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Brasino M, Cha JN. Real-time femtomolar detection of cancer biomarkers from photoconjugated antibody-phage constructs. Analyst 2018; 142:91-97. [PMID: 27731431 DOI: 10.1039/c6an01904h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here we describe novel covalent conjugates of antibody-phage for the detection of multiple cancer biomarkers using real time immuno-polymerase chain reaction (immuno-PCR). While the conventional process of immuno-PCR utilizes DNA-conjugated antibodies, chemical modification of antibodies not only reduces antibody affinity but also creates a heterogeneous population of products. However, phage naturally encapsulate genomic DNA, which can be used as a PCR template. To produce covalently conjugated antibody-phage constructs without recombinant antibody expression or chemical modification of antibodies, we incorporated a photocrosslinkable non-canonical amino acid within an antibody-binding domain displayed on one of the phage coat proteins. To correlate antigen presence to a specific DNA sequence, the phage genomes were modified with domains that recognized specific sets of primers. The crosslinked antibody-phage conjugates were then tested in a sandwich-type immunoassay using real-time PCR where low pg ml-1 concentrations of antigen could be detected and identified from a single solution containing a mixture of three different types of cancer biomarkers.
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Affiliation(s)
- M Brasino
- Materials Science and Engineering Program, University of Colorado, Boulder, USA.
| | - J N Cha
- Materials Science and Engineering Program, University of Colorado, Boulder, USA. and Department of Chemical and Biological Engineering, University of Colorado, Boulder, USA
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2
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Zhao M, Zhang S, Chen Z, Zhao C, Wang L, Liu S. Allosteric kissing complex-based electrochemical biosensor for sensitive, regenerative and versatile detection of proteins. Biosens Bioelectron 2018; 105:42-48. [PMID: 29351869 DOI: 10.1016/j.bios.2018.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/04/2018] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
Abstract
Herein, an allosteric kissing complex-based electrochemical biosensor was ingeniously proposed for the simple, sensitive, regenerative and versatile detection of proteins. Two hairpins (Hp1 and Hp2) were designed and the Hp1 was immobilized on the electrode surface, which could form a kissing complex with Hp2 through the apical loop-loop or kissing interaction of the RNA-RNA base sequences. The Hp2 possesses the appended single-stranded tails on each end, which hybridize with the recognition element-conjugated DNA strands to construct a protein responsive switch of Hp2 scaffold. After kissing complex formation between the Hp2 scaffold and the immobilized Hp1, the streptavidin-labeled alkaline phosphatase (SA-ALP) can be introduced onto the electrode surface for the generation of electrochemical signal. In the presence of target protein, its binding to the recognition elements linked onto the Hp2 scaffold endows the steric strain to open the Hp2 stem, propagated by the disruption of the kissing complex structure, resulting into a decreased electrochemical signal related with the protein quantification. Also, the Hp1 immobilized electrode can be directly regenerated after protein-induced kissing complex dissociation. The current kissing complex-based electrochemical biosensing strategy can be easily extended for the detection toward different protein targets of interest by simply changing the recognition elements conjugated onto the Hp2 scaffold. The sensitive and selective detection toward proteins could be achieved with the detection limits toward Anti-Dig antibody and thrombin of about 1ng/mL and 10pM, respectively. The developed kissing complex-based protein biosensing strategy should be a beneficial supplement in current biosensor field, providing a promising means for the applications in bioanalysis, disease diagnostics, and clinical biomedicine.
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Affiliation(s)
- Mingsha Zhao
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No.53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Shanshan Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No.53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Zhiqiang Chen
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No.53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Changzhi Zhao
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No.53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No.53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No.53, Rd. Zhengzhou, Qingdao, Shandong 266042, China.
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3
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Wen G, Ju H. Enhanced Photoelectrochemical Proximity Assay for Highly Selective Protein Detection in Biological Matrixes. Anal Chem 2016; 88:8339-45. [DOI: 10.1021/acs.analchem.6b02740] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Guangming Wen
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- School
of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, P.R. China
| | - Huangxian Ju
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
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4
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Mukhortava A, Schlierf M. Efficient Formation of Site-Specific Protein–DNA Hybrids Using Copper-Free Click Chemistry. Bioconjug Chem 2016; 27:1559-63. [DOI: 10.1021/acs.bioconjchem.6b00120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ann Mukhortava
- B CUBE − Center for
Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße
18, 01307 Dresden, Germany
| | - Michael Schlierf
- B CUBE − Center for
Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße
18, 01307 Dresden, Germany
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5
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Chang L, Li J, Wang L. Immuno-PCR: An ultrasensitive immunoassay for biomolecular detection. Anal Chim Acta 2016; 910:12-24. [DOI: 10.1016/j.aca.2015.12.039] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 12/29/2015] [Accepted: 12/31/2015] [Indexed: 12/11/2022]
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6
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Brasino MD, Cha JN. Isothermal rolling circle amplification of virus genomes for rapid antigen detection and typing. Analyst 2016; 140:5138-44. [PMID: 26040578 DOI: 10.1039/c5an00721f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, isothermal rolling circle amplification (RCA) of the multi-kilobase genome of engineered filamentous bacteriophage is used to report the presence and identification of specific protein analytes in solution. First, bacteriophages were chosen as sensing platforms because peptides or antibodies that bind medically relevant targets can be isolated through phage display or expressed as fusions to their p3 and p8 coat proteins. Second, the circular, single-stranded genome contained within the phage serves as a natural large DNA template for a RCA reaction to rapidly generate exponential amounts of double stranded DNA in a single isothermal step that can be easily detected using low-cost fluorescent nucleic acid stains. Amplifying the entire phage genome also provides high detection sensitivities. Furthermore, since the sequence of the viral DNA can be easily modified with multiple restriction enzyme sites, a simple DNA digest can be applied to detect and identify multiple antigens simultaneously. The methods developed here will lead to protein sensors that are highly scalable to produce, can be run without complex biological equipment and do not require the use of multiple antibodies or high-cost fluorescent DNA probes or nucleotides.
