1
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Jurado Z, Murray RM. Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence. ACS Synth Biol 2024. [PMID: 39287516 DOI: 10.1021/acssynbio.4c00211] [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: 09/19/2024]
Abstract
The malachite green aptamer (MGapt) is known for its utility in RNA measurement in vivo and in lysate-based cell-free protein systems. However, MGapt fluorescence dynamics do not accurately reflect RNA concentration. Our study finds that MGapt fluorescence is unstable in commercial PURE systems. We discovered that the chemical composition of the cell-free reaction strongly influences MGapt fluorescence, which leads to inaccurate RNA calculations. Specific to the commercial system, we posit that MGapt fluorescence is significantly affected by the system's chemical properties, governed notably by the presence of dithiothreitol (DTT). We propose a model that, on average, accurately predicts MGapt measurement within a 10% margin, leveraging DTT concentration as a critical factor. This model sheds light on the complex dynamics of MGapt in cell-free systems and underscores the importance of considering environmental factors in RNA measurements using aptamers.
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Affiliation(s)
- Zoila Jurado
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91106, United States
| | - Richard M Murray
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91106, United States
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2
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Nucleic acid-assisted CRISPR-Cas systems for advanced biosensing and bioimaging. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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3
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Assays to Estimate the Binding Affinity of Aptamers. Talanta 2022; 238:122971. [PMID: 34857318 DOI: 10.1016/j.talanta.2021.122971] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.
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4
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Araujo-Rocha M, Piro B, Noël V, Barbault F. Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement. J Phys Chem B 2021; 125:9499-9506. [PMID: 34403245 DOI: 10.1021/acs.jpcb.1c05341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aptamers are a class of bioreceptors intensively used in current analytical tools dedicated to molecular diagnostics due to their ability to perform large structural reorganization upon target binding. However, there is a lack of methodologies allowing us to rationalize their structure in order to improve the transduction efficiency in aptamer sensors. We choose here, as a model system, a three-strand DNA structure as the probe, composed of two DNA strands anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to ampicillin (AMP). The DNA structure has been designed to show strong structural change upon AMP binding to its aptamer. Using a set of computational techniques including molecular dynamics simulations, we deeply investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses of ion distributions along the trajectories unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates the ability of computational investigations for the first time to drive, in silico, the design of aptasensors.
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Affiliation(s)
| | - Benoît Piro
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Vincent Noël
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
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5
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Piccolo KA, McNeil B, Crouse J, Lim SJ, Bickers SC, Hopkins WS, Dieckmann T. Ligand specificity and affinity in the sulforhodamine B binding RNA aptamer. Biochem Biophys Res Commun 2020; 529:666-671. [PMID: 32736690 DOI: 10.1016/j.bbrc.2020.06.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 10/23/2022]
Abstract
Binding affinity and selectivity are critical properties of aptamers that must be optimized for any application. The sulforhodamine B binding RNA aptamer (SRB-2) is a somewhat promiscuous aptamer that can bind ligands that vary markedly in shape, size and charge. Here we categorize potential ligands based on their binding mode and structural characteristics required for high affinity and selectivity. Several known and potential ligands of SRB-2 were screened for binding affinity using LSPR, ITC and NMR spectroscopy. The study shows that rhodamine B has the ideal structural and electrostatic properties for selective and high-affinity binding of the SRB-2 aptamer.
