1
|
Wahid B, Tiwana MS. Bacteriophage-based bioassays: an expected paradigm shift in microbial diagnostics. Future Microbiol 2024; 19:811-824. [PMID: 38900594 PMCID: PMC11290765 DOI: 10.2217/fmb-2023-0246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/01/2024] [Indexed: 06/22/2024] Open
Abstract
Bacteriophages, as abundant and specific agents, hold significant promise as a solution to combat the growing threat of antimicrobial resistance. Their unique ability to selectively lyse bacterial cells without harming humans makes them a compelling alternative to traditional antibiotics and point-of-care diagnostics. The article reviews the current landscape of diagnostic technologies, identify gaps and highlight emerging possibilities demonstrates a comprehensive approach to advancing clinical diagnosis of microbial pathogens and covers an overview of existing phage-based bioassays. Overall, the provided data in this review effectively communicates the potential of bacteriophages in transforming therapeutic and diagnostic paradigms, offering a holistic perspective on the benefits and opportunities they present in combating microbial infections and enhancing public health.
Collapse
Affiliation(s)
- Braira Wahid
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton VIC Australia
| | | |
Collapse
|
2
|
Ntemafack A, Dzelamonyuy A, Nchinda G, Bopda Waffo A. Evolutionary Qβ Phage Displayed Nanotag Library and Peptides for Biosensing. Viruses 2023; 15:1414. [PMID: 37515102 PMCID: PMC10386108 DOI: 10.3390/v15071414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
We selected a novel biotin-binding peptide for sensing biotin, biotinylated proteins, and nucleotides. From a 15-mer library displayed on the RNA coliphage Qβ, a 15-amino acid long peptide (HGHGWQIPVWPWGQG) hereby referred to as a nanotag was identified to selectively bind biotin. The target selection was achieved through panning with elution by infection. The selected peptide was tested as a transducer for an immunogenic epitope of the foot-and-mouth disease virus (FMDV) on Qβ phage platform separated by a linker. The biotin-tag showed no significant influence on the affinity of the epitope to its cognate antibody (SD6). The nanotag-bound biotin selectively fused either to the C- or N-terminus of the epitope. The epitope would not bind or recognize SD6 while positioned at the N-terminus of the nanotag. Additionally, the biotin competed linearly with the SD6 antibody in a competitive ELISA. Competition assays using the selected recombinant phage itself as a probe or transducer enable the operationalization of this technology as a biosensor toolkit to sense and quantify SD6 analyte. Herein, the published Strep II nanotag (DVEWLDERVPLVET) was used as a control and has similar functionalities to our proposed novel biotin-tag thereby providing a new platform for developing devices for diagnostic purposes.
Collapse
Affiliation(s)
- Augustin Ntemafack
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA
| | - Aristide Dzelamonyuy
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA
| | - Godwin Nchinda
- Laboratory of Vaccinology and Biobanking, CIRCB BP 3077 Messa, Yaoundé P.O. Box 3077, Cameroon
- Department of Pharmaceutical Microbiology and Biotechnology, Nnamdi Azikiwe University, Awka 420110, Nigeria
- African Center of Excellence for Clinical and Translational Sciences (ACECTS), Yaoundé P.O. Box 13591, Cameroon
| | - Alain Bopda Waffo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA
| |
Collapse
|
3
|
Recombinant antibodies by phage display for bioanalytical applications. Biosens Bioelectron 2023; 222:114909. [PMID: 36462427 DOI: 10.1016/j.bios.2022.114909] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 10/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Antibody phage display, aimed at preparing antibodies to defined antigens, is a useful replacement for hybridoma technology. The phage system replaces all work stages that follow animal immunization with simple procedures for manipulating DNA and bacteria. It enables the time needed to generate stable antibody-producing clones to be shortened considerably, making the process noticeably cheaper. Antibodies prepared by phage display undergo several affinity selection steps and can be used as selective receptors in biosensors. This article briefly describes the techniques used in the making of phage antibodies to various antigens. The possibilities and prospects are discussed of using phage antibodies as selective agents in analytical systems, including biosensors.
Collapse
|
4
|
Tian L, Jackson K, Chan M, Saif A, He L, Didar TF, Hosseinidoust Z. Phage display for the detection, analysis, disinfection, and prevention of Staphylococcus aureus. SMART MEDICINE 2022; 1:e20220015. [PMID: 39188734 PMCID: PMC11235639 DOI: 10.1002/smmd.20220015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 09/25/2022] [Indexed: 08/28/2024]
Abstract
The World Health Organization has designated Staphylococcus aureus as a global health concern. This designation stems from the emergence of multiple drug-resistant strains that already account for hundreds of thousands of deaths globally. The development of novel treatment strategies to eradicate S. aureus or mitigate its pathogenic potential is desperately needed. In the effort to develop emerging strategies to combat S. aureus, phage display is uniquely positioned to assist in this endeavor. Leveraging bacteriophages, phage display enables researchers to better understand interactions between proteins and their antagonists. In doing so, researchers have the capacity to design novel inhibitors, biosensors, disinfectants, and immune modulators that can target specific S. aureus strains. In this review, we highlight how phage display can be leveraged to design novel solutions to combat S. aureus. We further discuss existing uses of phage display as a detection, intervention, and prevention platform against S. aureus and provide outlooks on how this technology can be optimized for future applications.
Collapse
Affiliation(s)
- Lei Tian
- Department of Chemical EngineeringMcMaster UniversityHamiltonOntarioCanada
| | - Kyle Jackson
- Department of Chemical EngineeringMcMaster UniversityHamiltonOntarioCanada
| | - Michael Chan
- Department of Chemical EngineeringMcMaster UniversityHamiltonOntarioCanada
| | - Ahmed Saif
- Department of Chemical EngineeringMcMaster UniversityHamiltonOntarioCanada
| | - Leon He
- Department of Chemical EngineeringMcMaster UniversityHamiltonOntarioCanada
| | - Tohid F. Didar
- School of Biomedical EngineeringMcMaster UniversityHamiltonOntarioCanada
- Michael DeGroote Institute for Infectious Disease ResearchMcMaster UniversityHamiltonOntarioCanada
- Department of Mechanical EngineeringMcMaster UniversityHamiltonOntarioCanada
| | - Zeinab Hosseinidoust
- Department of Chemical EngineeringMcMaster UniversityHamiltonOntarioCanada
- School of Biomedical EngineeringMcMaster UniversityHamiltonOntarioCanada
- Michael DeGroote Institute for Infectious Disease ResearchMcMaster UniversityHamiltonOntarioCanada
| |
Collapse
|
5
|
Al-Hindi RR, Teklemariam AD, Alharbi MG, Alotibi I, Azhari SA, Qadri I, Alamri T, Harakeh S, Applegate BM, Bhunia AK. Bacteriophage-Based Biosensors: A Platform for Detection of Foodborne Bacterial Pathogens from Food and Environment. BIOSENSORS 2022; 12:bios12100905. [PMID: 36291042 PMCID: PMC9599427 DOI: 10.3390/bios12100905] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 05/27/2023]
Abstract
Foodborne microorganisms are an important cause of human illness worldwide. Two-thirds of human foodborne diseases are caused by bacterial pathogens throughout the globe, especially in developing nations. Despite enormous developments in conventional foodborne pathogen detection methods, progress is limited by the assay complexity and a prolonged time-to-result. The specificity and sensitivity of assays for live pathogen detection may also depend on the nature of the samples being analyzed and the immunological or molecular reagents used. Bacteriophage-based biosensors offer several benefits, including specificity to their host organism, the detection of only live pathogens, and resistance to extreme environmental factors such as organic solvents, high temperatures, and a wide pH range. Phage-based biosensors are receiving increasing attention owing to their high degree of accuracy, specificity, and reduced assay times. These characteristics, coupled with their abundant supply, make phages a novel bio-recognition molecule in assay development, including biosensors for the detection of foodborne bacterial pathogens to ensure food safety. This review provides comprehensive information about the different types of phage-based biosensor platforms, such as magnetoelastic sensors, quartz crystal microbalance, and electrochemical and surface plasmon resonance for the detection of several foodborne bacterial pathogens from various representative food matrices and environmental samples.