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Affiliation(s)
- Michael D Brasino
- Materials Science and Engineering Program, University of Colorado, Boulder, USA
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7
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Advances in Anthrax Detection: Overview of Bioprobes and Biosensors. Appl Biochem Biotechnol 2015; 176:957-77. [PMID: 25987133 DOI: 10.1007/s12010-015-1625-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 04/08/2015] [Indexed: 12/22/2022]
Abstract
Anthrax is an infectious disease caused by Bacillus anthracis. Although anthrax commonly affects domestic and wild animals, it causes a rare but lethal infection in humans. A variety of techniques have been introduced and evaluated to detect anthrax using cultures, polymerase chain reaction, and immunoassays to address the potential threat of anthrax being used as a bioweapon. The high-potential harm of anthrax in bioterrorism requires sensitive and specific detection systems that are rapid, field-ready, and real-time monitoring. Here, we provide a systematic overview of anthrax detection probes with their potential applications in various ultra-sensitive diagnostic systems.
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8
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Detection of pathogen-specific antibodies by loop-mediated isothermal amplification. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2015; 22:374-80. [PMID: 25651920 DOI: 10.1128/cvi.00811-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a method for enzymatically replicating DNA that has great utility for clinical diagnosis at the point of care (POC), given its high sensitivity, specificity, speed, and technical requirements (isothermal conditions). Here, we adapted LAMP for measuring protein analytes by creating a protein-DNA fusion (referred to here as a "LAMPole") that attaches oligonucleotides (LAMP templates) to IgG antibodies. This fusion consists of a DNA element covalently bonded to an IgG-binding polypeptide (protein L/G domain). In our platform, LAMP is expected to provide the most suitable means for amplifying LAMPoles for clinical diagnosis at the POC, while quantitative PCR is more suitable for laboratory-based quantification of antigen-specific IgG abundance. As proof of concept, we measured serological responses to a protozoan parasite by quantifying changes in solution turbidity in real time. We observed a >6-log fold difference in signal between sera from vaccinated versus control mice and in a clinical patient sample versus a control. We assert that LAMPoles will be useful for increasing the sensitivity of measuring proteins, whether it be in a clinical laboratory or in a field setting, thereby improving acute diagnosis of a variety of infections.
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Pastoriza-Gallego M, Breton MF, Discala F, Auvray L, Betton JM, Pelta J. Evidence of unfolded protein translocation through a protein nanopore. ACS NANO 2014; 8:11350-11360. [PMID: 25380310 DOI: 10.1021/nn5042398] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein nanopores are mainly used to study transport, unfolding, intrinsically disordered proteins, protein-pore interactions, and protein-ligand complexes. This single-molecule sensor for biomedical and biotechnological applications is promising but until now direct proof of protein translocation through a narrow channel is lacking. Here, we report the translocation of a chimera molecule through the aerolysin nanopore in the presence of a denaturing agent, guanidium chloride (1.5 M) and KCl (1 M). The chimera molecule is composed of the recombinant MalE protein with a unique cysteine residue at the C-terminal position covalently linked to a single-stranded DNA oligonucleotide. Real-time polymerase chain reaction (PCR) was used to detect the presence of chimera molecules that have been effectively translocated from the cis to trans chamber of the set up. Comparing the electrical signature of the chimera related to the protein or oligonucleotide alone demonstrates that each type of molecule displays different dynamics in term of transport time, event frequency, and current blockade. This original approach provides the possibility to study protein translocation through different biological, artificial, and biomimetic nanopores or nanotubes. New future applications are now conceivable such as protein refolding at the nanopore exit, peptides and protein sequencing, and peptide characterization for diagnostics.
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Affiliation(s)
- Manuela Pastoriza-Gallego
- CNRS-UMR 8587, LAMBE, Université de Cergy-Pontoise , 2 avenue A. Chauvin, 95302 Cergy-Pontoise Cedex France
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10
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Pippig DA, Baumann F, Strackharn M, Aschenbrenner D, Gaub HE. Protein-DNA chimeras for nano assembly. ACS NANO 2014; 8:6551-6555. [PMID: 24897163 DOI: 10.1021/nn501644w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In synthetic biology, "understanding by building" requires exquisite control of the molecular constituents and their spatial organization. Site-specific coupling of DNA to proteins allows arrangement of different protein functionalities with emergent properties by self-assembly on origami-like DNA scaffolds or by direct assembly via Single-Molecule Cut & Paste (SMC&P). Here, we employed the ybbR-tag/Sfp system to covalently attach Coenzyme A-modified DNA to GFP and, as a proof of principle, arranged the chimera in different patterns by SMC&P. Fluorescence recordings of individual molecules proved that the proteins remained folded and fully functional throughout the assembly process. The high coupling efficiency and specificity as well as the negligible size (11 amino acids) of the ybbR-tag represent a mild, yet versatile, general and robust way of adding a freely programmable and highly selective attachment site to virtually any protein of interest.
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Affiliation(s)
- Diana A Pippig
- Center for Nanoscience and Department of Physics, University of Munich , Amalienstraße 54, 80799 Munich, Germany
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11
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Ren K, Wu J, Yan F, Ju H. Ratiometric electrochemical proximity assay for sensitive one-step protein detection. Sci Rep 2014; 4:4360. [PMID: 24618513 PMCID: PMC3950580 DOI: 10.1038/srep04360] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/25/2014] [Indexed: 11/17/2022] Open
Abstract
This work proposes the concept of ratiometric electrochemical proximity assay (REPA), which can be used for one-step, highly sensitive and selective detection of protein. The assay strategy was achieved on a sensing interface that was formed by hybridization of methylene blue (MB)-labeled antibody-DNA probe (MB-DNA1-Ab1) with ferrocene (Fc)-labeled DNA capture probe (Fc-P) modified gold electrode. On the interface the target protein could trigger the formation of immunocomplex between MB-DNA1-Ab1 and detection antibody-DNA probe (Ab2-DNA2) and subsequently the proximity hybridization of DNA1-DNA2, which led to the departure of MB-DNA1-Ab1 from the interface. The remained Fc-P could form a hairpin structure to take Fc group to electrode surface. Therefore, the recognition of target protein to Ab1 and Ab2 resulted in both the "signal-off" of MB and the "signal-on" of Fc for dual-signal electrochemical ratiometric readout. The proposed REPA could be carried out in one-step with 40-min duration and showed a wide detection range from 0.05 to 100 ng/mL with pg/mL limit of detection, displaying great potential for convenient point-of-care testing and commercial application.
