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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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2
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Li A, Bouhss A, Clément MJ, Bauvais C, Taylor JP, Bollot G, Pastré D. Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives. Front Mol Biosci 2023; 10:1298441. [PMID: 38033386 PMCID: PMC10687564 DOI: 10.3389/fmolb.2023.1298441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
In recent years, RNA has gained traction both as a therapeutic molecule and as a therapeutic target in several human pathologies. In this review, we consider the approach of targeting RNA using small molecules for both research and therapeutic purposes. Given the primary challenge presented by the low structural diversity of RNA, we discuss the potential for targeting RNA: protein interactions to enhance the structural and sequence specificity of drug candidates. We review available tools and inherent challenges in this approach, ranging from adapted bioinformatics tools to in vitro and cellular high-throughput screening and functional analysis. We further consider two critical steps in targeting RNA/protein interactions: first, the integration of in silico and structural analyses to improve the efficacy of molecules by identifying scaffolds with high affinity, and second, increasing the likelihood of identifying on-target compounds in cells through a combination of high-throughput approaches and functional assays. We anticipate that the development of a new class of molecules targeting RNA: protein interactions to prevent physio-pathological mechanisms could significantly expand the arsenal of effective therapeutic compounds.
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Affiliation(s)
- Aixiao Li
- Synsight, Genopole Entreprises, Evry, France
| | - Ahmed Bouhss
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
| | - Marie-Jeanne Clément
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
| | | | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | | | - David Pastré
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
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3
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Dobrovodský D, Di Primo C. Do conformational changes contribute to the surface plasmon resonance signal? Biosens Bioelectron 2023; 232:115296. [PMID: 37079993 DOI: 10.1016/j.bios.2023.115296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/23/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
Abstract
Surface plasmon resonance (SPR)-based biosensors are widely used instruments for characterizing molecular interactions. In theory the SPR signal depends only on mass changes for interacting molecules of same chemical nature. Whether conformational changes of interacting molecules also contribute to the SPR signal is still a subject of lively debates. Works have been published claiming that conformational changes were detected but all factors contributing to the SPR signal were not carefully considered, in addition to often using no or improper controls. In the present work we used a very well-characterized oligonucleotide, the thrombin-binding DNA aptamer (TBA), which upon binding of potassium ions folds into a two G-tetrad antiparallel G-quadruplex structure. All terms contributing to the maximal expected SPR response, Rmax, in particular the refractive index increment, RII, of both partners and the fraction of immobilized TBA target available, ca, were experimentally assessed. The resulting Rmax was then compared to the maximal experimental SPR response for potassium ions binding to TBA using appropriate controls. Regardless how the RIIs were measured, by SPR or refractometry, and how much TBA available for interacting with potassium ions was considered, the theoretical and the experimental SPR responses never matched, the former being always lower than the latter. Using a straightforward experimental model system and by thoroughly taking into account all contributing factors we therefore conclude that conformational changes can indeed contribute to the measured SPR signal.
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4
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Morishita EC. Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies. Expert Opin Drug Discov 2023; 18:207-226. [PMID: 36322542 DOI: 10.1080/17460441.2022.2134852] [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: 11/05/2022]
Abstract
INTRODUCTION The field of RNA-targeted small molecules is rapidly evolving, owing to the advances in experimental and computational technologies. With the identification of several bioactive small molecules that target RNA, including the FDA-approved risdiplam, the biopharmaceutical industry is gaining confidence in the field. This review, based on the literature obtained from PubMed, aims to disseminate information about the various technologies developed for targeting RNA with small molecules and propose areas for improvement to develop drugs more efficiently, particularly those linked to diseases with unmet medical needs. AREAS COVERED The technologies for the identification of RNA targets, screening of chemical libraries against RNA, assessing the bioactivity and target engagement of the hit compounds, structure determination, and hit-to-lead optimization are reviewed. Along with the description of the technologies, their strengths, limitations, and examples of how they can impact drug discovery are provided. EXPERT OPINION Many existing technologies employed for protein targets have been repurposed for use in the discovery of RNA-targeted small molecules. In addition, technologies tailored for RNA targets have been developed. Nevertheless, more improvements are necessary, such as artificial intelligence to dissect important RNA structures and RNA-small-molecule interactions and more powerful chemical probing and structure prediction techniques.
