10 closely related species is used demonstrating that in principal antibodies can be generated against individual organisms within microbial communities. CONCLUSIONS The approach presented here demonstrates that phage-selected antibodies against bacteria enable identification, enrichment of rare species, and depletion of abundant organisms making it tractable to virtually any microbe or microbial community. Combining antibody specificity with FACS provides a new approach for characterizing and manipulating microbial communities prior to genome sequencing.
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Affiliation(s)
- Devin W Close
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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Liu Y, Barua D, Liu P, Wilson BS, Oliver JM, Hlavacek WS, Singh AK. Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. PLoS One 2013; 8:e60159. [PMID: 23544131 PMCID: PMC3609784 DOI: 10.1371/journal.pone.0060159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
Heterogeneity in responses of cells to a stimulus, such as a pathogen or allergen, can potentially play an important role in deciding the fate of the responding cell population and the overall systemic response. Measuring heterogeneous responses requires tools capable of interrogating individual cells. Cell signaling studies commonly do not have single-cell resolution because of the limitations of techniques used such as Westerns, ELISAs, mass spectrometry, and DNA microarrays. Microfluidics devices are increasingly being used to overcome these limitations. Here, we report on a microfluidic platform for cell signaling analysis that combines two orthogonal single-cell measurement technologies: on-chip flow cytometry and optical imaging. The device seamlessly integrates cell culture, stimulation, and preparation with downstream measurements permitting hands-free, automated analysis to minimize experimental variability. The platform was used to interrogate IgE receptor (FcεRI) signaling, which is responsible for triggering allergic reactions, in RBL-2H3 cells. Following on-chip crosslinking of IgE-FcεRI complexes by multivalent antigen, we monitored signaling events including protein phosphorylation, calcium mobilization and the release of inflammatory mediators. The results demonstrate the ability of our platform to produce quantitative measurements on a cell-by-cell basis from just a few hundred cells. Model-based analysis of the Syk phosphorylation data suggests that heterogeneity in Syk phosphorylation can be attributed to protein copy number variations, with the level of Syk phosphorylation being particularly sensitive to the copy number of Lyn.
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Affiliation(s)
- Yanli Liu
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Dipak Barua
- Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Peng Liu
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Bridget S. Wilson
- Department of Pathology and Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Janet M. Oliver
- Department of Pathology and Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - William S. Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anup K. Singh
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
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Sørensen MD, Melchjorsen CJ, Mandrup OA, Kristensen P. Raising antibodies against circulating foetal cells from maternal peripheral blood. Prenat Diagn 2013; 33:284-91. [PMID: 23390071 DOI: 10.1002/pd.4060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Cells of foetal origin circulating in the maternal peripheral bloodstream present a unique source for non-invasive prenatal diagnostics. The aims of this study were to raise antibodies against identified circulating foetal cells from the maternal blood, test the properties of these antibodies and to determine the foetal cell type recognised by the antibodies. METHOD Cells from a male foetus were identified in a maternal blood sample by FISH analysis of the X- and Y- chromosomes. The identified cells were subjected to phage display selection using a novel single cell selection strategy. Selected antibodies were tested by immunocytochemistry on foetal and adult tissue arrays, an endothelial cell line, and peripheral blood mononuclear cells. RESULTS Three identified foetal cells subjected to antibody selection, yielded a total of 12 antibodies. Three antibodies gave distinct staining patterns on tissue arrays, and endothelial cells. One antibody, SF1.3, shows specific staining of a subpopulation of peripheral blood mononuclear cells, including a fraction of CD34 positive cells. CONCLUSION These findings indicate that the identified foetal cells could have been progenitor cells of haematopoietic origin. The antibody SF1.3 could be a potential tool toward non-invasive prenatal diagnostics.