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Affiliation(s)
- Kewei Ren
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093, P.R. China
- These authors contributed equally to this work
| | - Jie Wu
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093, P.R. China
- These authors contributed equally to this work
| | - Feng Yan
- Jiangsu Institute of Cancer Prevention and Cure, Nanjing 210009, P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093, P.R. China
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12
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Nong RY, Gu J, Darmanis S, Kamali-Moghaddam M, Landegren U. DNA-assisted protein detection technologies. Expert Rev Proteomics 2014; 9:21-32. [DOI: 10.1586/epr.11.78] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Zhou X, Liao Y, Xing D. Sensitive monitoring of RNA transcription levels using a graphene oxide fluorescence switch. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5584-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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14
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Flanigon J, Kamali-Moghaddam M, Burbulis I, Annink C, Steffen M, Oeth P, Brent R, van den Boom D, Landegren U, Cantor C. Multiplex protein detection with DNA readout via mass spectrometry. N Biotechnol 2012. [PMID: 23201185 DOI: 10.1016/j.nbt.2012.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Multiplex protein quantification has been constrained by issues of assay specificity, sensitivity and throughput. This research presents a novel approach that overcomes these limitations using antibody-oligonucleotide conjugates for immuno-polymerase chain reaction (immuno-PCR) or proximity ligation, coupled with competitive PCR and MALDI-TOF mass spectrometry. Employing these combinations of technologies, we demonstrate multiplex detection and quantification of up to eight proteins, spanning wide dynamic ranges from femtomolar concentrations, using only microliter sample volumes.
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Affiliation(s)
- James Flanigon
- Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
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15
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16
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Rossi EA, Goldenberg DM, Chang CH. Complex and defined biostructures with the dock-and-lock method. Trends Pharmacol Sci 2012; 33:474-81. [DOI: 10.1016/j.tips.2012.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/24/2012] [Accepted: 06/01/2012] [Indexed: 11/30/2022]
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17
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Singh AK, Stanker LH, Sharma SK. Botulinum neurotoxin: where are we with detection technologies? Crit Rev Microbiol 2012; 39:43-56. [PMID: 22676403 DOI: 10.3109/1040841x.2012.691457] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Because of its high toxicity, botulinum neurotoxin (BoNT) poses a significant risk to humans and it represents a possible biological warfare agent. Nevertheless, BoNT serotypes A and B are considered an effective treatment for a variety of neurological disorders. The growing applicability of BoNT as a drug, and its potential use as a biological threat agent, highlight the urgent need to develop sensitive detection assays and therapeutic counter measures. In the last decade, significant progress has been made in BoNT detection technologies but none have fully replaced the mouse lethality assay, the current "gold standard". Recently, new advances in robotics and the availability of new reagents have allowed development of methods for rapid toxin analysis. These technologies while promising need further refinement.
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Affiliation(s)
- Ajay K Singh
- Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
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Mashimo Y, Maeda H, Mie M, Kobatake E. Construction of semisynthetic DNA-protein conjugates with Phi X174 Gene-A* protein. Bioconjug Chem 2012; 23:1349-55. [PMID: 22616938 DOI: 10.1021/bc300118m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA-protein conjugates have frequently been used as versatile molecular tools for a variety of applications in biotechnology to harness synergistic effects of DNA and protein functions. With applications for DNA-protein conjugates growing, easy-to-use and economical methods for the synthesis of DNA-protein conjugates are required. In this study, we developed a method for site-specific labeling of single-stranded DNA (ssDNA) to a recombinant protein of interest (POI) through the Gene-A* protein (Gene-A*) from bacteriophage phi X174, without any chemical modifications of ssDNA. Gene-A* protein is an enzyme that site-selectively cleaves an oligodeoxyribonucleotide (ODN) containing a Gene-A* recognition sequence, at which point a tyrosine residue of Gene-A* is bonded to the 5'-phosphoryl group of the cleavage site via a stable phosphotyrosine linkage. Here, we constructed three kinds of recombinant proteins fused to Gene-A*: N-terminally Gene-A*-fused enhanced green fluorescent protein (EGFP), C-terminally Gene-A*-fused EGFP, and N-terminally Gene-A*-fused firefly luciferase (FLuc). The reaction yields of DNA-protein conjugation catalyzed by the Gene-A* moiety reached 80-90% in the three proteins, and kinetic study revealed that the reaction achieved a steady state after 10 min. Moreover, dot blot analyses were performed to evaluate the hybridization and aptamer-forming ability of ssDNA conjugated to the Gene-A* moiety of a recombinant Gene-A*-FLuc protein. This study demonstrated that a strategy using recombinant proteins fused to Gene-A* could offer a versatile, rapid, easy-to-use, and economical platform for producing DNA-protein conjugates.
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Affiliation(s)
- Yasumasa Mashimo
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology , 4259, Nagatsuta, Midori-ku, Yokohama-shi, 226-8501, Japan
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Akter F, Mie M, Grimm S, Nygren PÅ, Kobatake E. Detection of antigens using a protein-DNA chimera developed by enzymatic covalent bonding with phiX gene A*. Anal Chem 2012; 84:5040-6. [PMID: 22571843 DOI: 10.1021/ac300708r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The chemical reactions used to make antibody-DNA conjugates in many immunoassays diminish antigen-binding activity and yield heterogeneous products. Here, we address these issues by developing an antibody-based rolling circle amplification (RCA) strategy using a fusion of φX174 gene A* protein and Z(mab25) (A*-Zmab). The φX174 gene A* protein is an enzyme that can covalently link with DNA, while the Z(mab25) protein moiety can bind to specific species of antibodies. The DNA in an A*-Zmab conjugate was attached to the A* protein at a site chosen to not interfere with protein function, as determined by enzyme-linked immunosorbent assay (ELISA) and gel mobility shift analysis. The novel A*-Zmab-DNA conjugate retained its binding capabilities to a specific class of murine immunoglobulin γ1 (IgG1) but not to rabbit IgG. This indicates the generality of the A*-Zmab-based immuno-RCA assay that can be used in-sandwich ELISA format. Moreover, the enzymatic covalent method dramatically increased the yields of A*-Zmab-DNA conjugates up to 80% after a 15 min reaction. Finally, sensitive detection of human interferon-γ (IFN-γ) was achieved by immuno-RCA using our fusion protein in sandwich ELISA format. This new approach of the use of site-specific enzymatic DNA conjugation to proteins should be applicable to fabrication of novel immunoassays for biosensing.
