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Anders U, Gulotti-Georgieva M, Zelger-Paulus S, Hibti FE, Frydman C, Suckau D, Sigel RKO, Zenobi R. Screening for potential interaction partners with surface plasmon resonance imaging coupled to MALDI mass spectrometry. Anal Biochem 2021; 624:114195. [PMID: 33857502 DOI: 10.1016/j.ab.2021.114195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/14/2021] [Accepted: 04/02/2021] [Indexed: 11/29/2022]
Abstract
We coupled SPR imaging (SPRi) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) to identify new potential RNA binders. Here, we improve this powerful method, especially by optimizing the proteolytic digestion (type of reducing agent, its concentration, and incubation time), to work with complex mixtures, specifically a lysate of the rough mitochondrial fraction from yeast. The advantages of this hyphenated method compared to column-based or separate analyses are (i) rapid and direct visual readout from the SPRi array, (ii) possibility of high-throughput analysis of different interactions in parallel, (iii) high sensitivity, and (iv) no sample loss or contamination due to elution or micro-recovery procedures. The model system used is a catalytically active RNA (group IIB intron from Saccharomyces cerevisiae, Sc.ai5γ) and its cofactor Mss116. The protein supports the RNA folding process and thereby the subsequent excision of the intronic RNA from the coding part. Using the novel approach of coupling SPR with MALDI MS, we report the identification of potential RNA-binding proteins from a crude yeast mitochondrial lysate in a non-targeted approach. Our results show that proteins other than the well-known cofactor Mss116 interact with Sc.ai5γ (Dbp8, Prp8, Mrp13, and Cullin-3), suggesting that the intron folding and splicing are regulated by more than one cofactor in vivo.
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Affiliation(s)
- Ulrike Anders
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093, Zurich, Switzerland
| | - Maya Gulotti-Georgieva
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057, Zurich, Switzerland
| | - Susann Zelger-Paulus
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057, Zurich, Switzerland
| | - Fatima-Ezzahra Hibti
- Horiba France S.A.S, Avenue de La Vauve, Passage Jobin Yvon, CS 45002 - F-91120 Palaiseau, France
| | - Chiraz Frydman
- Horiba France S.A.S, Avenue de La Vauve, Passage Jobin Yvon, CS 45002 - F-91120 Palaiseau, France
| | - Detlev Suckau
- Bruker Daltonics, Fahrenheitstr. 4, D-28359 Bremen, Germany
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093, Zurich, Switzerland.
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Anders U, Schaefer JV, Hibti FE, Frydman C, Suckau D, Plückthun A, Zenobi R. SPRi-MALDI MS: characterization and identification of a kinase from cell lysate by specific interaction with different designed ankyrin repeat proteins. Anal Bioanal Chem 2016; 409:1827-1836. [DOI: 10.1007/s00216-016-0127-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/22/2016] [Accepted: 11/29/2016] [Indexed: 01/24/2023]
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Nevola L, Giralt E. Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 2015; 51:3302-15. [PMID: 25578807 DOI: 10.1039/c4cc08565e] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important and challenging targets in chemical biology and medicinal chemistry. The main difficulty encountered in the discovery of small molecule modulators derives from the large contact surfaces involved in PPIs when compared with those that participate in protein-small molecule interactions. Because of their intrinsic features, peptides can explore larger surfaces and therefore represent a useful alternative to modulate PPIs. The use of peptides as therapeutics has been held back by their instability in vivo and poor cell internalization. However, more than 200 peptide drugs and homologous compounds (proteins or antibodies) containing peptide bonds are (or have been) on the market, and many alternatives are now available to tackle these limitations. This review will focus on the latest progress in the field, spanning from "lead" identification methods to binding evaluation techniques, through an update of the most successful examples described in the literature.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain.
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Stigter E, de Jong G, van Bennekom W. Coupling surface-plasmon resonance and mass spectrometry to quantify and to identify ligands. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2012.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Surface plasmon resonance imaging in arrays coupled with mass spectrometry (SUPRA–MS): proof of concept of on-chip characterization of a potential breast cancer marker in human plasma. Anal Bioanal Chem 2012; 404:423-32. [DOI: 10.1007/s00216-012-6130-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 05/19/2012] [Accepted: 05/20/2012] [Indexed: 01/20/2023]
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Wang RE, Zhang Y, Cai J, Cai W, Gao T. Aptamer-based fluorescent biosensors. Curr Med Chem 2012; 18:4175-84. [PMID: 21838688 DOI: 10.2174/092986711797189637] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 01/24/2023]
Abstract
Selected from random pools of DNA or RNA molecules through systematic evolution of ligands by exponential enrichment (SELEX), aptamers can bind to target molecules with high affinity and specificity, which makes them ideal recognition elements in the development of biosensors. To date, aptamer-based biosensors have used a wide variety of detection techniques, which are briefly summarized in this article. The focus of this review is on the development of aptamer-based fluorescent biosensors, with emphasis on their design as well as properties such as sensitivity and specificity. These biosensors can be broadly divided into two categories: those using fluorescently-labeled aptamers and others that employ label-free aptamers. Within each category, they can be further divided into "signal-on" and "signal-off" sensors. A number of these aptamer-based fluorescent biosensors have shown promising results in biological samples such as urine and serum, suggesting their potential applications in biomedical research and disease diagnostics.