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Ahmad KM, Xiao Y, Soh HT. Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution. Nucleic Acids Res 2012; 40:11777-83. [PMID: 23042245 PMCID: PMC3526301 DOI: 10.1093/nar/gks899] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Multivalent molecular interactions can be exploited to dramatically enhance the performance of an affinity reagent. The enhancement in affinity and specificity achieved with a multivalent construct depends critically on the effectiveness of the scaffold that joins the ligands, as this determines their positions and orientations with respect to the target molecule. Currently, no generalizable design rules exist for construction of an optimal multivalent ligand for targets with known structures, and the design challenge remains an insurmountable obstacle for the large number of proteins whose structures are not known. As an alternative to such design-based strategies, we report here a directed evolution-based method for generating optimal bivalent aptamers. To demonstrate this approach, we fused two thrombin aptamers with a randomized DNA sequence and used a microfluidic in vitro selection strategy to isolate scaffolds with exceptionally high affinities. Within five rounds of selection, we generated a bivalent aptamer that binds thrombin with an apparent dissociation constant (Kd) <10 pM, representing a ∼200-fold improvement in binding affinity over the monomeric aptamers and a ∼15-fold improvement over the best designed bivalent construct. The process described here can be used to produce high-affinity multivalent aptamers and could potentially be adapted to other classes of biomolecules.
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Affiliation(s)
- Kareem M Ahmad
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 91306, USA
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Antibody phage display libraries: contributions to oncology. Int J Mol Sci 2012; 13:5420-5440. [PMID: 22754305 PMCID: PMC3382779 DOI: 10.3390/ijms13055420] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 04/05/2012] [Accepted: 04/24/2012] [Indexed: 12/16/2022] Open
Abstract
Since the advent of phage display technology, dating back to 1985, antibody libraries displayed on filamentous phage surfaces have been used to identify specific binders for many different purposes, including the recognition of tumors. Phage display represents a high-throughput technique for screening billions of random fusion antibodies against virtually any target on the surface or inside cancer cells, or even soluble markers found in patient serum. Many phage display derived binders targeting important tumor markers have been identified. Selection directed to tumoral cells’ surfaces lead to the identification of unknown tumoral markers. Also the improvement of methods that require smaller amounts of cells has opened the possibility to use this approach on patient samples. Robust techniques combining an antibody library displayed on the phage surface and protein microarray allowed the identification of auto antibodies recognized by patient sera. Many Ab molecules directly or indirectly targeting angiogenesis have been identified, and one of them, ramucirumab, has been tested in 27 phase I–III clinical trials in a broad array of cancers. Examples of such antibodies will be discussed here with emphasis on those used as probes for molecular imaging and other clinical trials.
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Cung K, Slater RL, Cui Y, Jones SE, Ahmad H, Naik RR, McAlpine MC. Rapid, multiplexed microfluidic phage display. LAB ON A CHIP 2012; 12:562-5. [PMID: 22182980 DOI: 10.1039/c2lc21129g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The development of a method for high-throughput, automated proteomic screening could impact areas ranging from fundamental molecular interactions to the discovery of novel disease markers and therapeutic targets. Surface display techniques allow for efficient handling of large molecular libraries in small volumes. In particular, phage display has emerged as a powerful technology for selecting peptides and proteins with enhanced, target-specific binding affinities. Yet, the process becomes cumbersome and time-consuming when multiple targets are involved. Here we demonstrate for the first time a microfluidic chip capable of identifying high affinity phage-displayed peptides for multiple targets in just a single round and without the need for bacterial infection. The chip is shown to be able to yield well-established control consensus sequences while simultaneously identifying new sequences for clinically important targets. Indeed, the confined parameters of the device allow not only for highly controlled assay conditions but also introduce a significant time-reduction to the phage display process. We anticipate that this easily-fabricated, disposable device has the potential to impact areas ranging from fundamental studies of protein, peptide, and molecular interactions, to applications such as fully automated proteomic screening.