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Affiliation(s)
- Farhima Akter
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Reed J, Hsueh C, Lam ML, Kjolby R, Sundstrom A, Mishra B, Gimzewski JK. Identifying individual DNA species in a complex mixture by precisely measuring the spacing between nicking restriction enzymes with atomic force microscope. J R Soc Interface 2012; 9:2341-50. [PMID: 22456455 DOI: 10.1098/rsif.2012.0024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We discuss a novel atomic force microscope-based method for identifying individual short DNA molecules (<5000 bp) within a complex mixture by measuring the intra-molecular spacing of a few sequence-specific topographical labels in each molecule. Using this method, we accurately determined the relative abundance of individual DNA species in a 15-species mixture, with fewer than 100 copies per species sampled. To assess the scalability of our approach, we conducted a computer simulation, with realistic parameters, of the hypothetical problem of detecting abundance changes in individual gene transcripts between two single-cell human messenger RNA samples, each containing roughly 9000 species. We found that this approach can distinguish transcript species abundance changes accurately in most cases, including transcript isoforms which would be challenging to quantitate with traditional methods. Given its sensitivity and procedural simplicity, our approach could be used to identify transcript-derived complementary DNAs, where it would have substantial technical and practical advantages versus established techniques in situations where sample material is scarce.
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Affiliation(s)
- Jason Reed
- California Nanosystems Institute (CNSI), University of California, Los Angeles, CA 90095, USA.
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Site-specific DNA-antibody conjugates for specific and sensitive immuno-PCR. Proc Natl Acad Sci U S A 2012; 109:3731-6. [PMID: 22345566 DOI: 10.1073/pnas.1120682109] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Antibody conjugates are widely used as diagnostics and imaging reagents. However, many such conjugates suffer losses in sensitivity and specificity due to nonspecific labeling techniques. We have developed methodology to site-specifically conjugate oligonucleotides to antibodies containing a genetically encoded unnatural amino acid with orthogonal chemical reactivity. These oligobody molecules were used in immuno-PCR assays to detect Her2(+) cells with greater sensitivity and specificity than nonspecifically coupled fragments, and can detect extremely rare Her2(+) cells in a complex cellular environment. Such designed antibody-oligonucleotide conjugates should provide sensitive and specific reagents for diagnostics, as well as enable other unique applications based on oligobody building blocks.
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22
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Rossi EA, Goldenberg DM, Chang CH. The dock-and-lock method combines recombinant engineering with site-specific covalent conjugation to generate multifunctional structures. Bioconjug Chem 2012; 23:309-23. [PMID: 22168393 DOI: 10.1021/bc2004999] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Advances in recombinant protein technology have facilitated the production of increasingly complex fusion proteins with multivalent, multifunctional designs for use in various in vitro and in vivo applications. In addition, traditional chemical conjugation remains a primary choice for linking proteins with polyethylene glycol (PEG), biotin, fluorescent markers, drugs, and others. More recently, site-specific conjugation of two or more interactive modules has emerged as a valid approach to expand the existing repertoires produced by either recombinant engineering or chemical conjugation alone, thus advancing the range of potential applications. Five such methods, each involving a specific binding event, are highlighted in this review, with a particular focus on the Dock-and-Lock (DNL) method, which exploits the natural interaction between the dimerization and docking domain (DDD) of cAMP-dependent protein kinase (PKA) and the anchoring domain (AD) of A-kinase anchoring proteins (AKAP). The various enablements of DNL to date include trivalent, tetravalent, pentavalent, and hexavalent antibodies of monospecificity or bispecificity; immnocytokines comprising multiple copies of interferon-alpha (IFNα); and site-specific PEGylation. These achievements attest to the power of the DNL platform technology to develop novel therapeutic and diagnostic agents from both proteins and nonproteins for unmet medical needs.
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Affiliation(s)
- Edmund A Rossi
- IBC Pharmaceuticals, Inc., Morris Plains, New Jersey, USA.
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Perrins RD, Orchard C, Zavodszky M, Kasry A, Nikolaev N, Harwood A, Borri P, Dale T. Doing more with less: a method for low total mass, affinity measurement using variable-length nanotethers. Anal Chem 2011; 83:8900-5. [PMID: 22029261 DOI: 10.1021/ac2012569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions between biomolecules are an important feature of biological systems and understanding these interactions is a key goal in biochemical studies. Using conventional techniques, such as surface plasmon resonance and isothermal titration calorimetry, the determination of the binding constants requires a significant amount of time and resources to produce and purify sufficient quantities of biomolecules in order to measure the affinity of biological interactions. Using DNA hybridization, we have demonstrated a new technique based on the use of nanotethers and time-resolved Forster resonance energy transfer (FRET) that significantly reduces the amount of material required to carry out quantitative binding assays. Test biomolecules were colocalized and attached to a surface using DNA tethers constructed from overlapping oligonucleotides. The length of the tethers defines the concentration of the tethered biomolecule. Effective end concentrations ranging from 56 nM to 3.8 μM were demonstrated. The use of variable length tethers may have wider applications in the quantitative measurement of affinity binding parameters.
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Affiliation(s)
- Richard D Perrins
- Cardiff School of Biosciences, Biomedical Sciences Building, Museum Avenue, Cardiff, CF10 3AX, UK
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24
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Seefeld TH, Zhou WJ, Corn RM. Rapid microarray detection of DNA and proteins in microliter volumes with surface plasmon resonance imaging measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:6534-40. [PMID: 21488682 PMCID: PMC3093654 DOI: 10.1021/la200649n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A four-chamber microfluidic biochip is fabricated for the rapid detection of multiple proteins and nucleic acids from microliter volume samples with the technique of surface plasmon resonance imaging (SPRI). The 18 mm × 18 mm biochip consists of four 3 μL microfluidic chambers attached to an SF10 glass substrate, each of which contains three individually addressable SPRI gold thin film microarray elements. The 12-element (4 × 3) SPRI microarray consists of gold thin film spots (1 mm(2) area; 45 nm thickness), each in individually addressable 0.5 μL volume microchannels. Microarrays of single-stranded DNA and RNA (ssDNA and ssRNA, respectively) are fabricated by either chemical and/or enzymatic attachment reactions in these microchannels; the SPRI microarrays are then used to detect femtomole amounts (nanomolar concentrations) of DNA and proteins (ssDNA binding protein and thrombin via aptamer-protein bioaffinity interactions). Microarrays of ssRNA microarray elements are also used for the ultrasensitive detection of zeptomole amounts (femtomolar concentrations) of DNA via the technique of RNase H-amplified SPRI. Enzymatic removal of ssRNA from the surface due to the hybridization adsorption of target ssDNA is detected as a reflectivity decrease in the SPR imaging measurements. The observed reflectivity loss is proportional to the log of the target ssDNA concentration with a detection limit of 10 fM or 30 zeptomoles (18 000 molecules). This enzymatic amplified ssDNA detection method is not limited by diffusion of ssDNA to the interface, and thus is extremely fast, requiring only 200 s in the microliter volume format.