Collapse
Affiliation(s)
- Rashad R. Al-Hindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Addisu D. Teklemariam
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mona G. Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ibrahim Alotibi
- Health Information Technology Department, Applied College, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sheren A. Azhari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Turki Alamri
- Family and Community Medicine Department, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bruce M. Applegate
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
- Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN 47907, USA
| | - Arun K. Bhunia
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
- Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN 47907, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
6
|
Bacteriophage Based Biosensors: Trends, Outcomes and Challenges. NANOMATERIALS 2020; 10:nano10030501. [PMID: 32168802 PMCID: PMC7153619 DOI: 10.3390/nano10030501] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 01/04/2023]
Abstract
Foodborne pathogens are one of the main concerns in public health, which can have a serious impact on community health and health care systems. Contamination of foods by bacterial pathogens (such as Staphylococcus aureus, Streptococci, Legionella pneumophila, Escherichia coli, Campylobacter jejuni and Salmonella typhimurium) results in human infection. A typical example is the current issue with Coronavirus, which has the potential for foodborne transmission and ruling out such concerns is often difficult. Although, the possible dissemination of such viruses via the food chain has been raised. Standard bacterial detection methods require several hours or even days to obtain the results, and the delay may result in food poisoning to eventuate. Conventional biochemical and microbiological tests are expensive, complex, time-consuming and not always reliable. Therefore, there are urgent demands to develop simple, cheap, quick, sensitive, specific and reliable tests for the detection of these pathogens in foods. Recent advances in smart materials, nanomaterials and biomolecular modeling have been a quantum leap in the development of biosensors in overcoming the limitations of a conventional standard laboratory assay. This research aimed to critically review bacteriophage-based biosensors, used for the detection of foodborne pathogens, as well as their trends, outcomes and challenges are discussed. The future perspective in the use of simple and cheap biosensors is in the development of lab-on-chips, and its availability in every household to test the quality of their food.
Collapse
|
7
|
Hierarchical Cluster Analysis of Medical Chemicals Detected by a Bacteriophage-Based Colorimetric Sensor Array. NANOMATERIALS 2020; 10:nano10010121. [PMID: 31936438 PMCID: PMC7023180 DOI: 10.3390/nano10010121] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/31/2019] [Accepted: 01/06/2020] [Indexed: 12/13/2022]
Abstract
M13 bacteriophage-based colorimetric sensors, especially multi-array sensors, have been successfully demonstrated to be a powerful platform for detecting extremely small amounts of target molecules. Colorimetric sensors can be fabricated easily using self-assembly of genetically engineered M13 bacteriophage which incorporates peptide libraries on its surface. However, the ability to discriminate many types of target molecules is still required. In this work, we introduce a statistical method to efficiently analyze a huge amount of numerical results in order to classify various types of target molecules. To enhance the selectivity of M13 bacteriophage-based colorimetric sensors, a multi-array sensor system can be an appropriate platform. On this basis, a pattern-recognizing multi-array biosensor platform was fabricated by integrating three types of sensors in which genetically engineered M13 bacteriophages (wild-, RGD-, and EEEE-type) were utilized as a primary building block. This sensor system was used to analyze a pattern of color change caused by a reaction between the sensor array and external substances, followed by separating the specific target substances by means of hierarchical cluster analysis. The biosensor platform could detect drug contaminants such as hormone drugs (estrogen) and antibiotics. We expect that the proposed biosensor system could be used for the development of a first-analysis kit, which would be inexpensive and easy to supply and could be applied in monitoring the environment and health care.
Collapse
|
8
|
Putra BR, Szot-Karpińska K, Kudła P, Yin H, Boswell JA, Squires AM, Da Silva MA, Edler KJ, Fletcher PJ, Parker SC, Marken F. Bacteriophage M13 Aggregation on a Microhole Poly(ethylene terephthalate) Substrate Produces an Anionic Current Rectifier: Sensitivity toward Anionic versus Cationic Guests. ACS APPLIED BIO MATERIALS 2019; 3:512-521. [DOI: 10.1021/acsabm.9b00952] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Budi Riza Putra
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor 16680, West Java, Indonesia
| | - Katarzyna Szot-Karpińska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Patryk Kudła
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Han Yin
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | - Jacob A. Boswell
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | - Adam M. Squires
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | | | - Karen J. Edler
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | - Philip J. Fletcher
- Material & Chemical Characterisation Facility MC2, University of Bath, Bath BA2 7AY, U.K
| | - Stephen C. Parker
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| | - Frank Marken
- Department of Chemistry, University of Bath, Claverton Down BA2 7AY, U.K
| |
Collapse
|
9
|
Lee K, Choi S, Kim C, Kang WS, Son W, Bae SC, Oh JW, Lee SK, Cha C. Implementation of Combinatorial Genetic and Microenvironmental Engineering to Microbial-Based Field-Deployable Microbead Biosensors for Highly Sensitive and Remote Chemical Detection. ACS Sens 2019; 4:2716-2723. [PMID: 31512857 DOI: 10.1021/acssensors.9b01183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bioreporters, microbial species genetically engineered to provide measurable signals in response to specific chemicals, have been widely investigated as sensors for biomedical and environmental monitoring. More specifically, the bioreporter encapsulated within a biocompatible material, such as a hydrogel that can provide a suitable microenvironment for its prolonged activity as well as efficient scalable production, has been viewed as a more broadly applicable mode of biosensors. In this study, alginate-based microbeads encapsulated with the bacterial bioreporter capable of expressing green fluorescence protein in response to nitro compounds (e.g., trinitrotoluene and dinitrotoluene) are developed as biosensors. To significantly enhance the sensitivity of the microbial-based microbead biosensors, "multifaceted" modification strategies are simultaneously employed: (1) multiple genetic modifications of the bioreporter, (2) tuning the physicomechanical properties of the encapsulating microbeads, (3) controlling the initial cell density within the microbeads, and (4) enrichment of nitro compounds inside microbeads via functional nanomaterials. These microbial and microenvironmental engineering approaches combine to significantly enhance the sensing capability, even allowing highly sensitive remote detection under a low-vapor phase. Thus, the strategy developed herein is expected to contribute to various cell-based biosensors.
Collapse
Affiliation(s)
| | | | - Chuntae Kim
- Department of Nano Fusion Technology, Pusan National University, Busan 46241, Korea
| | | | | | | | - Jin-Woo Oh
- Department of Nano Fusion Technology, Pusan National University, Busan 46241, Korea
| | | | | |
Collapse
|
10
|
Hanif A, Farooq R, Rehman MU, Khan R, Majid S, Ganaie MA. Aptamer based nanobiosensors: Promising healthcare devices. Saudi Pharm J 2019; 27:312-319. [PMID: 30976173 PMCID: PMC6438676 DOI: 10.1016/j.jsps.2018.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/22/2018] [Indexed: 12/20/2022] Open
Abstract
Nanobiosensors based on aptamer are extensively being studied as potent analytical tools in clinical analysis. These biosensors provide high sensitivity, fast response, specificity and desired portability in addition to simplicity and decreased cost compared to conventional methods. The purpose of this manuscript is to provide readers with an overview of current advances about electrochemical, electrochemiluminescent and photoelectrochemical aptasensors from the sea of available literature. These are mainly used for determination of protein-based biomarkers, especially for cancer diagnosis. Here in we have given special emphasis on nanosize-based aptasensors which have been reported to show considerable improvement in the analytical performance.