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Affiliation(s)
- Kyle A Piccolo
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Brooke McNeil
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Jeff Crouse
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Su Ji Lim
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sarah C Bickers
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada; Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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6
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Thevendran R, Navien TN, Meng X, Wen K, Lin Q, Sarah S, Tang TH, Citartan M. Mathematical approaches in estimating aptamer-target binding affinity. Anal Biochem 2020; 600:113742. [PMID: 32315616 DOI: 10.1016/j.ab.2020.113742] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/25/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
The performance of aptamers as versatile tools in numerous analytical applications is critically dependent on their high target binding specificity and selectivity. However, only the technical or methodological aspects of measuring aptamer-target binding affinities are focused, ignoring the equally important mathematical components that play pivotal roles in affinity measurements. In this study, we aim to provide a comprehensive review regarding the utilization of different mathematical models and equations, along with a detailed description of the computational steps involved in mathematically deriving the binding affinity of aptamers against their specific target molecules. Mathematical models ranging from one-site binding to multiple aptameric binding site-based models are explained in detail. Models applied in several different approaches of affinity measurements such as thermodynamics and kinetic analysis, including cooperativity and competitive-assay based mathematical models have been elaborately discussed. Mathematical models incorporating factors that could potentially affect affinity measurements are also further scrutinized.
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Affiliation(s)
- Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Xin Meng
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Kechun Wen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Shigdar Sarah
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria, 3216, Australia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia; Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States.
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7
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Wu L, Xu Z, Meng Q, Xiao Y, Cao Q, Rathi B, Liu H, Han G, Zhang J, Yan J. A new aptamer/black phosphorous interdigital electrode for malachite green detection. Anal Chim Acta 2019; 1099:39-45. [PMID: 31986275 DOI: 10.1016/j.aca.2019.11.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/05/2019] [Accepted: 11/09/2019] [Indexed: 01/13/2023]
Abstract
Malachite Green (MG), a cationic triphenylmethane dye, has adverse effects on the immune and reproductive system. Thus, it is essential to develop a rapid, sensitive and high-selective method for determination of MG. Black phosphorus (BP) has high charge-carrier mobility (∼1000 cm2 V-1 s-1) and high adsorption capacity for cationic dyes (i.e. MG) through both electrostatic and hydrophobic interactions. Thus, it potentially plays as a high-sensitive sensing platform for detecting MG. However, BP degrades within 12 h under humid condition, which limits its applications. To overcome this issue, cysteine (CYS) is used for protecting BP from oxidation and ceasing its degradation. To the best of our knowledge, it is the first time that CYS is used to functionalize BP, and a silicon interdigital electrode is fabricated with the functionalized BP and aptamer. The BP-based interdigital electrode shows a lowest detection limit of 0.3 ng L-1 toward MG. This work provides a new route to prepare a large scale and selective biosensor for MG monitoring on site in future.
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Affiliation(s)
- Lidong Wu
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
| | - Zhiyuan Xu
- College of Information, North China University of Technology, Beijing, 100043, China
| | - Qingyi Meng
- College of Information, North China University of Technology, Beijing, 100043, China
| | - Yushi Xiao
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Chinese Academy of Fishery Sciences, Beijing, 100141, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Qiang Cao
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Chinese Academy of Fishery Sciences, Beijing, 100141, China; College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Brijesh Rathi
- Department of Chemistry, Hansraj College University of Delhi, Delhi, 110007, India
| | - Huan Liu
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Gang Han
- Key Laboratory of Control of Quality and Safety for Aquatic Products, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Jing Zhang
- College of Information, North China University of Technology, Beijing, 100043, China
| | - Jiang Yan
- College of Information, North China University of Technology, Beijing, 100043, China
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8
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Karunanayake Mudiyanselage APKK, Wu R, Leon-Duque MA, Ren K, You M. "Second-generation" fluorogenic RNA-based sensors. Methods 2019; 161:24-34. [PMID: 30660865 PMCID: PMC6589113 DOI: 10.1016/j.ymeth.2019.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 02/07/2023] Open
Abstract
A fluorogenic aptamer can specifically interact with a fluorophore to activate its fluorescence. These nucleic acid-based fluorogenic modules have been dramatically developed over the past decade, and have been used as versatile reporters in the sensor development and for intracellular imaging. In this review, we summarize the design principles, applications, and challenges of the first-generation fluorogenic RNA-based sensors. Moreover, we discuss some strategies to develop next-generation biosensors with improved sensitivity, selectivity, quantification property, and eukaryotic robustness. Using genetically encoded catalytic hairpin assembly strategy as an example, we further introduce a standard protocol to design, characterize, and apply these fluorogenic RNA-based sensors for in vitro detection and cellular imaging of target biomolecules. By incorporating natural RNA machineries, nucleic acid nanotechnology, and systematic evolution approaches, next-generation fluorogenic RNA-based devices can be potentially engineered to be widely applied in cell biology and biomedicine.