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Affiliation(s)
- Kellye Cung
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
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Ahmad KM, Oh SS, Kim S, McClellen FM, Xiao Y, Soh HT. Probing the limits of aptamer affinity with a microfluidic SELEX platform. PLoS One 2011; 6:e27051. [PMID: 22110600 PMCID: PMC3215713 DOI: 10.1371/journal.pone.0027051] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 10/10/2011] [Indexed: 01/14/2023] Open
Abstract
Nucleic acid-based aptamers offer many potential advantages relative to antibodies and other protein-based affinity reagents, including facile chemical synthesis, reversible folding, improved thermal stability and lower cost. However, their selection requires significant time and resources and selections often fail to yield molecules with affinities sufficient for molecular diagnostics or therapeutics. Toward a selection technique that can efficiently and reproducibly generate high performance aptamers, we have developed a microfluidic selection process (M-SELEX) that can be used to obtain high affinity aptamers against diverse protein targets. Here, we isolated DNA aptamers against three protein targets with different isoelectric points (pI) using a common protocol. After only three rounds of selection, we discovered novel aptamer sequences that bind to platelet derived growth factor B (PDGF-BB; pI = 9.3) and thrombin (pI = 8.3) with respective dissociation constants (Kd) of 0.028 nM and 0.33 nM, which are both superior to previously reported aptamers against these targets. In parallel, we discovered a new aptamer that binds to apolipoprotein E3 (ApoE; pI = 5.3) with a Kd of 3.1 nM. Furthermore, we observe that the net protein charge may exert influence on the affinity of the selected aptamers. To further explore this relationship, we performed selections against PDGF-BB under different pH conditions using the same selection protocol, and report an inverse correlation between protein charge and aptamer Kd.
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Affiliation(s)
- Kareem M. Ahmad
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Seung Soo Oh
- Materials Department, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Seon Kim
- Department of Electrical and Computer Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Forrest M. McClellen
- Chemistry and Biochemistry Department, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Yi Xiao
- Materials Department, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail: (YX); (HTS)
| | - H. Tom Soh
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
- Materials Department, University of California Santa Barbara, Santa Barbara, California, United States of America
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail: (YX); (HTS)
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Oh SS, Ahmad KM, Cho M, Kim S, Xiao Y, Soh HT. Improving aptamer selection efficiency through volume dilution, magnetic concentration, and continuous washing in microfluidic channels. Anal Chem 2011; 83:6883-9. [PMID: 21774453 PMCID: PMC3165111 DOI: 10.1021/ac201269f] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The generation of nucleic acid aptamers with high affinity typically entails a time-consuming, iterative process of binding, separation, and amplification. It would therefore be beneficial to develop an efficient selection strategy that can generate these high-quality aptamers rapidly, economically, and reproducibly. Toward this goal, we have developed a method that efficiently generates DNA aptamers with slow off-rates. This methodology, called VDC-MSELEX, pairs the volume dilution challenge process with microfluidic separation for magnetic bead-assisted aptamer selection. This method offers improved aptamer selection efficiencies through the application of highly stringent selection conditions: it retrieves a small number (<10(6)) of magnetic beads suspended in a large volume (>50 mL) and concentrates them into a microfluidic chamber (8 μL) with minimal loss for continuous washing. We performed three rounds of the VDC-MSELEX using streptavidin (SA) as the target and obtained new DNA aptamer sequences with low nanomolar affinity that specifically bind to the SA proteins.