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25
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Ghosh I, Considine N, Maunus E, Sun L, Zhang A, Buswell J, Evans TC, Xu MQ. Site-specific protein labeling by intein-mediated protein ligation. Methods Mol Biol 2011; 705:87-107. [PMID: 21125382 DOI: 10.1007/978-1-61737-967-3_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Intein-mediated protein ligation (IPL) employs an intein to create a protein possessing a C-terminal thioester that can be ligated to a protein or peptide with an amino-terminal cysteine via a native peptide bond. Here we present a procedure to conduct isolation and labeling of recombinant proteins expressed in E. coli using synthetic short peptides possessing a fluorescent moiety. This approach can be readily utilized for site-specific conjugation of a fluorophore to the C-terminus of a protein of interest, without the drawback of non-specific chemical labeling. This chapter also gives a general review of the critical parameters of intein-mediated cleavage and ligation reactions.
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Affiliation(s)
- Inca Ghosh
- New England BioLabs, Ipswich, MA 01938, USA.
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26
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Diezmann F, Seitz O. DNA-guided display of proteins and protein ligands for the interrogation of biology. Chem Soc Rev 2011; 40:5789-801. [DOI: 10.1039/c1cs15054e] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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27
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Niemeyer CM. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew Chem Int Ed Engl 2010; 49:1200-16. [PMID: 20091721 DOI: 10.1002/anie.200904930] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.
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Affiliation(s)
- Christof M Niemeyer
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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28
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Kim J, Yoon MY. Recent advances in rapid and ultrasensitive biosensors for infectious agents: lesson from Bacillus anthracis diagnostic sensors. Analyst 2010; 135:1182-90. [PMID: 20498871 DOI: 10.1039/c0an00030b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we review the cumulative efforts to develop rapid and ultrasensitive diagnostic systems, especially for the infectious agent, Bacillus anthracis, as a model system. This Minireview focuses on demonstrating the features of various probes for target molecule detection and recent methods of signal generation within the biosensors. Also, we discuss the possibility of using peptides as next-generation probe molecules.
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Affiliation(s)
- Joungmok Kim
- Department of Chemistry, Research Institute for Natural Sciences, Hanyang University, Seoul 133-791, Korea
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29
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Niemeyer C. Halbsynthetische DNA-Protein-Konjugate für Biosensorik und Nanofabrikation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904930] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Chao J, Huang WY, Wang J, Xiao SJ, Tang YC, Liu JN. Click-chemistry-conjugated oligo-angiomax in the two-dimensional DNA lattice and its interaction with thrombin. Biomacromolecules 2010; 10:877-83. [PMID: 19275167 DOI: 10.1021/bm8014076] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The recently arising antithrombin drug, angiomax, was successfully conjugated with a 5'-amino oligonucleotide through click chemistry. This oligo-angiomax conjugate was assembled into a two-dimensional DNA lattice with other oligonucleotides together. Besides the plane sheet of DNA lattices, an interesting angiomax-involved DNA tubing structure, constructed by 40 to 50 angiomax stripes which are parallel to the longitudinal axis of the tube, was also imaged. After incubation of thrombins with the angiomax-involved DNA lattice, the binding of thrombins to arrayed angiomax peptides was observed. Finally a chromogenic substrate bioassay was employed to estimate the antithrombin activities as assembled oligo-angiomax DNA lattice approximately 1.1, oligo-angiomax approximately 2.7 angiomax. The functionalized DNA lattices have the potential to be used as a powerful platform for investigation of biomolecular interactions such as drug-protein, protein-protein, DNA-RNA, and DNA-protein interactions in the nano- and subnanoscales.
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Affiliation(s)
- Jie Chao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, Jiangsu, People's Republic of China
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31
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Shan J, Toye P. A Novel Immuno-Polymerase Chain Reaction Protocol Incorporating a Highly Purified Streptavidin-DNA Conjugate. J Immunoassay Immunochem 2009; 30:322-37. [DOI: 10.1080/15321810903084764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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32
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Dahdah DB, Morin I, Moreau MJJ, Dixon NE, Schaeffer PM. Site-specific covalent attachment of DNA to proteins using a photoactivatable Tus-Ter complex. Chem Commun (Camb) 2009:3050-2. [PMID: 19462083 DOI: 10.1039/b900905a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Investigations into the photocrosslinking kinetics of the protein Tus with various bromodeoxyuridine-substituted Ter DNA variants highlight the potential use of this complex as a photoactivatable connector between proteins of interest and specific DNA sequences.
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Affiliation(s)
- Dahdah B Dahdah
- Comparative Genomics Centre, School of Pharmacy & Molecular Sciences, James Cook University, Townsville, QLD 4811, Australia
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33
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Yu RC, Resnekov O, Abola AP, Andrews SS, Benjamin KR, Bruck J, Burbulis IE, Colman-Lerner A, Endy D, Gordon A, Holl M, Lok L, Pesce CG, Serra E, Smith RD, Thomson TM, Tsong AE, Brent R. The Alpha Project: a model system for systems biology research. IET Syst Biol 2009; 2:222-33. [PMID: 19045818 DOI: 10.1049/iet-syb:20080127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
One goal of systems biology is to understand how genome-encoded parts interact to produce quantitative phenotypes. The Alpha Project is a medium-scale, interdisciplinary systems biology effort that aims to achieve this goal by understanding fundamental quantitative behaviours of a prototypic signal transduction pathway, the yeast pheromone response system from Saccharomyces cerevisiae. The Alpha Project distinguishes itself from many other systems biology projects by studying a tightly bounded and well-characterised system that is easily modified by genetic means, and by focusing on deep understanding of a discrete number of important and accessible quantitative behaviours. During the project, the authors have developed tools to measure the appropriate data and develop models at appropriate levels of detail to study a number of these quantitative behaviours. The authors have also developed transportable experimental tools and conceptual frameworks for understanding other signalling systems. In particular, the authors have begun to interpret system behaviours and their underlying molecular mechanisms through the lens of information transmission, a principal function of signalling systems. The Alpha Project demonstrates that interdisciplinary studies that identify key quantitative behaviours and measure important quantities, in the context of well-articulated abstractions of system function and appropriate analytical frameworks, can lead to deeper biological understanding. The authors' experience may provide a productive template for systems biology investigations of other cellular systems.