Collapse
Affiliation(s)
- Aamir Hanif
- City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region
| | - Rabia Farooq
- Department of Biochemistry, Govt Medical College (GMC) Srinagar, J&K 190010, India
| | - Muneeb U. Rehman
- Department of Biochemistry, Govt Medical College (GMC) Srinagar, J&K 190010, India
| | - Rehan Khan
- Nanotherapeutics, Institute of Nanoscience & Technology (DST-INST), Habitat Centre Phase 10, Mohali, Punjab, India
| | - Sabhiya Majid
- Department of Biochemistry, Govt Medical College (GMC) Srinagar, J&K 190010, India
| | - Majid Ahmad Ganaie
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| |
Collapse
|
11
|
Sarkes DA, Jahnke JP, Stratis-Cullum DN. Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates. J Vis Exp 2017. [PMID: 29286465 PMCID: PMC5755526 DOI: 10.3791/56061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Biopanning bacterial display libraries is a proven technique for peptide affinity reagent discovery for recognition of both biotic and abiotic targets. Peptide affinity reagents can be used for similar applications to antibodies, including sensing and therapeutics, but are more robust and able to perform in more extreme environments. Specific enrichment of peptide capture agents to a protein target of interest is enhanced using semi-automated sorting methods which improve binding and wash steps and therefore decrease the occurrence of false positive binders. A semi-automated sorting method is described herein for use with a commercial automated magnetic-activated cell sorting device with an unconstrained bacterial display sorting library expressing random 15-mer peptides. With slight modifications, these methods are extendable to other automated devices, other sorting libraries, and other organisms. A primary goal of this work is to provide a comprehensive methodology and expound the thought process applied in analyzing and minimizing the resulting pool of candidates. These techniques include analysis of on-cell binding using fluorescence-activated cell sorting (FACS), to assess affinity and specificity during sorting and in comparing individual candidates, and the analysis of peptide sequences to identify trends and consensus sequences for understanding and potentially improving the affinity to and specificity for the target of interest.
Collapse
Affiliation(s)
- Deborah A Sarkes
- Sensors and Electron Devices Directorate, US Army Research Laboratory;
| | - Justin P Jahnke
- Sensors and Electron Devices Directorate, US Army Research Laboratory
| | | |
Collapse
|
12
|
Zhao N, Spencer J, Schmitt MA, Fisk JD. Hyperthermostable binding molecules on phage: Assay components for point-of-care diagnostics for active tuberculosis infection. Anal Biochem 2017; 521:59-71. [DOI: 10.1016/j.ab.2016.12.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/25/2016] [Accepted: 12/23/2016] [Indexed: 11/24/2022]
|
13
|
Sarkes DA, Hurley MM, Stratis-Cullum DN. Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives. Molecules 2016; 21:E1504. [PMID: 27834872 PMCID: PMC6272918 DOI: 10.3390/molecules21111504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022] Open
Abstract
Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC) agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms. Here, we have discovered peptide affinity reagents against abrax, a derivative of abrin with reduced toxicity. Using on-cell Fluorescence Activated Cell Sorting (FACS) assays, we show that the peptides are highly selective for abrax over RiVax, a similar derivative of ricin originally designed as a vaccine, with significant structural homology to abrax. We rank the newly discovered peptides for strongest affinity and analyze three observed consensus sequences with varying affinity and specificity. The strongest (Tier 1) consensus was FWDTWF, which is highly aromatic and hydrophobic. To better understand the observed selectivity, we use the XPairIt peptide-protein docking protocol to analyze binding location predictions of the individual Tier 1 peptides and consensus on abrax and RiVax. The binding location profiles on the two proteins are quite distinct, which we determine is due to differences in pocket size, pocket environment (including hydrophobicity and electronegativity), and steric hindrance. This study provides a model system to show that peptide capture candidates can be quite selective for a structurally similar protein system, even without further maturation, and offers an in silico method of analysis for understanding binding and down-selecting candidates.
Collapse
Affiliation(s)
- Deborah A Sarkes
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Margaret M Hurley
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| |
Collapse
|
14
|
Zhang R, Zhang CJ, Feng G, Hu F, Wang J, Liu B. Specific Light-Up Probe with Aggregation-Induced Emission for Facile Detection of Chymase. Anal Chem 2016; 88:9111-7. [PMID: 27541711 DOI: 10.1021/acs.analchem.6b02073] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human chymases are important proteases abundant in mast cell granules. The elevated level of chymases and other serine proteases is closely related to inflammatory and immunoregulatory functions. Monitoring of the chymase level is very important, however, the existing methods remain limited and insufficient. In this work, a light-up probe of TPETH-2(CFTERD3) (where CFTERD is Cys-Phe-Thr-Glu-Arg-Asp) was developed for chymase detection. The probe has low fluorescent signal in aqueous media, but its solubility can be changed after hydrolysis by chymase, giving significant fluorescence turn-on with a high signal-to-noise (S/N) ratio. The probe has excellent selectivity to chymase compared to other proteins and can effectively differentiate chymase from other enzymes (e.g., chymotrypsin and trypsin) in the same family (E.C. 3.4.21). The detection limit is calculated to be 0.1 ng/mL in PBS buffer with a linear range of 0-9.0 ng/mL. A comparison study using TPETH-2(CFTERD2) as the probe reveals the importance of molecular design in realizing the high S/N ratio. TPETH-2(CFTERD3) thus represents a simple turn-on probe for chymase detection, with real-time and direct readout and also excellent sensitivity and selectivity.
Collapse
Affiliation(s)
- Ruoyu Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Chong-Jing Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Guangxue Feng
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Fang Hu
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Jigang Wang
- Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART) , Singapore 138602, Singapore
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 4 Engineering Drive 4, Singapore 117585, Singapore.,Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR) , 2 Fusionopolis Way, Innovis, Singapore 138634, Singapore
| |
Collapse
|
15
|
Wen AM, Steinmetz NF. Design of virus-based nanomaterials for medicine, biotechnology, and energy. Chem Soc Rev 2016; 45:4074-126. [PMID: 27152673 PMCID: PMC5068136 DOI: 10.1039/c5cs00287g] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review provides an overview of recent developments in "chemical virology." Viruses, as materials, provide unique nanoscale scaffolds that have relevance in chemical biology and nanotechnology, with diverse areas of applications. Some fundamental advantages of viruses, compared to synthetically programmed materials, include the highly precise spatial arrangement of their subunits into a diverse array of shapes and sizes and many available avenues for easy and reproducible modification. Here, we will first survey the broad distribution of viruses and various methods for producing virus-based nanoparticles, as well as engineering principles used to impart new functionalities. We will then examine the broad range of applications and implications of virus-based materials, focusing on the medical, biotechnology, and energy sectors. We anticipate that this field will continue to evolve and grow, with exciting new possibilities stemming from advancements in the rational design of virus-based nanomaterials.
Collapse
Affiliation(s)
- Amy M Wen
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA. and Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| |
Collapse
|
16
|
Kogot JM, Pennington JM, Sarkes DA, Kingery DA, Pellegrino PM, Stratis-Cullum DN. Screening and characterization of anti-SEB peptides using a bacterial display library and microfluidic magnetic sorting. J Mol Recognit 2015; 27:739-45. [PMID: 25319622 PMCID: PMC4274986 DOI: 10.1002/jmr.2400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 04/22/2014] [Accepted: 05/27/2014] [Indexed: 11/06/2022]
Abstract
Bacterial peptide display libraries enable the rapid and efficient selection of peptides that have high affinity and selectivity toward their targets. Using a 15-mer random library on the outer surface of Escherichia coli (E.coli), high-affinity peptides were selected against a staphylococcal enterotoxin B (SEB) protein after four rounds of biopanning. On-cell screening analysis of affinity and specificity were measured by flow cytometry and directly compared to the synthetic peptide, off-cell, using peptide-ELISA. DNA sequencing of the positive clones after four rounds of microfluidic magnetic sorting (MMS) revealed a common consensus sequence of (S/T)CH(Y/F)W for the SEB-binding peptides R338, R418, and R445. The consensus sequence in these bacterial display peptides has similar amino acid characteristics with SEB peptide sequences isolated from phage display. The Kd measured by peptide-ELISA off-cell was 2.4 nM for R418 and 3.0 nM for R445. The bacterial peptide display methodology using the semiautomated MMS resulted in the discovery of selective peptides with affinity for a food safety and defense threat. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Journal of Molecular Recognition published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Joshua M Kogot
- US Army Research Laboratory; Sensors and Electron Devices, Adelphi, MD, USA
| | | | | | | | | | | |
Collapse
|
17
|
Bernard JML, Francis MB. Chemical strategies for the covalent modification of filamentous phage. Front Microbiol 2014; 5:734. [PMID: 25566240 PMCID: PMC4274979 DOI: 10.3389/fmicb.2014.00734] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/04/2014] [Indexed: 01/16/2023] Open
Abstract
Historically filamentous bacteriophage have been known to be the workhorse of phage display due to their ability to link genotype to phenotype. More recently, the filamentous phage scaffold has proven to be powerful outside the realm of phage display technology in fields such as molecular imaging, cancer research and materials, and vaccine development. The ability of the virion to serve as a platform for a variety of applications heavily relies on the functionalization of the phage coat proteins with a wide variety of functionalities. Genetic modification of the coat proteins has been the most widely used strategy for functionalizing the virion; however, complementary chemical modification strategies can help to diversify the range of materials that can be developed. This review emphasizes the recent advances that have been made in the chemical modification of filamentous phage as well as some of the challenges that are involved in functionalizing the virion.