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Affiliation(s)
- Seung Soo Oh
- Materials Department, University of California, Santa Barbara, CA 93106
| | - Kareem M. Ahmad
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106
| | - Minseon Cho
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Seon Kim
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106
| | - Yi Xiao
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - H. Tom Soh
- Materials Department, University of California, Santa Barbara, CA 93106
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
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Olson CA, Adams JD, Takahashi TT, Qi H, Howell SM, Wu TT, Roberts RW, Sun R, Soh HT. Rapid mRNA-Display Selection of an IL-6 Inhibitor Using Continuous-Flow Magnetic Separation. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Olson CA, Adams JD, Takahashi TT, Qi H, Howell SM, Wu TT, Roberts RW, Sun R, Soh HT. Rapid mRNA-display selection of an IL-6 inhibitor using continuous-flow magnetic separation. Angew Chem Int Ed Engl 2011; 50:8295-8. [PMID: 21761516 DOI: 10.1002/anie.201101149] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Indexed: 11/10/2022]
Affiliation(s)
- C Anders Olson
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, USA
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36
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Ferguson BS, Buchsbaum SF, Wu TT, Hsieh K, Xiao Y, Sun R, Soh HT. Genetic analysis of H1N1 influenza virus from throat swab samples in a microfluidic system for point-of-care diagnostics. J Am Chem Soc 2011; 133:9129-35. [PMID: 21561070 PMCID: PMC3110979 DOI: 10.1021/ja203981w] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to obtain sequence-specific genetic information about rare target organisms directly from complex biological samples at the point-of-care would transform many areas of biotechnology. Microfluidics technology offers compelling tools for integrating multiple biochemical processes in a single device, but despite significant progress, only limited examples have shown specific, genetic analysis of clinical samples within the context of a fully integrated, portable platform. Herein we present the Magnetic Integrated Microfluidic Electrochemical Detector (MIMED) that integrates sample preparation and electrochemical sensors in a monolithic disposable device to detect RNA-based virus directly from throat swab samples. By combining immunomagnetic target capture, concentration, and purification, reverse-transcriptase polymerase chain reaction (RT-PCR) and single-stranded DNA (ssDNA) generation in the sample preparation chamber, as well as sequence-specific electrochemical DNA detection in the electrochemical cell, we demonstrate the detection of influenza H1N1 in throat swab samples at loads as low as 10 TCID(50), 4 orders of magnitude below the clinical titer for this virus. Given the availability of affinity reagents for a broad range of pathogens, our system offers a general approach for multitarget diagnostics at the point-of-care.
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Wang J, Liu Y, Teesalu T, Sugahara KN, Kotamrajua VR, Adams JD, Ferguson BS, Gong Q, Oh SS, Csordas AT, Cho M, Ruoslahti E, Xiao Y, Soh HT. Selection of phage-displayed peptides on live adherent cells in microfluidic channels. Proc Natl Acad Sci U S A 2011; 108:6909-14. [PMID: 21486998 PMCID: PMC3084056 DOI: 10.1073/pnas.1014753108] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Affinity reagents that bind to specific molecular targets are an essential tool for both diagnostics and targeted therapeutics. There is a particular need for advanced technologies for the generation of reagents that specifically target cell-surface markers, because transmembrane proteins are notoriously difficult to express in recombinant form. We have previously shown that microfluidics offers many advantages for generating affinity reagents against purified protein targets, and we have now significantly extended this approach to achieve successful in vitro selection of T7 phage-displayed peptides that recognize markers expressed on live, adherent cells within a microfluidic channel. As a model, we have targeted neuropilin-1 (NRP-1), a membrane-bound receptor expressed at the surface of human prostate carcinoma cells that plays central roles in angiogenesis, cell migration, and invasion. We show that, compared to conventional biopanning methods, microfluidic selection enables more efficient discovery of peptides with higher affinity and specificity by providing controllable and reproducible means for applying stringent selection conditions against minimal amounts of target cells without loss. Using our microfluidic system, we isolate peptide sequences with superior binding affinity and specificity relative to the well known NRP-1-binding RPARPAR peptide. As such microfluidic systems can be used with a wide range of biocombinatorial libraries and tissue types, we believe that our method represents an effective approach toward efficient biomarker discovery from patient samples.