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Affiliation(s)
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Mark A Leon-Duque
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA.
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9
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2019; 58:1266-1279. [PMID: 30102012 PMCID: PMC6391945 DOI: 10.1002/anie.201806482] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/16/2022]
Abstract
The cellular functions of RNA are not limited to their role as blueprints for protein synthesis. In particular, noncoding RNA, such as, snRNAs, lncRNAs, miRNAs, play important roles. With increasing numbers of RNAs being identified, it is well known that the transcriptome outnumbers the proteome by far. This emphasizes the great importance of functional RNA characterization and the need to further develop tools for these investigations, many of which are still in their infancy. Fluorescent light-up aptamers (FLAPs) are RNA sequences that can bind nontoxic, cell-permeable small-molecule fluorogens and enhance their fluorescence over many orders of magnitude upon binding. FLAPs can be encoded on the DNA level using standard molecular biology tools and are subsequently transcribed into RNA by the cellular machinery, so that they can be used as fluorescent RNA tags (FLAP-tags). In this Minireview, we give a brief overview of the fluorogens that have been developed and their binding RNA aptamers, with a special focus on published crystal structures. A summary of current and future cellular FLAP applications with an emphasis on the study of RNA-RNA and RNA-protein interactions using split-FLAP and Förster resonance energy transfer (FRET) systems is given.
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Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
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10
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
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11
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Yerramilli VS, Kim KH. Labeling RNAs in Live Cells Using Malachite Green Aptamer Scaffolds as Fluorescent Probes. ACS Synth Biol 2018. [PMID: 29513000 DOI: 10.1021/acssynbio.7b00237] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNAs mediate many different processes that are central to cellular function. The ability to quantify or image RNAs in live cells is very useful in elucidating such functions of RNA. RNA aptamer-fluorogen systems have been increasingly used in labeling RNAs in live cells. Here, we use the malachite green aptamer (MGA), an RNA aptamer that can specifically bind to malachite green (MG) dye and induces it to emit far-red fluorescence signals. Previous studies on MGA showed a potential for the use of MGA for genetically tagging other RNA molecules in live cells. However, these studies also exhibited low fluorescence signals and high background noise. Here we constructed and tested RNA scaffolds containing multiple tandem repeats of MGA as a strategy to increase the brightness of the MGA aptamer-fluorogen system as well as to make the system fluoresce when tagging various RNA molecules, in live cells. We demonstrate that our MGA scaffolds can induce fluorescence signals by up to ∼20-fold compared to the basal level as a genetic tag for other RNA molecules. We also show that our scaffolds function reliably as genetically encoded fluorescent tags for mRNAs of fluorescent proteins and other RNA aptamers.
