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Binding Characterization of Cyclic Peptide Ligands to Target Proteins and Chemical Epitopes Using ELISA and Fluorescence Polarization Assays. Methods Mol Biol 2021; 2371:335-354. [PMID: 34596857 DOI: 10.1007/978-1-0716-1689-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Enzyme-linked immunosorbent assay (ELISA) is a plate-based immunological assay designed to detect and quantify peptides, proteins, antibodies, and hormones. Fluorescence polarization (FP) is a solution-phase technique that can be used to determine equilibrium dissociation constant of ligand for the protein of interest. Here we describe the protocols for different ELISAs and for Fluorescence Polarization, and how they can be used to determine relative or absolute binding of macrocyclic peptides to the target proteins. In ELISA, the target protein is used as the antigen, and the binding of antigen is quantified using cyclic peptides and enzyme-linked antibodies. In Fluorescence Polarization assays, a cyclic ligand is fluorescent dye-labeled and titrated with serial concentrations of the non-labeled target protein to determine the equilibrium dissociation constant (KD) of ligand for protein. Detailed descriptions of sample preparation and the ELISA and FP experiments are provided in this chapter.
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Davis AN, Samlali K, Kapadia JB, Perreault J, Shih SCC, Kharma N. Digital Microfluidics Chips for the Execution and Real-Time Monitoring of Multiple Ribozymatic Cleavage Reactions. ACS OMEGA 2021; 6:22514-22524. [PMID: 34514224 PMCID: PMC8427639 DOI: 10.1021/acsomega.1c00239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/22/2021] [Indexed: 06/08/2023]
Abstract
In this paper, we describe the design and performance of two digital microfluidics (DMF) chips capable of executing multiple ribozymatic reactions, with proper controls, in response to short single-stranded DNA inducers. Since the fluorescence output of a reaction is measurable directly from the chip, without the need for gel electrophoresis, a complete experiment involving up to eight reactions (per chip) can be carried out reliably, relatively quickly, and efficiently. The ribozymes can also be used as biosensors of the concentration of oligonucleotide inputs, with high sensitivity, low limits of quantification and of detection, and excellent signal-to-noise ratio. The presented chips are readily usable devices that can be used to automate, speed up, and reduce the costs of ribozymatic reaction experiments.
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Affiliation(s)
- Alen N. Davis
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
| | - Kenza Samlali
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
| | - Jay B. Kapadia
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
| | - Jonathan Perreault
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
- Armand-Frappier
Health Biotechnology Center, Institut national
de la recherche scientifique, Laval, Québec H7V 1B7, Canada
| | - Steve C. C. Shih
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Nawwaf Kharma
- Department
of Electrical and Computer Engineering, Concordia University, Montreal, Québec H3G 1M8, Canada
- Centre
for Applied Synthetic Biology, Concordia
University, Montréal, Québec H4B 1R6, Canada
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Ultrasensitive monitoring of ribozyme cleavage product using molecular-beacon-ligation system. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11434-007-0074-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Crockett AO, Wittwer CT. Fluorescein-labeled oligonucleotides for real-time pcr: using the inherent quenching of deoxyguanosine nucleotides. Anal Biochem 2001; 290:89-97. [PMID: 11180941 DOI: 10.1006/abio.2000.4957] [Citation(s) in RCA: 197] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorescein-labeled oligonucleotide probes can be used to continuously monitor the polymerase chain reaction. Depending on the sequence, the fluorescence intensity of the probe is either increased or decreased by hybridization. The greatest effect is probe quenching by hybridization to amplicons containing deoxyguanosine nucleotides (Gs), giving a sequence-specific decrease in fluorescence as product accumulates. Quenching of the probes by Gs is position dependent. A 25% decrease in fluorescence of 5'-labeled probes was observed with a G at the first position of the 3'-dangling end. Additional Gs can increase quenching to about 40%. This change in fluorescence with hybridization allows real-time quantification and mutation detection with a simple single labeled probe. Quantification of the initial template copy number is possible by monitoring fluorescence at each cycle at a constant temperature. Mutation detection by Tm estimates from melting curve analysis for factor V Leiden, hemoglobin C, hemoglobin S, the thermolabile mutation of methylenetetrahydrofolate reductase, and the cystic fibrosis-associated deletion F508del is demonstrated. By using the inherent quenching of deoxyguanosine nucleotides in the amplicon, complicated probe designs involving internal quenching can be avoided.
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Affiliation(s)
- A O Crockett
- Department of Pathology, University of Utah Medical School, Salt Lake City, Utah 84132, USA
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