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Affiliation(s)
- R C Yu
- Molecular Sciences Institute, Berkeley, USA
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34
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Flavell RR, Muir TW. Expressed protein ligation (EPL) in the study of signal transduction, ion conduction, and chromatin biology. Acc Chem Res 2009; 42:107-16. [PMID: 18939858 DOI: 10.1021/ar800129c] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Expressed protein ligation (EPL) is a semisynthetic technique in which a recombinant protein thioester, generated by thiolysis of an intein fusion protein, is reacted with a synthetic or recombinant peptide with an N-terminal cysteine to produce a native peptide bond. This method has been used extensively for the incorporation of biophysical probes, unnatural amino acids, and post-translational modifications in proteins. In the 10 years since this technique was developed, the applications of EPL to studying protein structure and function have grown ever more sophisticated. In this Account, we review the use of EPL in selected systems in which substantial mechanistic insights have recently been gained through the use of the semisynthetic protein derivatives. EPL has been used in many studies to unravel the complexity of signaling networks and subcellular trafficking. Herein, we highlight this application to two different systems. First, we describe how phosphorylated or otherwise modified proteins in the TGF-beta signaling network were prepared and how they were applied to understanding the complexities of this pathway, from receptor activation to nuclear import. Second, Rab-GTPases are multiply modified with lipid derivatives, and EPL-based techniques were used to incorporate these modifications, allowing for the elucidation of the biophysical basis of membrane association and dissociation. We also review the use of EPL to understand the biology of two other systems, the potassium channel KcsA and histones. EPL was used to incorporate d-alanine and an amide-to-ester backbone modification in the selectivity filter of the KcsA potassium channel, providing insight into the mechanism of selectivity in ion conduction. In the case of histones, which are among the most heavily post-translationally modified proteins, the modifications play a key role in the regulation of gene transcription and chromatin structure. We describe how native chemical ligation and EPL were used to generate acetylated, phosphorylated, methylated, and ubiquitylated histones and how these modified histones were used to interrogate chromatin biology. Collectively, these studies demonstrate the utility of EPL in protein science. These techniques and concepts are applicable to many other systems, and ongoing advances promise to extend this semisynthetic technique to increasingly complex biological problems.
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Affiliation(s)
- Robert R. Flavell
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, New York 10065
| | - Tom W. Muir
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, New York 10065
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35
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Abstract
Synthetic protein-DNA conjugates are valuable tools with applications in fields including nanobiotechnology, bioanalytical chemistry, and molecular diagnostics, and various synthetic methods for their production have been developed during the past three decades. The present article reviews current methodologies for the synthesis of covalent protein-DNA conjugates with particular focus on the regiospecificity and stoichiometry of these reactions.
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36
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Takeda S, Tsukiji S, Ueda H, Nagamune T. Covalent split protein fragment-DNA hybrids generated through N-terminus-specific modification of proteins by oligonucleotides. Org Biomol Chem 2008; 6:2187-94. [PMID: 18528581 DOI: 10.1039/b720013g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Semisynthetic protein-DNA hybrid molecules have recently attracted much attention as valuable tools for bioanalytical chemistry and nanobiotechnology. Here we describe a synthetic method for conjugating oligonucleotides to the N-terminus of recombinant proteins. Our strategy involves the conversion of amine-terminated oligonucleotides to thioester-functionalized oligonucleotides by using a bifunctional reagent bearing an N-hydroxysuccinimide ester and benzyl thioester group, followed by native chemical ligation with proteins containing an N-terminal cysteine. We applied this technique to construct split luciferase fragment-DNA hybrid systems in which the catalytic activity of split luciferase is restored by the re-assembly of each fragment through a specific DNA-protein or DNA-DNA interaction. Split protein fragment-DNA hybrids will offer new opportunities to explore the potential of protein-DNA conjugates for various applications.
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Affiliation(s)
- Shuji Takeda
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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37
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Adler M, Wacker R, Niemeyer CM. Sensitivity by combination: immuno-PCR and related technologies. Analyst 2008; 133:702-18. [PMID: 18493669 DOI: 10.1039/b718587c] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The versatility of immunoassays for the detection of antigens can be combined with the signal amplification power of nucleic acid amplification techniques in a broad range of innovative detection strategies. This review summarizes the spectrum of both, DNA-modification techniques used for assay enhancement and the resulting key applications. In particular, it focuses on the highly sensitive immuno-PCR (IPCR) method. This technique is based on chimeric conjugates of specific antibodies and nucleic acid molecules, the latter of which are used as markers to be amplified by PCR or related techniques for signal generation and read-out. Various strategies for the combination of antigen detection and nucleic acid amplification are discussed with regard to their laboratory analytic performance, including novel approaches to the conjugation of antibodies with DNA, and alternative pathways for signal amplification and detection. A critical assessment of advantages and drawbacks of these methods for a number of applications in clinical diagnostics and research is conducted. The examples include the detection of viral and bacterial antigens, tumor markers, toxins, pathogens, cytokines and other targets in different biological sample materials.