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Affiliation(s)
- R E Wang
- Department of Chemistry, Washington University in St. Louis, MO, USA
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Dragusanu M, Petre BA, Slamnoiu S, Vlad C, Tu T, Przybylski M. On-line bioaffinity-electrospray mass spectrometry for simultaneous detection, identification, and quantification of protein-ligand interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1643-1648. [PMID: 20692851 DOI: 10.1016/j.jasms.2010.06.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 06/18/2010] [Accepted: 06/18/2010] [Indexed: 05/29/2023]
Abstract
We describe here an on-line combination of a surface acoustic wave (SAW) biosensor with electrospray ionization mass spectrometry (SAW-ESI-MS) that enables the direct detection, identification, and quantification of affinity-bound ligands from a protein-ligand complex on a biosensor chip. A trapping column was used between the SAW-biosensor and the electrospray mass spectrometer equipped with a micro-guard column, which provides simultaneous sample concentration and desalting for the mass spectrometric analysis of the dissociated ligand. First applications of the on-line SAW-ESI-MS combination include (1), differentiation of β-amyloid (Aβ) epitope peptides bound to anti-Aβ antibodies; (2), the identification of immobilized Substance P peptide-calmodulin complex; (3), identification and quantification of the interaction of 3-nitrotyrosine-modified peptides with nitrotyrosine-specific antibodies; and (4), identification of immobilized anti-α-synuclein-human α-synuclein complex. Quantitative determinations of protein-ligand complexes by SAW yielded dissociation constants (K(D)) from micro-to low nanomolar sample concentrations. The on-line bioaffinity-ESI-MS combination presented here is expected to enable broad bioanalytical application to the simultaneous, label-free determination and quantification of biopolymer-ligand interactions, as diverse as antigen-antibody and lectin-carbohydrate complexes.
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Affiliation(s)
- Mihaela Dragusanu
- Laboratory of Analytical Chemistry and Biopolymer Structure Analysis, Department of Chemistry, University of Konstanz, Konstanz, Germany
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Zhou J, Battig MR, Wang Y. Aptamer-based molecular recognition for biosensor development. Anal Bioanal Chem 2010; 398:2471-80. [PMID: 20644915 DOI: 10.1007/s00216-010-3987-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 06/21/2010] [Accepted: 06/29/2010] [Indexed: 11/30/2022]
Abstract
Nucleic acid aptamers are an emerging class of synthetic ligands and have recently attracted significant attention in numerous fields. One is in biosensor development. In principle, nucleic acid aptamers can be discovered to recognize any molecule of interest with high affinity and specificity. In addition, unlike most ligands evolved in nature, synthetic nucleic acid aptamers are usually tolerant of harsh chemical, physical, and biological conditions. These distinguished characteristics make aptamers attractive molecular recognition ligands for biosensing applications. This review first concisely introduces methods for aptamer discovery including upstream selection and downstream truncation, then discusses aptamer-based biosensor development from the viewpoint of signal production.
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Affiliation(s)
- Jing Zhou
- Department of Chemical, Materials and Biomolecular Engineering, University of Connecticut, 191 Auditorium Road, Storrs, CT 06269-3222, USA
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Gronewold TMA, Baumgartner A, Hierer J, Sierra S, Blind M, Schäfer F, Blümer J, Tillmann T, Kiwitz A, Kaiser R, Zabe-Kühn M, Quandt E, Famulok M. Kinetic binding analysis of aptamers targeting HIV-1 proteins by a combination of a microbalance array and mass spectrometry (MAMS). J Proteome Res 2009; 8:3568-77. [PMID: 19469583 DOI: 10.1021/pr900265r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
An enhanced chip-based detection platform was developed by integrating a surface acoustic wave biosensor of the Love-wave type with protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). The system was applied to characterize the interaction of aptamers with their cognate HIV-1 proteins. The aptamers, which target two proteins of HIV-1, were identified using an automated in vitro selection platform. For aptamers S66A-C6 and S68B-C5, which target the V3 loop of the HIV-1 envelope protein gp120, KD values of 406 and 791 nM, respectively, were measured. Aptamer S69A-C15 was shown to bind HIV-1 reverse transcriptase (HIV-1 RT) with a KD value of 637 nM when immobilized on the biosensor surface. HIV-1 RT was identified with high significance using MALDI-ToF MS even in crude protein mixtures. The V3-loop of gp120 could be directly identified when using chip-bound purified protein samples. From crude protein mixtures, it could be identified indirectly with high significance via its fusion-partner glutathione-S-transferase (GST). Our data show that the combination of the selectivity of aptamers with a sensitive detection by MS enables the reliable and quantitative analysis of kinetic binding events of protein solutions in real time.