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Affiliation(s)
- Jinpeng Wang
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Yanli Liu
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
- Department of Materials, University of California, Santa Barbara, CA 93106
| | - Tambet Teesalu
- Vascular Mapping Laboratory, Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106
| | - Kazuki N. Sugahara
- Vascular Mapping Laboratory, Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106
| | - Venkata Ramana Kotamrajua
- Vascular Mapping Laboratory, Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106
| | - Jonathan D. Adams
- Department of Physics, University of California, Santa Barbara, CA 93106
| | - Brian S. Ferguson
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Qiang Gong
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106; and
| | - Seung Soo Oh
- Department of Materials, University of California, Santa Barbara, CA 93106
| | - Andrew T. Csordas
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106; and
| | - Minseon Cho
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Erkki Ruoslahti
- Vascular Mapping Laboratory, Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Yi Xiao
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
- Department of Materials, University of California, Santa Barbara, CA 93106
| | - H. Tom Soh
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
- Department of Materials, University of California, Santa Barbara, CA 93106
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Cochran R, Cochran F. Phage display and molecular imaging: expanding fields of vision in living subjects. Biotechnol Genet Eng Rev 2011; 27:57-94. [PMID: 21415893 DOI: 10.1080/02648725.2010.10648145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In vivo molecular imaging enables non-invasive visualization of biological processes within living subjects, and holds great promise for diagnosis and monitoring of disease. The ability to create new agents that bind to molecular targets and deliver imaging probes to desired locations in the body is critically important to further advance this field. To address this need, phage display, an established technology for the discovery and development of novel binding agents, is increasingly becoming a key component of many molecular imaging research programs. This review discusses the expanding role played by phage display in the field of molecular imaging with a focus on in vivo applications. Furthermore, new methodological advances in phage display that can be directly applied to the discovery and development of molecular imaging agents are described. Various phage library selection strategies are summarized and compared, including selections against purified target, intact cells, and ex vivo tissue, plus in vivo homing strategies. An outline of the process for converting polypeptides obtained from phage display library selections into successful in vivo imaging agents is provided, including strategies to optimize in vivo performance. Additionally, the use of phage particles as imaging agents is also described. In the latter part of the review, a survey of phage-derived in vivo imaging agents is presented, and important recent examples are highlighted. Other imaging applications are also discussed, such as the development of peptide tags for site-specific protein labeling and the use of phage as delivery agents for reporter genes. The review concludes with a discussion of how phage display technology will continue to impact both basic science and clinical applications in the field of molecular imaging.
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Affiliation(s)
- R Cochran
- Department of Bioengineering, Cancer Center, Bio-X Program, Stanford University, Stanford CA, USA
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Paegel BM. Microfluidic landscapes for evolution. Curr Opin Chem Biol 2010; 14:568-73. [PMID: 20800535 DOI: 10.1016/j.cbpa.2010.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 07/28/2010] [Accepted: 07/29/2010] [Indexed: 01/11/2023]
Abstract
Evolution at its heart is an iterative algorithm composed of three steps: selection, amplification and mutagenesis. This algorithm can be applied to complex inputs such as populations of whole organisms and viruses, or mixtures of bare nucleic acids and proteins. The output is the same: evolutionary adaptation of new and improved function subject to selection. Recent breakthroughs in microfluidic technology have introduced automation and process monitoring to in vitro evolution, and reproducible preparation of emulsions and other multi-phase reaction landscapes. It is at this intersection of compartmentalization and in vitro evolution where miniaturization is again redefining experimental design in contemporary chemistry and biology.
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Affiliation(s)
- Brian M Paegel
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
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40
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Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc Natl Acad Sci U S A 2010; 107:15373-8. [PMID: 20705898 DOI: 10.1073/pnas.1009331107] [Citation(s) in RCA: 190] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We describe the integration of microfluidic selection with high-throughput DNA sequencing technology for rapid and efficient discovery of nucleic acid aptamers. The Quantitative Selection of Aptamers through Sequencing method tracks the copy number and enrichment-fold of more than 10 million individual sequences through multiple selection rounds, enabling the identification of high-affinity aptamers without the need for the pool to fully converge to a small number of sequences. Importantly, this method allows the discrimination of sequences that arise from experimental biases rather than true high-affinity target binding. As a demonstration, we have identified aptamers that specifically bind to PDGF-BB protein with K(d) < 3 nM within 3 rounds. Furthermore, we show that the aptamers identified by Quantitative Selection of Aptamers through Sequencing have approximately 3-8-fold higher affinity and approximately 2-4-fold higher specificity relative to those discovered through conventional cloning methods. Given that many biocombinatorial libraries are encoded with nucleic acids, we extrapolate that our method may be extended to other types of libraries for a range of molecular functions.