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Affiliation(s)
- Michael Adler
- Chimera Biotec GmbH, Emil-Figge-Str. 76 A, D-44227, Dortmund, Germany
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38
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Chang CH, Rossi EA, Goldenberg DM. The dock and lock method: a novel platform technology for building multivalent, multifunctional structures of defined composition with retained bioactivity. Clin Cancer Res 2007; 13:5586s-5591s. [PMID: 17875793 DOI: 10.1158/1078-0432.ccr-07-1217] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The idea, approach, and proof-of-concept of the dock and lock (DNL) method, which has the potential for making a large number of bioactive molecules with multivalency and multifunctionality, are reviewed. The key to the DNL method seems to be the judicious application of a pair of distinct protein domains that are involved in the natural association between protein kinase A (PKA; cyclic AMP-dependent protein kinase) and A-kinase anchoring proteins. In essence, the dimerization and docking domain found in the regulatory subunit of PKA and the anchoring domain of an interactive A-kinase anchoring protein are each attached to a biological entity, and the resulting derivatives, when combined, readily form a stably tethered complex of a defined composition that fully retains the functions of individual constituents. Initial validation of the DNL method was provided by the successful generation of several trivalent bispecific binding proteins, each consisting of two identical Fab fragments linked site-specifically to a different Fab. The integration of genetic engineering and conjugation chemistry achieved with the DNL method may not only enable the creation of novel human therapeutics but could also provide the promise and challenge for the construction of improved recombinant products over those currently commercialized, including cytokines, vaccines, and monoclonal antibodies.
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39
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Duckworth B, Chen Y, Wollack J, Sham Y, Mueller J, Taton T, Distefano M. A Universal Method for the Preparation of Covalent Protein–DNA Conjugates for Use in Creating Protein Nanostructures. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701942] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Duckworth B, Chen Y, Wollack J, Sham Y, Mueller J, Taton T, Distefano M. A Universal Method for the Preparation of Covalent Protein–DNA Conjugates for Use in Creating Protein Nanostructures. Angew Chem Int Ed Engl 2007; 46:8819-22. [DOI: 10.1002/anie.200701942] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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41
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Burbulis I, Yamaguchi K, Yu R, Resnekov O, Brent R. Quantifying small numbers of antibodies with a 'near-universal' protein-DNA chimera. Nat Methods 2007; 4:1011-3. [PMID: 17982460 DOI: 10.1038/nmeth1127] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Accepted: 10/10/2007] [Indexed: 12/31/2022]
Abstract
We present general means to greatly increase the sensitivity of antibody-based assays. Augmentation relies on a 'tadpole' protein-DNA chimera whose protein moiety binds most classes of mammalian antibodies but not avian immunoglobulin Y (IgY). We used this tadpole in affinity capture assays followed by real-time PCR to quantify numerous molecules, including prostate-specific antigen (PSA) in human serum, with great sensitivity and accuracy.
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Affiliation(s)
- Ian Burbulis
- Center for Quantitative Genome Function and Molecular Sciences Institute, 2168 Shattuck Avenue, Berkeley, California 94704, USA
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42
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Fischer NO, Tarasow TM, Tok JBH. Protein detection via direct enzymatic amplification of short DNA aptamers. Anal Biochem 2007; 373:121-8. [PMID: 17980857 DOI: 10.1016/j.ab.2007.09.035] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 09/26/2007] [Accepted: 09/27/2007] [Indexed: 10/22/2022]
Abstract
Aptamers are single-stranded nucleic acids that fold into defined tertiary structures to bind target molecules with high specificities and affinities. DNA aptamers have garnered much interest as recognition elements for biodetection and diagnostic applications due to their small size, ease of discovery and synthesis, and chemical and thermal stability. Here we describe the design and application of a short DNA molecule capable of both protein target binding and amplifiable bioreadout processes. Because both recognition and readout capabilities are incorporated into a single DNA molecule, tedious conjugation procedures required for protein-DNA hybrids can be omitted. The DNA aptamer is designed to be amplified directly by either polymerase chain reaction (PCR) or rolling circle amplification (RCA) processes, taking advantage of real-time amplification monitoring techniques for target detection. A combination of both RCA and PCR provides a wide protein target dynamic range (1 microM to 10 pM).
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Affiliation(s)
- Nicholas O Fischer
- BioSecurity and NanoSciences Laboratory, Chemistry, Materials, and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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43
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Reed J, Mishra B, Pittenger B, Magonov S, Troke J, Teitell MA, Gimzewski JK. Single molecule transcription profiling with AFM. NANOTECHNOLOGY 2007; 18:44032. [PMID: 20721301 PMCID: PMC2922717 DOI: 10.1088/0957-4484/18/4/044032] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.
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Affiliation(s)
- Jason Reed
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Bud Mishra
- Department of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | | | | | - Joshua Troke
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
| | - Michael A Teitell
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
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44
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Lovrinovic M, Niemeyer CM. Microtiter plate-based screening for the optimization of DNA-protein conjugate synthesis by means of expressed protein ligation. Chembiochem 2007; 8:61-7. [PMID: 17121402 DOI: 10.1002/cbic.200600303] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report a rapid microtiter plate screening assay for the optimization of the synthesis of covalent DNA-protein conjugates by means of expressed protein ligation (EPL). The EPL method allows for the site-specific coupling of cysteine-modified DNA oligomers with recombinant intein-fusion proteins, the latter containing a C-terminal thioester that enables a mild and highly specific reaction with N-terminal cysteine compounds. To screen for optimal reaction conditions, we developed a microtiter plate-based assay that utilizes DNA-directed immobilization of the products formed in the ligation reaction of cysteine-modified DNA oligonucleotides with the model protein thioester of the maltose-binding protein (MBP), recombinantly expressed as an intein-fusion protein in E. coli. The screening assay allowed the rapid quantitative monitoring of various reaction parameters, such as the ratio of the reactants, reaction times, pH and ion strength of the buffer, the influence of various thiol additives and the nature of the chemical linker within the cysteine-bearing DNA oligonucleotide. As the consequence of the assay-based optimization, the ligation of MBP with the oligonucleotide was improved to near quantitative yields.