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Arney JW, Weeks KM. RNA-Ligand Interactions Quantified by Surface Plasmon Resonance with Reference Subtraction. Biochemistry 2022; 61:1625-1632. [PMID: 35802500 PMCID: PMC9357220 DOI: 10.1021/acs.biochem.2c00177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structured RNAs bind ligands and are attractive targets for small-molecule drugs. A wide variety of analytical methods have been used to characterize RNA-ligand interactions, but our experience is that most have significant limitations in terms of material requirements and applicability to complex RNAs. Surface plasmon resonance (SPR) potentially overcomes these limitations, but we find that the standard experimental framework measures notable nonspecific electrostatic-mediated interactions, frustrating analysis of weak RNA binders. SPR measurements are typically quantified relative to a non-target reference channel. Here, we show that referencing to a channel containing a non-binding control RNA enables subtraction of nonspecific binding contributions, allowing measurements of accurate and specific binding affinities. We validated this approach for small-molecule binders of two riboswitch RNAs with affinities ranging from nanomolar to millimolar, including low-molecular-mass fragment ligands. SPR implemented with reference subtraction reliably discriminates specific from nonspecific binding, uses RNA and ligand material efficiently, and enables rapid exploration of the ligand-binding landscape for RNA targets.
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Affiliation(s)
- J. Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
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6
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Cai Z, Zafferani M, Akande OM, Hargrove AE. Quantitative Structure-Activity Relationship (QSAR) Study Predicts Small-Molecule Binding to RNA Structure. J Med Chem 2022; 65:7262-7277. [PMID: 35522972 PMCID: PMC9150105 DOI: 10.1021/acs.jmedchem.2c00254] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The diversity of RNA structural elements and their documented role in human diseases make RNA an attractive therapeutic target. However, progress in drug discovery and development has been hindered by challenges in the determination of high-resolution RNA structures and a limited understanding of the parameters that drive RNA recognition by small molecules, including a lack of validated quantitative structure-activity relationships (QSARs). Herein, we develop QSAR models that quantitatively predict both thermodynamic- and kinetic-based binding parameters of small molecules and the HIV-1 transactivation response (TAR) RNA model system. Small molecules bearing diverse scaffolds were screened against TAR using surface plasmon resonance. Multiple linear regression (MLR) combined with feature selection afforded robust models that allowed direct interpretation of the properties critical for both binding strength and kinetic rate constants. These models were validated with new molecules, and their accurate performance was confirmed via comparison to ensemble tree methods, supporting the general applicability of this platform.
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Affiliation(s)
- Zhengguo Cai
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Martina Zafferani
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Olanrewaju M. Akande
- Social
Science Research Institute, 140 Science Drive, Durham, North Carolina 27708, United States
| | - Amanda E. Hargrove
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States,. Phone: 919-660-1521. Fax: 919-660-1605
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Dursun AD, Dogan S, Kavruk M, Busra Tasbasi B, Sudagidan M, Deniz Yilmaz M, Yilmaz B, Ozalp VC, Tuna BG. Surface plasmon resonance aptasensor for soluble ICAM-1 protein in blood samples. Analyst 2022; 147:1663-1668. [DOI: 10.1039/d1an02332b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aptamer sequence for soluble ICAM-1 was selected by the SELEX procedure. The ICAM-1 aptamer was used to develop a magnetic separation from blood samples by silica shell nanoparticles and subsequent real-time detection by SPR biosensing.