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Cho EJ, Lee JW, Ellington AD. Applications of aptamers as sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2009; 2:241-64. [PMID: 20636061 DOI: 10.1146/annurev.anchem.1.031207.112851] [Citation(s) in RCA: 577] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Aptamers are ligand-binding nucleic acids whose affinities and selectivities can rival those of antibodies. They have been adapted to analytical applications not only as alternatives to antibodies, but as unique reagents in their own right. In particular, aptamers can be readily site-specifically modified during chemical or enzymatic synthesis to incorporate particular reporters, linkers, or other moieties. Also, aptamer secondary structures can be engineered to undergo analyte-dependent conformational changes, which, in concert with the ability to specifically place chemical agents, opens up a wealth of possible signal transduction schemas, irrespective of whether the detection modality is optical, electrochemical, or mass based. Finally, because aptamers are nucleic acids, they are readily adapted to sequence- (and hence signal-) amplification methods. However, application of aptamers without a basic knowledge of their biochemistry or technical requirements can cause serious analytical difficulties.
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Affiliation(s)
- Eun Jeong Cho
- The Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, Texas 78712, USA.
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Mok W, Li Y. Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays. SENSORS 2008; 8:7050-7084. [PMID: 27873915 PMCID: PMC3787431 DOI: 10.3390/s8117050] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/25/2008] [Accepted: 10/30/2008] [Indexed: 02/03/2023]
Abstract
As the key constituents of the genetic code, the importance of nucleic acids to life has long been appreciated. Despite being composed of only four structurally similar nucleotides, single-stranded nucleic acids, as in single-stranded DNAs and RNAs, can fold into distinct three-dimensional shapes due to specific intramolecular interactions and carry out functions beyond serving as templates for protein synthesis. These functional nucleic acids (FNAs) can catalyze chemical reactions, regulate gene expression, and recognize target molecules. Aptamers, whose name is derived from the Latin word aptus meaning “to fit”, are oligonucleotides that can bind their target ligands with high affinity and specificity. Since aptamers exist in nature but can also be artificially isolated from pools of random nucleic acids through a process called in vitro selection, they can potentially bind a diverse array of compounds. In this review, we will discuss the research that is being done to develop aptamers against various biomolecules, the progress in engineering biosensors by coupling aptamers to signal transducers, and the prospect of employing these sensors for a range of chemical and biological applications. Advances in aptamer technology emphasizes that nucleic acids are not only the fundamental molecules of life, they can also serve as research tools to enhance our understanding of life. The possibility of using aptamer-based tools in drug discovery and the identification of infectious agents can ultimately augment our quality of life.
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Affiliation(s)
- Wendy Mok
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada.
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada.
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada.
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Boireau W, Rouleau A, Lucchi G, Ducoroy P. Revisited BIA-MS combination: entire "on-a-chip" processing leading to the proteins identification at low femtomole to sub-femtomole levels. Biosens Bioelectron 2008; 24:1121-7. [PMID: 18829299 DOI: 10.1016/j.bios.2008.06.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/13/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
Abstract
We present the results of a study in which biomolecular interaction analysis (BIA, Biacoretrade mark 2000) was combined with mass spectrometry (MS) using entire "on-a-chip" procedure. Most BIA-MS studies included an elution step of the analyte prior MS analysis. Here, we report a low-cost approach combining Biacore analysis with homemade chips and MS in situ identification onto the chips without elution step. First experiments have been made with rat serum albumin to determine the sensitivity and validation of the concept has been obtained with an antibody/antigen couple. Our "on-a-chip" procedure allowed complete analysis by MS/MS(2) of the biochip leading to protein identifications at low femtomole to sub-femtomole levels. Using this technique, identification of protein complexes were routinely obtained giving the opportunity to the "on-a-chip" processing to complete the BIA-MS approach in the discovery and analysis of protein complexes.
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Affiliation(s)
- W Boireau
- Institut FEMTO-ST, Université de Franche Comté, Clinical-Innovation Proteomic Platform, 32 Av de I'Observatoire, CNRS, 25044 Besançon, France
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