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Affiliation(s)
- Susan L Deutscher
- Biochemistry Department, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri 65211, USA.
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Csordas A, Gerdon A, Adams J, Qian J, Oh S, Xiao Y, Soh H. Detection of Proteins in Serum by Micromagnetic Aptamer PCR (MAP) Technology. Angew Chem Int Ed Engl 2010; 49:355-8. [DOI: 10.1002/anie.200904846] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Andrew Csordas
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara (USA)
| | | | - Jonathan D. Adams
- Department of Physics, University of California, Santa Barbara (USA)
| | | | - Seung Soo Oh
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
| | - Yi Xiao
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
| | - H. Tom Soh
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
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Mark D, Haeberle S, Roth G, Von Stetten F, Zengerle R. Microfluidic Lab-on-a-Chip Platforms: Requirements, Characteristics and Applications. MICROFLUIDICS BASED MICROSYSTEMS 2010. [DOI: 10.1007/978-90-481-9029-4_17] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Mark D, Haeberle S, Roth G, von Stetten F, Zengerle R. Microfluidic lab-on-a-chip platforms: requirements, characteristics and applications. Chem Soc Rev 2010; 39:1153-82. [PMID: 20179830 DOI: 10.1039/b820557b] [Citation(s) in RCA: 765] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel Mark
- HSG-IMIT-Institut für Mikro- und Informationstechnik, Wilhelm-Schickard-Strasse 10, 78052 Villingen-Schwenningen, Germany
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Csordas A, Gerdon A, Adams J, Qian J, Oh S, Xiao Y, Soh H. Detection of Proteins in Serum by Micromagnetic Aptamer PCR (MAP) Technology. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Andrew Csordas
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara (USA)
| | | | - Jonathan D. Adams
- Department of Physics, University of California, Santa Barbara (USA)
| | | | - Seung Soo Oh
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
| | - Yi Xiao
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
| | - H. Tom Soh
- Materials Department, Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106 (USA)
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Adams JD, Tom Soh H. Perspectives on utilizing unique features of microfluidics technology for particle and cell sorting. ACTA ACUST UNITED AC 2009; 14:331-340. [PMID: 20161387 DOI: 10.1016/j.jala.2009.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Sample preparation is often the most tedious and demanding step in an assay, but it also plays an essential role in determining the quality of results. As biological questions and analytical methods become increasingly sophisticated, there is a rapidly growing need for systems that can reliably and reproducibly separate cells and particles with high purity, throughput and recovery. Microfluidics technology represents a compelling approach in this regard, allowing precise control of separation forces for high performance separation in inexpensive, or even disposable, devices. In addition, microfluidics technology enables the fabrication of arrayed and integrated systems that operate either in parallel or in tandem, in a capacity that would be difficult to achieve in macro-scale systems. In this report, we use recent examples from our work to illustrate the potential of microfluidic cell- and particle-sorting devices. We demonstrate the potential of chip-based high-gradient magnetophoresis that enable high-purity separation through reversible trapping of target particles paired with high-stringency washing with minimal loss. We also describe our work in the development of devices that perform simultaneous multi-target sorting, either through precise control of magnetic and fluidic forces or through the integration of multiple actuation forces into a single monolithic device. We believe that such devices may serve as a powerful "front-end" module of highly integrated analytical platforms capable of providing actionable diagnostic information directly from crude, unprocessed samples - the success of such systems may hold the key to advancing point-of-care diagnostics and personalized medicine.
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Affiliation(s)
- Jonathan D Adams
- Department of Physics, University of California, Santa Barbara, CA, 93106, USA
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