Collapse
Affiliation(s)
- Jenna M L Bernard
- Department of Chemistry, University of California at Berkeley Berkeley, CA, USA ; Materials Sciences Division - Lawrence Berkeley National Laboratories Berkeley, CA, USA
| | - Matthew B Francis
- Department of Chemistry, University of California at Berkeley Berkeley, CA, USA ; Materials Sciences Division - Lawrence Berkeley National Laboratories Berkeley, CA, USA
| |
Collapse
|
18
|
Ahmed N, Dhanapala P, Sadli N, Barrow CJ, Suphioglu C. Mimtags: the use of phage display technology to produce novel protein-specific probes. J Immunol Methods 2014; 405:121-9. [PMID: 24530568 DOI: 10.1016/j.jim.2014.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/04/2014] [Accepted: 02/04/2014] [Indexed: 11/16/2022]
Abstract
In recent times the use of protein-specific probes in the field of proteomics has undergone evolutionary changes leading to the discovery of new probing techniques. Protein-specific probes serve two main purposes: epitope mapping and detection assays. One such technique is the use of phage display in the random selection of peptide mimotopes (mimtags) that can tag epitopes of proteins, replacing the use of monoclonal antibodies in detection systems. In this study, phage display technology was used to screen a random peptide library with a biologically active purified human interleukin-4 receptor (IL-4R) and interleukin-13 (IL-13) to identify mimtag candidates that interacted with these proteins. Once identified, the mimtags were commercially synthesised, biotinylated and used for in vitro immunoassays. We have used phage display to identify M13 phage clones that demonstrated specific binding to IL-4R and IL-13 cytokine. A consensus in binding sequences was observed and phage clones characterised had identical peptide sequence motifs. Only one was synthesised for use in further immunoassays, demonstrating significant binding to either IL-4R or IL-13. We have successfully shown the use of phage display to identify and characterise mimtags that specifically bind to their target epitope. Thus, this new method of probing proteins can be used in the future as a novel tool for immunoassay and detection technique, which is cheaper and more rapidly produced and therefore a better alternative to the use of monoclonal antibodies.
Collapse
Affiliation(s)
- Nayyar Ahmed
- NeuroAllergy Research Laboratory (NARL), Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216, Australia; School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216 Australia
| | - Pathum Dhanapala
- NeuroAllergy Research Laboratory (NARL), Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216, Australia; School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216 Australia
| | - Nadia Sadli
- NeuroAllergy Research Laboratory (NARL), Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216, Australia; School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216 Australia
| | - Colin J Barrow
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216 Australia
| | - Cenk Suphioglu
- NeuroAllergy Research Laboratory (NARL), Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216, Australia; School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, Victoria 3216 Australia.
| |
Collapse
|
19
|
Screening of peptide ligands for pyrroloquinoline quinone glucose dehydrogenase using antagonistic template-based biopanning. Int J Mol Sci 2013; 14:23244-56. [PMID: 24287902 PMCID: PMC3876041 DOI: 10.3390/ijms141223244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/31/2013] [Accepted: 11/11/2013] [Indexed: 01/05/2023] Open
Abstract
We have developed a novel method, antagonistic template-based biopanning, for screening peptide ligands specifically recognizing local tertiary protein structures. We chose water-soluble pyrroloquinoline quinone (PQQ) glucose dehydrogenase (GDH-B) as a model enzyme for this screening. Two GDH-B mutants were constructed as antagonistic templates; these have some point mutations to induce disruption of local tertiary structures within the loop regions that are located at near glucose-binding pocket. Using phage display, we selected 12-mer peptides that specifically bound to wild-type GDH-B but not to the antagonistic templates. Consequently, a peptide ligand showing inhibitory activity against GDH-B was obtained. These results demonstrate that the antagonistic template-based biopanning is useful for screening peptide ligands recognizing the specific local tertiary structure of proteins.
Collapse
|
20
|
Blackstock D, Park M, Sun Q, Tsai SL, Chen W. Engineering protein modules for diagnostic applications. Curr Opin Chem Eng 2013. [DOI: 10.1016/j.coche.2013.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
21
|
Peptide-Based Surface Plasmon Resonance Biosensor for Detection of Staphylococcal Enterotoxin B. FOOD ANAL METHOD 2013. [DOI: 10.1007/s12161-013-9739-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
22
|
Domaille DW, Lee JH, Cha JN. High density DNA loading on the M13 bacteriophage provides access to colorimetric and fluorescent protein microarray biosensors. Chem Commun (Camb) 2013; 49:1759-61. [PMID: 23340548 DOI: 10.1039/c3cc38871a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the synthesis, characterization, and protein sensing capabilities of M13 bacteriophage-DNA bioconjugates. DNA oligonucleotides were conjugated to M13 through acyl hydrazone linkages. In one case, DNAzymes retained their catalytic ability when anchored to the virus coat, and in a separate study, the dynamic nature of the hydrazone allowed for liberation of DNA from the phage under mild conditions.
Collapse
Affiliation(s)
- Dylan W Domaille
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, CO, USA
| | | | | |
Collapse
|
23
|
Singh A, Poshtiban S, Evoy S. Recent advances in bacteriophage based biosensors for food-borne pathogen detection. SENSORS 2013. [PMID: 23364199 DOI: 10.3390/s130201763; 10.3390/s130201763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Foodborne diseases are a major health concern that can have severe impact on society and can add tremendous financial burden to our health care systems. Rapid early detection of food contamination is therefore relevant for the containment of food-borne pathogens. Conventional pathogen detection methods, such as microbiological and biochemical identification are time-consuming and laborious, while immunological or nucleic acid-based techniques require extensive sample preparation and are not amenable to miniaturization for on-site detection. Biosensors have shown tremendous promise to overcome these limitations and are being aggressively studied to provide rapid, reliable and sensitive detection platforms for such applications. Novel biological recognition elements are studied to improve the selectivity and facilitate integration on the transduction platform for sensitive detection. Bacteriophages are one such unique biological entity that show excellent host selectivity and have been actively used as recognition probes for pathogen detection. This review summarizes the extensive literature search on the application of bacteriophages (and recently their receptor binding proteins) as probes for sensitive and selective detection of foodborne pathogens, and critically outlines their advantages and disadvantages over other recognition elements.
Collapse
Affiliation(s)
- Amit Singh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada.
| | | | | |
Collapse
|
24
|
Singh A, Poshtiban S, Evoy S. Recent advances in bacteriophage based biosensors for food-borne pathogen detection. SENSORS 2013; 13:1763-86. [PMID: 23364199 PMCID: PMC3649382 DOI: 10.3390/s130201763] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 01/16/2013] [Accepted: 01/29/2013] [Indexed: 12/20/2022]
Abstract
Foodborne diseases are a major health concern that can have severe impact on society and can add tremendous financial burden to our health care systems. Rapid early detection of food contamination is therefore relevant for the containment of food-borne pathogens. Conventional pathogen detection methods, such as microbiological and biochemical identification are time-consuming and laborious, while immunological or nucleic acid-based techniques require extensive sample preparation and are not amenable to miniaturization for on-site detection. Biosensors have shown tremendous promise to overcome these limitations and are being aggressively studied to provide rapid, reliable and sensitive detection platforms for such applications. Novel biological recognition elements are studied to improve the selectivity and facilitate integration on the transduction platform for sensitive detection. Bacteriophages are one such unique biological entity that show excellent host selectivity and have been actively used as recognition probes for pathogen detection. This review summarizes the extensive literature search on the application of bacteriophages (and recently their receptor binding proteins) as probes for sensitive and selective detection of foodborne pathogens, and critically outlines their advantages and disadvantages over other recognition elements.