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Affiliation(s)
- Ali Dogan Dursun
- Department of Physiology, School of Medicine, Atilim University, Ankara, Turkey
- Vocational School of Health Services, Atilim University, Ankara, Turkey
| | - Soner Dogan
- Department of Medical Biology, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Murat Kavruk
- Department of Nutrition and Dietetics, School of Health Sciences, Atilim University, Ankara, Turkey
| | - B. Busra Tasbasi
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Konya, Turkey
| | - Mert Sudagidan
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Konya, Turkey
| | - M. Deniz Yilmaz
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Konya, Turkey
- Department of Bioengineering, Konya Food and Agriculture University, Konya, Turkey
| | - Bayram Yilmaz
- Department of Physiology, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Veli C. Ozalp
- Department of Biology, School of Medicine, Atilim University, Ankara, Turkey
| | - Bilge G. Tuna
- Department of Biophysics, School of Medicine, Yeditepe University, Istanbul, Turkey
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Santos T, Salgado GF, Cabrita EJ, Cruz C. G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions. Pharmaceuticals (Basel) 2021; 14:769. [PMID: 34451866 PMCID: PMC8401999 DOI: 10.3390/ph14080769] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Affiliation(s)
- Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Gilmar F. Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France;
| | - Eurico J. Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
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9
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Recent Advancements in Aptamer-Based Surface Plasmon Resonance Biosensing Strategies. BIOSENSORS-BASEL 2021; 11:bios11070233. [PMID: 34356703 PMCID: PMC8301862 DOI: 10.3390/bios11070233] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022]
Abstract
Surface plasmon resonance (SPR) can track molecular interactions in real time, and is a powerful as well as widely used biological and chemical sensing technique. Among the different SPR-based sensing applications, aptamer-based SPR biosensors have attracted significant attention because of their simplicity, feasibility, and low cost for target detection. Continuous developments in SPR aptasensing research have led to the emergence of abundant technical and design concepts. To understand the recent advances in SPR for biosensing, this paper reviews SPR-based research from the last seven years based on different sensing-type strategies and sub-directions. The characteristics of various SPR-based applications are introduced. We hope that this review will guide the development of SPR aptamer sensors for healthcare.
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10
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Liao J, Han L, Xu C. Comparison of the sensitivity by SPR in a metal-ITO-BlueP/TMDC structure. APPLIED OPTICS 2021; 60:5161-5168. [PMID: 34143085 DOI: 10.1364/ao.425903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
A surface plasmon resonance (SPR) sensor based on blue phosphorus (BlueP)/transition metal dichalcogenides (TMDCs) of two-dimensional (2D) materials is proposed to increase the performance. In this sensor, BlueP/TMDCs are coated on indium tin oxide (ITO) and different metals (Au/Ag/Cu) to improve the sensitivity. By optimizing structural parameters, with the BlueP/WS2 monolayer and Au thin film, the angular sensitivity can reach as high as 226.0°/RIU. The phase sensitivity also can be as high as 3.6001×106deg/RIU with BlueP/MoS2 4 layers, 228 nm ITO, and 25 nm Au thin film, which is 6.77 times that of the Au-ITO structure and 54.40 times that of the traditional SPR of Au thin film. The SPR sensor has potential applications in disease diagnosis, drug development, gene sequencing and treatment, environmental monitoring, food safety testing, doping testing, and other fields.
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11
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Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners. Biochem Soc Trans 2021; 48:1529-1543. [PMID: 32820806 PMCID: PMC7458403 DOI: 10.1042/bst20191059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 02/01/2023]
Abstract
Interactions between proteins and RNA are at the base of numerous cellular regulatory and functional phenomena. The investigation of the biological relevance of non-coding RNAs has led to the identification of numerous novel RNA-binding proteins (RBPs). However, defining the RNA sequences and structures that are selectively recognised by an RBP remains challenging, since these interactions can be transient and highly dynamic, and may be mediated by unstructured regions in the protein, as in the case of many non-canonical RBPs. Numerous experimental and computational methodologies have been developed to predict, identify and verify the binding between a given RBP and potential RNA partners, but navigating across the vast ocean of data can be frustrating and misleading. In this mini-review, we propose a workflow for the identification of the RNA binding partners of putative, newly identified RBPs. The large pool of potential binders selected by in-cell experiments can be enriched by in silico tools such as catRAPID, which is able to predict the RNA sequences more likely to interact with specific RBP regions with high accuracy. The RNA candidates with the highest potential can then be analysed in vitro to determine the binding strength and to precisely identify the binding sites. The results thus obtained can furthermore validate the computational predictions, offering an all-round solution to the issue of finding the most likely RNA binding partners for a newly identified potential RBP.