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Affiliation(s)
- Marina Lovrinovic
- Universität Dortmund, Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany
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45
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Branen JR, Hass MJ, Douthit ER, Maki WC, Branen AL. Detection of Escherichia coli O157, Salmonella enterica serovar Typhimurium, and staphylococcal enterotoxin B in a single sample using enzymatic bio-nanotransduction. J Food Prot 2007; 70:841-50. [PMID: 17477251 DOI: 10.4315/0362-028x-70.4.841] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Enzymatic bio-nanotransduction is a biological detection scheme based on the production of nucleic acid nano-signals (RNA) in response to specific biological recognition events. In this study, we applied an enzymatic bio-nanotransduction system to the detection of important food-related pathogens and a toxin. Escherichia coli O157:H7, Salmonella enterica serovar Typhimurium, and staphylococcal enterotoxin B (SEB) were chosen because of the implications of these targets to food safety. Primary antibodies to each of the targets were used to functionalize magnetic beads and produce biological recognition elements (antibodies) conjugated to nano-signal-producing DNA templates. Immunomagnetic capture that was followed by in vitro transcription of DNA templates bound to target molecules produced RNA nano-signals specific for every target in the sample. Discrimination of RNA nano-signals with a standard enzyme-linked oligonucleotide fluorescence assay provided a correlation between nano-signal profiles and target concentrations. The estimated limit of detection was 2.4 x 10(3) CFU/ml for E. coli O157:H7, 1.9 X 10(4) CFU/ml for S. enterica serovar Typhimurium, and 0.11 ng/ml for SEB with multianalyte detection in buffer. Low levels of one target were also detected in the presence of interference from high levels of the other targets. Finally, targets were detected in milk, and detection was improved for E. coli 0157 by heat treatment of the milk.
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Branen JR, Hass MJ, Maki WC, Branen AL. An enzymatic bionanotransduction system for multianalyte biological detection. J Appl Microbiol 2007; 102:892-908. [PMID: 17381732 DOI: 10.1111/j.1365-2672.2007.03300.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM The aim of this study was to develop and optimize a system for the detection of multiple biological targets in a single sample based on enzymatic bionanotransduction. METHOD AND RESULTS We used biological recognition elements (antibodies, DNA sequences) linked to DNA templates with T7 promoter regions for detection of specific target molecules. In vitro transcription of DNA templates bound to target molecules produced RNA nanosignals specific for every target in the sample. An enzyme-linked oligonucleotide fluorescence assay (ELOFA) provided a correlation between nanosignal profiles and target concentrations. The system was capable of detecting and distinguishing three species of specific immunoglobulin G (IgG) molecules at a level of 0.2 ng, mixed protein and DNA targets and single sample detection of Escherichia coli O157 micro-organisms and Staphylococcal enterotoxin B (SEB). CONCLUSIONS This report provided proof of concept for the use of enzymatic bionanotransduction with multianalyte biological detection based on differential nanosignal hybridization along with the application of this system to pathogen/toxin detection. SIGNIFICANCE AND IMPACT OF THE STUDY This system has the potential to be used as a tool for detection of multiple foodborne and environmental pathogens, toxins and targets of interest in a single sample.
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Affiliation(s)
- J R Branen
- University of Idaho, Post Falls, Idaho, USA.
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Lovrinovic M, Fruk L, Schröder H, Niemeyer CM. Site-specific labeling of DNA–protein conjugates by means of expressed protein ligation. Chem Commun (Camb) 2007:353-5. [PMID: 17220968 DOI: 10.1039/b614978b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Site-specific bioconjugation of protein thioesters with a DNA oligonucleotide was achieved by Expressed Protein Ligation (EPL) and the new thiol group formed upon EPL in the conjugate was selectively coupled with small molecule labels using maleimide chemistry.
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Affiliation(s)
- Marina Lovrinovic
- Universität Dortmund, Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
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Tominaga J, Kemori Y, Tanaka Y, Maruyama T, Kamiya N, Goto M. An enzymatic method for site-specific labeling of recombinant proteins with oligonucleotides. Chem Commun (Camb) 2006:401-3. [PMID: 17220984 DOI: 10.1039/b613793h] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA was site-specifically conjugated to a substrate peptide of microbial transglutaminase fused to the N- or C-terminus of target proteins without the loss of the proteins' functions of interest.
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Affiliation(s)
- Jo Tominaga
- Department of Applied Chemistry, Graduate School of Engineering, 744 Motooka, Fukuoka, 819-0395, Japan
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Scholler N, Garvik B, Quarles T, Jiang S, Urban N. Method for generation of in vivo biotinylated recombinant antibodies by yeast mating. J Immunol Methods 2006; 317:132-43. [PMID: 17113097 PMCID: PMC1784068 DOI: 10.1016/j.jim.2006.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 09/13/2006] [Accepted: 10/04/2006] [Indexed: 11/21/2022]
Abstract
We describe here a novel method for generation of yeast-secreted, in vivo biotinylated recombinant antibodies, or biobodies. Biobodies are secreted by diploid yeast resulting from the fusion of two haploid yeast of opposite mating type. One yeast carries a cDNA encoding an antibody recognition sequence fused to an IgA1 hinge and a biotin acceptor site (BCCP) at the C-terminus; the other carries a cDNA encoding an E. coli biotin ligase (BirA) fused to KEX2 golgi-localization sequences, so that BirA can catalyze the biotin transfer to the recognition sequence-fused BCCP within the yeast secretory compartment. We illustrate this technology with biobodies against HE4, a biomarker for ovarian carcinoma. Anti-HE4 biobodies were derived from clones or pools of anti-HE4-specific yeast-display scFv, constituting respectively monoclonal (mBb) or polyclonal (pBb) biobodies. Anti-HE4 biobodies were secreted directly biotinylated thus bound to labeled-streptavidin and streptavidin-coated surfaces without Ni-purification. Anti-HE4 biobodies demonstrated specificity and sensitivity by ELISA assays, flow cytometry analysis and Western blots prior to any maturation; dissociation equilibrium constants as measured by surface plasmon resonance sensor were of K(d)=4.8 x 10(-9) M and K(d)=5.1 x 10(-9) M before and after Ni-purification respectively. Thus, yeast mating permits cost-effective generation of biotinylated recombinant antibodies of high affinity.
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Affiliation(s)
- Nathalie Scholler
- Translational Outcomes Research Group, Molecular Diagnostics Program, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
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Becker CFW, Wacker R, Bouschen W, Seidel R, Kolaric B, Lang P, Schroeder H, Müller O, Niemeyer CM, Spengler B, Goody RS, Engelhard M. Direct readout of protein-protein interactions by mass spectrometry from protein-DNA microarrays. Angew Chem Int Ed Engl 2006; 44:7635-9. [PMID: 16245381 DOI: 10.1002/anie.200502908] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christian F W Becker
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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