Collapse
Affiliation(s)
- Amit Singh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada.
| | | | | |
Collapse
|
25
|
Temur E, Zengin A, Boyacı İH, Dudak FC, Torul H, Tamer U. Attomole sensitivity of staphylococcal enterotoxin B detection using an aptamer-modified surface-enhanced Raman scattering probe. Anal Chem 2012; 84:10600-6. [PMID: 23140575 DOI: 10.1021/ac301924f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this report, we present a new homogeneous detection method for staphylococcal enterotoxin B (SEB) utilizing core-shell-structured iron-gold magnetic nanoparticles and a gold nanorod surface-enhanced Raman scattering (SERS) probe in solution. Peptide ligand (aptamer) functionalized magnetic gold nanorod particles were used as scavengers for target SEB. After the SEB molecules were separated from the matrix, the sandwich assay procedure was tested by gold nanorod particles that act as SERS probes. The binding constant between SEB and peptide-nanoparticle complex was determined as 8.0 × 10(7) M(-1). The correlation between the SEB concentration and SERS signal was found to be linear within the range of 2.5 fM to 3.2 nM. The limit of detection for the homogeneous assay was determined as 224 aM (ca. 2697 SEB molecules/20 μL sample volume). Also, gold-coated surfaces were used as capture substrates and performances of the two methods were compared. Furthermore, the developed method was evaluated for investigating the SEB specificity on bovine serum albumin (BSA) and avidin and detecting SEB in artificially contaminated milk, blood, and urine.
Collapse
Affiliation(s)
- Erhan Temur
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Turkey
| | | | | | | | | | | |
Collapse
|
26
|
Henry M, Debarbieux L. Tools from viruses: bacteriophage successes and beyond. Virology 2012; 434:151-61. [PMID: 23063405 DOI: 10.1016/j.virol.2012.09.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/14/2012] [Accepted: 09/20/2012] [Indexed: 01/21/2023]
Abstract
Viruses are ubiquitous and can infect any of the three existing cellular lineages (Archaea, Bacteria and Eukarya). Despite the persisting negative public perception of these entities, scientists learnt how to domesticate some of them. The study of molecular mechanisms essential to the completion of viral cycles has greatly contributed to deciphering fundamental processes in biology. Nowadays, viruses have entered the biotechnological era and numerous applications have already been developed. Viral-derived tools are used to manipulate genetic information, detect, diagnose, control and cure infectious diseases, or even design new structural assemblies. With the recent advances in the field of metagenomics, an overwhelming amount of information on novel viruses has become available. As current tools have been historically developed from a limited number of viruses, the potential of discoveries from new archaeal, bacterial and eukaryotic viruses may be limited only by our understanding of the multiple facets of viral cycles.
Collapse
Affiliation(s)
- Marine Henry
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, F-75015 Paris, France
| | | |
Collapse
|
27
|
Muzard J, Platt M, Lee GU. M13 bacteriophage-activated superparamagnetic beads for affinity separation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2403-2411. [PMID: 22619210 DOI: 10.1002/smll.201200099] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/13/2012] [Indexed: 06/01/2023]
Abstract
The growth of the biopharmaceutical industry has created a demand for new technologies for the purification of genetically engineered proteins.The efficiency of large-scale, high-gradient magnetic fishing could be improved if magnetic particles offering higher binding capacity and magnetization were available. This article describes several strategies for synthesizing microbeads that are composed of a M13 bacteriophage layer assembled on a superparamagnetic core. Chemical cross-linking of the pVIII proteins to a carboxyl-functionalized bead produces highly responsive superparamagnetic particles (SPM) with a side-on oriented, adherent virus monolayer. Also, the genetic manipulation of the pIII proteins with a His(6) peptide sequence allows reversible assembly of the bacteriophage on a nitrilotriacetic-acid-functionalized core in an end-on configuration. These phage-magnetic particles are successfully used to separate antibodies from high-protein concentration solutions in a single step with a >90% purity. The dense magnetic core of these particles makes them five times more responsive to magnetic fields than commercial materials composed of polymer-(iron oxide) composites and a monolayer of phage could produce a 1000 fold higher antibody binding capacity. These new bionanomaterials appear to be well-suited to large-scale high-gradient magnetic fishing separation and promise to be cost effective as a result of the self-assembling and self-replicating properties of genetically engineered M13 bacteriophage.
Collapse
Affiliation(s)
- Julien Muzard
- UCD Centre for Nanomedicine, School of Chemistry & Chemical Biology - University, College Dublin Belfield, Dublin 4, Ireland
| | | | | |
Collapse
|
28
|
Lee JH, Domaille DW, Cha JN. Amplified protein detection and identification through DNA-conjugated M13 bacteriophage. ACS NANO 2012; 6:5621-5626. [PMID: 22587008 DOI: 10.1021/nn301565e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Sensitive protein detection and accurate identification continues to be in great demand for disease screening in clinical and laboratory settings. For these diagnostics to be of clinical value, it is necessary to develop sensors that have high sensitivity but favorable cost-to-benefit ratios. However, many of these sensing platforms are thermally unstable or require significant materials synthesis, engineering, or fabrication. Recently, we demonstrated that naturally occurring M13 bacteriophage can serve as biological scaffolds for engineering protein diagnostics. These viruses have five copies of the pIII protein, which can bind specifically to target antigens, and thousands of pVIII coat proteins, which can be genetically or chemically modified to react with signal-producing materials, such as plasmon-shifting gold nanoparticles (Au NPs). In this report, we show that DNA-conjugated M13 bacteriophage can act as inexpensive protein sensors that can rapidly induce a color change in the presence of a target protein yet also offer the ability to identify the detected antigen in a separate step. Many copies of a specific DNA oligonucleotide were appended to each virus to create phage-DNA conjugates that can hybridize with DNA-conjugated gold nanoparticles. In the case of a colorimetric positive result, the identity of the antigen can also be easily determined by using a DNA microarray. This saves precious resources by establishing a rapid, quantitative method to first screen for the presence of antigen followed by a highly specific typing assay if necessary.
Collapse
Affiliation(s)
- Ju Hun Lee
- Department of Nanoengineering and Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive M/C 0448, La Jolla, California 92093, USA
| | | | | |
Collapse
|
29
|
Liu Y, Matharu Z, Howland MC, Revzin A, Simonian AL. Affinity and enzyme-based biosensors: recent advances and emerging applications in cell analysis and point-of-care testing. Anal Bioanal Chem 2012; 404:1181-96. [PMID: 22722742 DOI: 10.1007/s00216-012-6149-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/17/2012] [Accepted: 05/24/2012] [Indexed: 01/09/2023]
Abstract
The applications of biosensors range from environmental testing and biowarfare agent detection to clinical testing and cell analysis. In recent years, biosensors have become increasingly prevalent in clinical testing and point-of-care testing. This is driven in part by the desire to decrease the cost of health care, to shift some of the analytical tests from centralized facilities to "frontline" physicians and nurses, and to obtain more precise information more quickly about the health status of a patient. This article gives an overview of recent advances in the field of biosensors, focusing on biosensors based on enzymes, aptamers, antibodies, and phages. In addition, this article attempts to describe efforts to apply these biosensors to clinical testing and cell analysis.
Collapse
Affiliation(s)
- Ying Liu
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA
| | | | | | | | | |
Collapse
|
30
|
Short peptides as biosensor transducers. Anal Bioanal Chem 2011; 402:3055-70. [DOI: 10.1007/s00216-011-5589-8] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/25/2011] [Accepted: 11/20/2011] [Indexed: 12/27/2022]
|
31
|
Dudak FC, Kılıç N, Demir K, Yaşar F, Boyacı İH. Enhancing the affinity of SEB-binding peptides by repeating their sequence. Biopolymers 2011; 98:145-54. [DOI: 10.1002/bip.22012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 09/29/2011] [Accepted: 11/04/2011] [Indexed: 11/08/2022]
|
32
|
Li K, Chen Y, Li S, Nguyen HG, Niu Z, You S, Mello CM, Lu X, Wang Q. Chemical modification of M13 bacteriophage and its application in cancer cell imaging. Bioconjug Chem 2010; 21:1369-77. [PMID: 20499838 DOI: 10.1021/bc900405q] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The M13 bacteriophage has been demonstrated to be a robust scaffold for bionanomaterial development. In this paper, we report on the chemical modifications of three kinds of reactive groups, i.e., the amino groups of lysine residues or N-terminal, the carboxylic acid groups of aspartic acid or glutamic acid residues, and the phenol group of tyrosine residues, on M13 surface. The reactivity of each group was identified through conjugation with small fluorescent molecules. Furthermore, the regioselectivity of each reaction was investigated by HPLC-MS-MS. By optimizing the reaction condition, hundreds of fluorescent moieties could be attached to create a highly fluorescent M13 bacteriophage. In addition, cancer cell targeting motifs such as folic acid could also be conjugated onto the M13 surface. Therefore, dual-modified M13 particles with folic acid and fluorescent molecules were synthesized via the selective modification of two kinds of reactive groups. Such dual-modified M13 particles showed very good binding affinity to human KB cancer cells, which demonstrated the potential applications of M13 bacteriophage in bioimaging and drug delivery.