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12
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Delannoy López DM, Tran DT, Viault G, Dairi S, Peixoto PA, Capello Y, Minder L, Pouységu L, Génot E, Di Primo C, Deffieux D, Quideau S. Real-Time Analysis of Polyphenol-Protein Interactions by Surface Plasmon Resonance Using Surface-Bound Polyphenols. Chemistry 2021; 27:5498-5508. [PMID: 33443311 DOI: 10.1002/chem.202005187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 11/11/2022]
Abstract
A selection of bioactive polyphenols of different structural classes, such as the ellagitannins vescalagin and vescalin, the flavanoids catechin, epicatechin, epigallocatechin gallate (EGCG), and procyanidin B2, and the stilbenoids resveratrol and piceatannol, were chemically modified to bear a biotin unit for enabling their immobilization on streptavidin-coated sensor chips. These sensor chips were used to evaluate in real time by surface plasmon resonance (SPR) the interactions of three different surface-bound polyphenolic ligands per sensor chip with various protein analytes, including human DNA topoisomerase IIα, flavonoid leucoanthocyanidin dioxygenase, B-cell lymphoma 2 apoptosis regulator protein, and bovine serum albumin. The types and levels of SPR responses unveiled major differences in the association, or lack thereof, and dissociation between a given protein analyte and different polyphenolic ligands. Thus, this multi-analysis SPR technique is a valuable methodology to rapidly screen and qualitatively compare various polyphenol-protein interactions.
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Affiliation(s)
| | - Dong Tien Tran
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Guillaume Viault
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Sofiane Dairi
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | | | - Yoan Capello
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Laëtitia Minder
- INSERM, CNRS, IECB (US001, UMS 3033), Univ. Bordeaux, 2 rue Robert Escarpit, 33607, Pessac Cedex, France
| | - Laurent Pouységu
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Elisabeth Génot
- Centre de Recherche Cardio-Thoracique de Bordeaux (INSERM U1045), Univ. Bordeaux, 2 rue Robert Escarpit, 33607, Pessac Cedex, France
| | - Carmelo Di Primo
- INSERM, CNRS (U1212, UMR 5320), IECB, Univ. Bordeaux, 2 rue Robert Escarpit, 33607, Pessac Cedex, France
| | - Denis Deffieux
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Stéphane Quideau
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France.,Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France
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Gao Y, Cao D, Pawnikar S, Akhter S, Miao Y, Liang B. Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations. STAR Protoc 2021; 2:100315. [PMID: 33659898 PMCID: PMC7890042 DOI: 10.1016/j.xpro.2021.100315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Here, we describe a generic protocol for monitoring protein-RNA interaction using a cleavable GFP fusion of a recombinant RNA-binding protein. We detail each expression and purification step, including high salt and heparin column for contaminant RNA removal. After the assembly of RNA into the ribonucleoprotein complex, the MicroScale Thermophoresis assay enables the binding affinity to be obtained quickly with a small amount of sample. Further Gaussian accelerated molecular dynamics simulations allow us to analyze protein:RNA interactions in detail. For complete details on the use and execution of this protocol, please refer to Gao et al. (2020). Using cleavable GFP fusion to monitor RNA-binding protein expression and purification High salt and heparin column to remove contamination RNA from RNA-binding proteins Use the MicroScale Thermophoresis (MST) assay to obtain the binding affinity (Kd) Simulate protein:RNA interactions with Gaussian accelerated molecular dynamics (GaMD)
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Affiliation(s)
- Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
| | - Sana Akhter
- Center for Computational Biology and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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14
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Giant Goos-Hänchen Shifts in Au-ITO-TMDCs-Graphene Heterostructure and Its Potential for High Performance Sensor. SENSORS 2020; 20:s20041028. [PMID: 32075012 PMCID: PMC7070563 DOI: 10.3390/s20041028] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/08/2020] [Accepted: 02/09/2020] [Indexed: 02/07/2023]
Abstract
In order to improve the performance of surface plasmon resonance (SPR) biosensor, the structure based on two-dimensional (2D) of graphene and transition metal dichalcogenides (TMDCs) are proposed to greatly enhance the Goos-Hänchen (GH) shift. It is theoretically proved that GH shift can be significantly enhanced in SPR structure coated with gold (Au)-indium tin oxide (ITO)-TMDCs-graphene heterostructure. In order to realize high GH shifts, the number of TMDCs and graphene layer are optimized. The highest GH shift (−801.7 λ) is obtained by Au-ITO-MoSe2-graphene hybrid structure with MoSe2 monolayer and graphene bilayer, respectively. By analyzing the GH variation, the index sensitivity of such configuration can reach as high as 8.02 × 105 λ/RIU, which is 293.24 times of the Au-ITO structure and 177.43 times of the Au-ITO-graphene structure. The proposed SPR biosensor can be widely used in the precision metrology and optical sensing.
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15
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Methods to identify and characterize RNA-targeting small molecules. Methods 2019; 167:1-2. [PMID: 31381979 DOI: 10.1016/j.ymeth.2019.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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