Collapse
Affiliation(s)
- Kai Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology (DUT), Dalian, P. R. China
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Dudak FC, Soykut EA, Oğuz ME, Yaşar F, Boyaci IH. Thermodynamic and structural analysis of interactions between peptide ligands and SEB. J Mol Recognit 2010; 23:369-78. [PMID: 19941320 DOI: 10.1002/jmr.1003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Staphylococcal enterotoxin B (SEB) is an exotoxin produced by Staphylococcus aureus and commonly associated with food poisoning. In this study, SEB-binding peptides were identified by screening a phage displayed peptide library. The binding of peptides to SEB was tested with isothermal titration calorimetry (ITC) and of the five selected peptides, three showed affinity to SEB, with one measured to have the highest affinity constant (10(5) M(-1)). ITC revealed that the interaction of peptide ligands with SEB was driven entropically and the binding was dominated by hydrophobic interactions. Circular dichroism (CD) measurements and molecular dynamics (MD) simulations, together, give a structural insight into the interaction of peptides with SEB. While SEB binding peptides showed random coil structure before binding, after complex formation they had more ordered structures. The peptide with highest affinity to SEB showed stable conformation during MD simulation. Taken together, our approach about thermodynamic and structural characterization of peptide ligands can be used to develop aptamers, with high affinity and selectivity, for biosensor applications.
Collapse
Affiliation(s)
- Fahriye Ceyda Dudak
- Department of Food Engineering, Hacettepe University, Beytepe 06800, Ankara, Turkey
| | | | | | | | | |
Collapse
|
34
|
Generation of Fab fragment-like molecular recognition proteins against staphylococcal enterotoxin B by phage display technology. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2010; 17:1708-17. [PMID: 20844088 DOI: 10.1128/cvi.00229-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Antigen-binding fragments (Fab fragments) and single-chain variable fragments (scFv) against staphylococcal enterotoxin B (SEB) were produced by phage display technology. SEB epitopes were first identified by phage display approach using the commercial anti-SEB monoclonal antibody ab53981 as the target. Heptamer and dodecamer mimotope peptides recognized by ab53981 were screened from Ph.D-7 or Ph.D-12 random peptide phage libraries expressed in Escherichia coli. The isolated 7-mer and 12-mer mimotopes were shown to share a sequence homologous to ⁸PDELHK¹⁴S in the amino acid sequence of SEB. The N-terminal 15-mer peptide of SEB was determined to be an epitope of ab53981. After immunization of mice with maltose-binding protein-tagged N-terminal 15-mer peptide, a phage display Fab library was constructed using cDNA prepared from the mRNAs of spleen cells. Three phage clones displaying the Fab molecule which recognized SEB were isolated through three rounds of panning. Only one of them produced a soluble Fab fragment from the transformed cells, and the fragment fused with a histidine tag sequence was produced in E. coli cells and converted into scFv. Surface plasmon resonance analysis showed that the dissociation constants of these proteins with SEB were (4.1 ± 1.1) × 10⁻⁹ M and (8.4 ± 2.3) × 10⁻¹⁰ M, respectively. The produced molecule was applied to the determination of SEB by enzyme-linked immunosorbent assay and Western blot analysis.
Collapse
|
35
|
Van Dorst B, Mehta J, Bekaert K, Rouah-Martin E, De Coen W, Dubruel P, Blust R, Robbens J. Recent advances in recognition elements of food and environmental biosensors: a review. Biosens Bioelectron 2010; 26:1178-94. [PMID: 20729060 DOI: 10.1016/j.bios.2010.07.033] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 07/08/2010] [Accepted: 07/11/2010] [Indexed: 12/12/2022]
Abstract
A sensitive monitoring of contaminants in food and environment, such as chemical compounds, toxins and pathogens, is essential to assess and avoid risks for both, human and environmental health. To accomplish this, there is a high need for sensitive, robust and cost-effective biosensors that make real time and in situ monitoring possible. Due to their high sensitivity, selectivity and versatility, affinity-based biosensors are interesting for monitoring contaminants in food and environment. Antibodies have long been the most popular affinity-based recognition elements, however recently a lot of research effort has been dedicated to the development of novel recognition elements with improved characteristics, like specificity, stability and cost-efficiency. This review discusses three of these innovative affinity-based recognition elements, namely, phages, nucleic acids and molecular imprinted polymers and gives an overview of biosensors for food and environmental applications where these novel affinity-based recognition elements are applied.
Collapse
Affiliation(s)
- Bieke Van Dorst
- University of Antwerp, Department of Biology, Laboratory of Ecophysiology, Biochemistry and Toxicology, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Johnson EM, Ellis WR, Powers LS, Wysocki VH. Affinity capture mass spectrometry of biomarker proteins using peptide ligands from biopanning. Anal Chem 2010; 81:5999-6005. [PMID: 19572565 DOI: 10.1021/ac900868q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Affinity capture mass spectrometry was used to isolate and ionize protein A from Staphylococcus aureus from both a commercial source and cell culture lysate using matrix assisted laser desorption/ionization (MALDI) mass spectrometry. Two surfaces are compared: gold surfaces with immunoglobulin G covalently immobilized and silica surfaces with a covalently bound small peptide discovered via biopanning. A detection limit of 2.22 bacterial cells/mL of culture fluid was determined for the immobilized peptide surfaces. This study emphasizes the ability to use peptide ligands to effectively capture a biomarker protein out of a complex mixture. This demonstrates the potential to use biopanning to generate capture ligands for a large variety of target proteins and subsequently detect the captured protein using MALDI mass spectrometry.
Collapse
Affiliation(s)
- Erin M Johnson
- Departments of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | | | | | | |
Collapse
|
37
|
Li K, Nguyen HG, Lu X, Wang Q. Viruses and their potential in bioimaging and biosensing applications. Analyst 2009; 135:21-7. [PMID: 20024176 DOI: 10.1039/b911883g] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Successful development of ultrasensitive constructs for bioimaging and biosensing is a challenging task. Recently, viruses have drawn increasing attention due to their exquisite three-dimensional structures and unique properties, including multivalency, orthogonal reactivities, and responsiveness to genetic modifications. With such well-characterized structures, functional units, such as imaging and binding motifs, can be engineered on the surface of viruses in a programmable, polyvalent manner, which leads to novel nanosized sensing/imaging systems with enhanced signaling and targeting performance. This review highlights some recent progress in the applications of viruses in bioimaging and biosensing.
Collapse
Affiliation(s)
- Kai Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, PR China
| | | | | | | |
Collapse
|
38
|
|
39
|
Synthesis of a virus electrode for measurement of prostate specific membrane antigen. Methods Mol Biol 2009; 504:255-74. [PMID: 19159102 DOI: 10.1007/978-1-60327-569-9_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Though relatively unexploited in biosensor applications, phage display technology can provide versatile recognition scaffolds for detection of cancer markers and other analytes. This chapter details protocols for covalent attachment of viruses directly to electrodes for reagent-free detection of analytes in real-time. Customization of binding specificity leverages selections with large phage display libraries prior to covalent attachment of the selected virus to the electrode. The methods described here utilize electrochemical impedance spectroscopy (EIS) to detect molecular recognition between M13 phage bound to a Au electrode and the following analytes: prostate specific membrane antigen (PSMA), positive and negative control antibodies (p-Ab and n-Ab, respectively). Because of a thick layer built on the Au electrode, the real impedance (Zre) increases reliably with S/N ratios upon noncovalent binding to PSMA (approximately 14) and p-Ab (approximately 20).
Collapse
|
40
|
Ricin detection using phage displayed single domain antibodies. SENSORS 2009; 9:542-55. [PMID: 22389616 PMCID: PMC3280762 DOI: 10.3390/s90100542] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 01/13/2009] [Accepted: 01/14/2009] [Indexed: 11/16/2022]
Abstract
Phage-displayed single domain antibodies (sdAb) were compared to monomeric solubly expressed sdAb and llama polyclonal antibodies for the detection of ricin. SdAb are comprised of the variable domain derived from camelid heavy chain only antibodies (HcAb). Although HcAb lack variable light chains, they as well as their derivative sdAb are able to bind antigens with high affinity. The small size of sdAb (∼16 kDa), while advantageous in many respects, limits the number of labels that can be incorporated. The ability to incorporate multiple labels is a beneficial attribute for reporter elements. Opportunely, sdAb are often selected using phage display methodology. Using sdAb displayed on bacteriophage M13 as the reporter element gives the potential for incorporating a very high number of labels. We have demonstrated the use of both sdAb and phage- displayed sdAb for the detection of ricin using both enzyme linked immunosorbent assays (ELISAs) and Luminex fluid array assays. The phage-displayed sdAb led to five to ten fold better detection of ricin in both the ELISA and Luminex assays, resulting in limits of detection of 1 ng/mL and 64 pg/mL respectively. The phage-displayed sdAb were also dramatically more effective for the visualization of binding to target in nitrocellulose dot blot assays, a method frequently used for epitope mapping.
Collapse
|
41
|
Lamboy JA, Tam PY, Lee LS, Jackson PJ, Avrantinis SK, Lee HJ, Corn RM, Weiss GA. Chemical and genetic wrappers for improved phage and RNA display. Chembiochem 2009; 9:2846-52. [PMID: 18973165 DOI: 10.1002/cbic.200800366] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An Achilles heel inherent to all molecular display formats, background binding between target and display system introduces false positives into screens and selections. For example, the negatively charged surfaces of phage, mRNA, and ribosome display systems bind with unacceptably high nonspecificity to positively charged target molecules, which represent an estimated 35% of proteins in the human proteome. Here we report the first systematic attempt to understand why a broad class of molecular display selections fail, and then solve the underlying problem for both phage and RNA display. Firstly, a genetic strategy was used to introduce a short, charge-neutralizing peptide into the solvent-exposed, negatively charged phage coat. The modified phage (KO7(+)) reduced or eliminated nonspecific binding to the problematic high-pI proteins. In the second, chemical approach, nonspecific interactions were blocked by oligolysine wrappers in the cases of phage and total RNA. For phage display applications, the peptides Lys(n) (where n=16 to 24) emerged as optimal for wrapping the phage. Lys(8), however, provided effective wrappers for RNA binding in assays against the RNA binding protein HIV-1 Vif. The oligolysine peptides blocked nonspecific binding to allow successful selections, screens, and assays with five previously unworkable protein targets.
Collapse
Affiliation(s)
- Jorge A Lamboy
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, CA 92697-2025, USA
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Abstract
Viruses have recently proven useful for the detection of target analytes such as explosives, proteins, bacteria, viruses, spores, and toxins with high selectivity and sensitivity. Bacteriophages (often shortened to phages), viruses that specifically infect bacteria, are currently the most studied viruses, mainly because target-specific nonlytic phages (and the peptides and proteins carried by them) can be identified by using the well-established phage display technique, and lytic phages can specifically break bacteria to release cell-specific marker molecules such as enzymes that can be assayed. In addition, phages have good chemical and thermal stability, and can be conjugated with nanomaterials and immobilized on a transducer surface in an analytical device. This Review focuses on progress made in the use of phages in chemical and biological sensors in combination with traditional analytical techniques. Recent progress in the use of virus-nanomaterial composites and other viruses in sensing applications is also highlighted.
Collapse
Affiliation(s)
- Chuanbin Mao
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
| | | | | |
Collapse
|
43
|
Yang LMC, Diaz JE, McIntire TM, Weiss GA, Penner RM. Direct electrical transduction of antibody binding to a covalent virus layer using electrochemical impedance. Anal Chem 2008; 80:5695-705. [PMID: 18590279 DOI: 10.1021/ac8008109] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrochemical impedance spectroscopy is used to detect the binding of a 148.2 kDa antibody to a "covalent virus layer" (CVL) immobilized on a gold electrode. The CVL consisted of M13 phage particles covalently anchored to a 3 mm diameter gold disk electrode. The ability of the CVL to distinguish this antibody ("p-Ab") from a second, nonbinding antibody ("n-Ab") was evaluated as a function of the frequency and phase of the measured current relative to the applied voltage. The binding of p-Ab to the CVL was correlated with a change in the resistance, reducing it at low frequency (1-40 Hz) while increasing it at high frequency (2-140 kHz). The capacitance of the CVL was virtually uncorrelated with p-Ab binding. At both low and high frequency, the electrode resistance was linearly dependent on the p-Ab concentration from 20 to 266 nM but noise compromised the reproducibility of the p-Ab measurement at frequencies below 40 Hz. A "signal-to-noise" ratio for antibody detection was computed based upon the ratio between the measured resistance change upon p-Ab binding and the standard deviation of this change obtained from multiple measurements. In spite of the fact that the impedance change upon p-Ab binding in the low frequency domain was more than 100 times larger than that measured at high frequency, the S/N ratio at high frequency was higher and virtually independent of frequency from 4 to 140 kHz. Attempts to release p-Ab from the CVL using 0.05 M HCl, as previously described for mass-based detection, caused a loss of sensitivity that may be associated with a transition of these phage particles within the CVL from a linear to a coiled conformation at low pH.
Collapse
Affiliation(s)
- Li-Mei C Yang
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | | | | | | | | |
Collapse
|
44
|
Handa H, Gurczynski S, Jackson MP, Auner G, Mao G. Recognition of Salmonella Typhimurium by Immobilized Phage P22 Monolayers. SURFACE SCIENCE 2008; 602:1392-1400. [PMID: 19461940 PMCID: PMC2682717 DOI: 10.1016/j.susc.2008.01.036] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Phages are promising alternatives to antibodies as the biorecognition element in a variety of biosensing applications. In this study, a monolayer of bacteriophage P22 whose tailspike proteins specifically recognize Salmonella serotypes was covalently bound to glass substrates through a bifunctional cross linker 3-aminopropyltrimethoxysilane. The specific binding of Salmonella typhimurium to the phage monolayer was studied by enzyme-linked immunosorbent assay and atomic force microscopy. Escherichia coli and a Gram-positive bacterium Listeria monocytogenes were also studied as control bacteria. The P22 particles show strong binding affinity to Salmonella typhimurium. In addition, the dried P22 monolayer maintained 50% binding capacity to Salmonella typhimurium after a one-week storage time. This is a promising method to prepare phage monolayer coatings on surface plasmon resonance and acoustic biosensor substrates in order to utilize the nascent phage display technology.
Collapse
Affiliation(s)
- Hitesh Handa
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
| | - Stephen Gurczynski
- Department of Immunology and Microbiology, Wayne State University, Detroit, MI 48201, USA
| | - Matthew P. Jackson
- Department of Immunology and Microbiology, Wayne State University, Detroit, MI 48201, USA
| | - Gregory Auner
- Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, USA
| | - Guangzhao Mao
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
| |
Collapse
|
45
|
Soykut EA, Dudak FC, Boyaci IH. Selection of staphylococcal enterotoxin B (SEB)-binding peptide using phage display technology. Biochem Biophys Res Commun 2008; 370:104-8. [PMID: 18359289 PMCID: PMC7117543 DOI: 10.1016/j.bbrc.2008.03.065] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2008] [Accepted: 03/08/2008] [Indexed: 11/17/2022]
Abstract
In this study, peptides were selected to recognize staphylococcal enterotoxin B (SEB) which cause food intoxication and can be used as a biological war agent. By using commercial M13 phage library, single plaque isolation of 38 phages was done and binding affinities were investigated with phage-ELISA. The specificities of the selected phage clones showing high affinity to SEB were checked by using different protein molecules which can be found in food samples. Furthermore, the affinities of three selected phage clones were determined by using surface plasmon resonance (SPR) sensors. Sequence analysis was realized for three peptides showing high binding affinity to SEB and WWRPLTPESPPA, MNLHDYHRLFWY, and QHPQINQTLYRM amino acid sequences were obtained. The peptide sequence with highest affinity to SEB was synthesized with solid phase peptide synthesis technique and thermodynamic constants of the peptide-SEB interaction were determined by using isothermal titration calorimetry (ITC) and compared with those of antibody-SEB interaction. The binding constant of the peptide was determined as 4.2+/-0.7 x 10(5)M(-1) which indicates a strong binding close to that of antibody.
Collapse
Affiliation(s)
- Esra Acar Soykut
- Department of Food Engineering, Hacettepe University, Beytepe 06532, Ankara, Turkey
| | | | | |
Collapse
|
46
|
Yang LMC, Diaz JE, McIntire TM, Weiss GA, Penner RM. Covalent virus layer for mass-based biosensing. Anal Chem 2008; 80:933-43. [PMID: 18198846 DOI: 10.1021/ac071470f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
M13 virus particles were covalently attached to a planar gold-coated quartz crystal microbalance (QCM) through reaction with a self-assembled monolayer of N-hydroxysuccinimide thioctic ester, followed by incorporation of the blocking agent bovine serum albumin. This immobilization chemistry produced a phage multilayer having a coverage equivalent to approximately 6.5 close-packed monolayers of the virus. The properties of this "covalent virus surface" or CVS for the mass-based detection of a 148.2 kDa antibody were then evaluated in a phosphate buffer using a flow injection analysis system. The mass of the CVS increased with exposure to an antibody (p-Ab) known to bind the phage particles with high affinity. Bound p-Ab was removed by washing with 0.5 M HCl thereby regenerating the sensor surface. A calibration plot for p-Ab binding was constructed by repetitively exposing the surface to p-Ab at concentrations between 6.6 and 200 nM and HCl rinsing after each exposure. The mass-concentration relationship was linear with a sensitivity of 0.018 microg/(cm2 nM) and a limit of detection of 7 nM or 1.3 pmol. The CVS could be saturated with high doses of p-Ab enabling the determination that an average of approximately 140 binding sites are available per M13 phage particle. Exposure of the CVS to a second, nonbinding antibody (n-Ab) did not cause a measurable mass change. These results demonstrate that the covalent virus layer is a rugged, selective, and sensitive means for carrying out mass-based biodetection.
Collapse
Affiliation(s)
- Li-Mei C Yang
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | | | | | | | | |
Collapse
|
47
|
Zourob M, Elwary S, Turner A. Acoustic Wave (TSM) Biosensors: Weighing Bacteria. PRINCIPLES OF BACTERIAL DETECTION: BIOSENSORS, RECOGNITION RECEPTORS AND MICROSYSTEMS 2008. [PMCID: PMC7121835 DOI: 10.1007/978-0-387-75113-9_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
This chapter is focused on the development and use of acoustic wave biosensor platforms for the detection of bacteria, specifically those based on the thickness shear mode (TSM) resonator. We demonstrated the mechanical and electrical implications of bacterial positioning at the solid-liquid interface of a TSM biosensor and presented a model of the TSM with bacteria attached operating as coupled oscillators. The experiments and model provide an understanding of the nature of the signals produced by acoustic wave devices when they are used for testing bacteria. The paradox of “negative mass” could be a real threat to the interpretation of experimental results related to the detection of bacteria. The knowledge of the true nature of “negative mass” linked to the strength of bacteria attachment will contribute significantly to our understanding of the results of “weighing bacteria.” The results of this work can be used for bacterial detection and control of processes of bacterial settlement, bacterial colonization, biofilm formation, and bacterial infection in which bacterial attachment plays a role.
Collapse
Affiliation(s)
| | - Souna Elwary
- Consultant to Biophage Pharma Inc, Montreal, Canada
| | | |
Collapse
|
48
|
Giraudi G, Anfossi L, Baggiani C, Giovannoli C, Tozzi C. Solid-phase extraction of ochratoxin A from wine based on a binding hexapeptide prepared by combinatorial synthesis. J Chromatogr A 2007; 1175:174-80. [DOI: 10.1016/j.chroma.2007.10.057] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 10/18/2007] [Accepted: 10/22/2007] [Indexed: 11/17/2022]
|
49
|
Rodriguez-Mozaz S, Lopez de Alda MJ, Barceló D. Advantages and limitations of on-line solid phase extraction coupled to liquid chromatography–mass spectrometry technologies versus biosensors for monitoring of emerging contaminants in water. J Chromatogr A 2007; 1152:97-115. [PMID: 17275010 DOI: 10.1016/j.chroma.2007.01.046] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Revised: 12/22/2006] [Accepted: 01/12/2007] [Indexed: 11/29/2022]
Abstract
On-line solid phase extraction (SPE) coupled to liquid chromatography-mass spectrometry (LC-MS) and biosensors are advanced technologies that have found increasing application in the analysis of environmental contaminants although their application to the determination of emerging contaminants (previously unknown or unrecognized pollutants) has been still limited. This review covers the most recent advances occurred in the areas of on-line SPE-LC-MS and biosensors, discusses and compares the main strengths and limitations of the two approaches, and examines their most relevant applications to the analysis of emerging contaminants in environmental waters. So far, the on-line configuration most frequently used has been SPE coupled to liquid chromatography-(tandem) mass spectrometry. Sorbents used for on-line SPE have included both traditional (alkyl-bonded silicas and polymers) and novel (restricted access materials (RAMs), molecularly imprinted synthetic polymers (MIPs), and immobilized receptors or antibodies (immunosorbents) materials. The biosensor technologies most frequently applied have been based on the use of antibodies and, to a lesser extent, enzymes, bacteria, receptors and DNA as recognition elements, and the use of optical and electrochemical transducing elements. Emerging contaminants investigated by means of these two techniques have included pharmaceuticals, endocrine disrupting compounds such as estrogens, alkylphenols and bisphenol A, pesticides transformation products, disinfection by-products, and bacterial toxins and mycotoxins, among others. Both techniques offer advantageous, and frequently comparable, features such as high sensitivity and selectivity, minimum sample manipulation, and automation. Biosensors are, in addition, relatively cheap and fast, which make them ideally suited for routine testing and screening of samples; however, in most cases, they can not compete yet with on-line SPE procedures in terms of accuracy, reproducibility, reliability (confirmation) of results, and capacity for multi-analyte determination.
Collapse
Affiliation(s)
- Sara Rodriguez-Mozaz
- Department of Environmental Chemistry, IIQAB-CSIC, C/Jordi Girona 18-26, 08034 Barcelona, Spain
| | | | | |
Collapse
|
50
|
Kulagina NV, Shaffer KM, Anderson GP, Ligler FS, Taitt CR. Antimicrobial peptide-based array for Escherichia coli and Salmonella screening. Anal Chim Acta 2006; 575:9-15. [PMID: 17723565 DOI: 10.1016/j.aca.2006.05.082] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 05/12/2006] [Accepted: 05/22/2006] [Indexed: 11/23/2022]
Abstract
Numerous bacteria, plants, and higher organisms produce antimicrobial peptides (AMPs) as part of their innate immune system, providing a chemical defense mechanism against microbial invasion. Many AMPs exert their antimicrobial activity by binding to components of the microbe's surface and disrupting the membrane. The goal of this study was to incorporate AMPs into screening assays for detection of pathogenic species. Surface-immobilized AMPs such as polymyxins B and E could be used to detect Salmonella typhimurium and Escherichia coli O157:H7 in two assay formats: direct and sandwich. Both types of assay confirmed that the peptides were immobilized in active form and could bind cells in a concentration-dependent manner. Cell binding to the AMPs was peptide-density dependent. This method for monitoring pathogen binding was extended to include other cationic AMPs such as cecropin A, magainin I and parasin. Detection limits (LODs) for E. coli O157:H7 and S. typhimurium obtained with AMPs during sandwich assays were in the ranges of 5x10(4) to 5x10(5) and 1x10(5) to 5x10(6)cells mL(-1), respectively. The different AMPs showed significantly different affinities for the two bacterial species; the potential for classification of pathogens based on different binding patterns to AMPs is discussed.
Collapse
Affiliation(s)
- Nadezhda V Kulagina
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC 20375-5348, USA
| | | | | | | | | |
Collapse
|