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Affiliation(s)
- V. Siddartha Yerramilli
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| | - Kyung Hyuk Kim
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
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12
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Challier L, Miranda-Castro R, Barbe B, Fave C, Limoges B, Peyrin E, Ravelet C, Fiore E, Labbé P, Coche-Guérente L, Ennifar E, Bec G, Dumas P, Mavré F, Noël V. Multianalytical Study of the Binding between a Small Chiral Molecule and a DNA Aptamer: Evidence for Asymmetric Steric Effect upon 3'- versus 5'-End Sequence Modification. Anal Chem 2016; 88:11963-11971. [PMID: 27934108 DOI: 10.1021/acs.analchem.6b04046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nucleic acid aptamers are involved in a broad field of applications ranging from therapeutics to analytics. Deciphering the binding mechanisms between aptamers and small ligands is therefore crucial to improve and optimize existing applications and to develop new ones. Particularly interesting is the enantiospecific binding mechanism involving small molecules with nonprestructured aptamers. One archetypal example is the chiral binding between l-tyrosinamide and its 49-mer aptamer for which neither structural nor mechanistic information is available. In the present work, we have taken advantage of a multiple analytical characterization strategy (i.e., using electroanalytical techniques such as kinetic rotating droplet electrochemistry, fluorescence polarization, isothermal titration calorimetry, and quartz crystal microbalance) for interpreting the nature of binding process. Screening of the binding thermodynamics and kinetics with a wide range of aptamer sequences revealed the lack of symmetry between the two ends of the 23-mer minimal binding sequence, showing an unprecedented influence of the 5' aptamer modification on the bimolecular binding rate constant kon and no significant effect on the dissociation rate constant koff. The results we have obtained lead us to conclude that the enantiospecific binding reaction occurs through an induced-fit mechanism, wherein the ligand promotes a primary nucleation binding step near the 5'-end of the aptamer followed by a directional folding of the aptamer around its target from 5'-end to 3'-end. Functionalization of the 5'-end position by a chemical label, a polydA tail, a protein, or a surface influences the kinetic/thermodynamic constants up to 2 orders of magnitude in the extreme case of a surface immobilized aptamer, while significantly weaker effect is observed for a 3'-end modification. The reason is that steric hindrance must be overcome to nucleate the binding complex in the presence of a modification near the nucleation site.
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Affiliation(s)
- Lylian Challier
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Rebeca Miranda-Castro
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Bertrand Barbe
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Pierre Labbé
- Département de Chimie Moléculaire, CNRS, UMR 5250, Université Grenoble Alpes , FR 2607, 570 rue de la chimie, B.P. 53, 38400 Grenoble, France
| | - Liliane Coche-Guérente
- Département de Chimie Moléculaire, CNRS, UMR 5250, Université Grenoble Alpes , FR 2607, 570 rue de la chimie, B.P. 53, 38400 Grenoble, France
| | - Eric Ennifar
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - Guillaume Bec
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - Philippe Dumas
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - François Mavré
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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Amano R, Takada K, Tanaka Y, Nakamura Y, Kawai G, Kozu T, Sakamoto T. Kinetic and Thermodynamic Analyses of Interaction between a High-Affinity RNA Aptamer and Its Target Protein. Biochemistry 2016; 55:6221-6229. [PMID: 27766833 DOI: 10.1021/acs.biochem.6b00748] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AML1 (RUNX1) protein is an essential transcription factor involved in the development of hematopoietic cells. Several genetic aberrations that disrupt the function of AML1 have been frequently observed in human leukemia. AML1 contains a DNA-binding domain known as the Runt domain (RD), which recognizes the RD-binding double-stranded DNA element of target genes. In this study, we identified high-affinity RNA aptamers that bind to RD by systematic evolution of ligands by exponential enrichment. The binding assay using surface plasmon resonance indicated that a shortened aptamer retained the ability to bind to RD when 1 M potassium acetate was used. A thermodynamic study using isothermal titration calorimetry (ITC) showed that the aptamer-RD interaction is driven by a large enthalpy change, and its unfavorable entropy change is compensated by a favorable enthalpy change. Furthermore, the binding heat capacity change was identified from the ITC data at various temperatures. The aptamer binding showed a large negative heat capacity change, which suggests that a large apolar surface is buried upon such binding. Thus, we proposed that the aptamer binds to RD with long-range electrostatic force in the early stage of the association and then changes its conformation and recognizes a large surface area of RD. These findings about the biophysics of aptamer binding should be useful for understanding the mechanism of RNA-protein interaction and optimizing and modifying RNA aptamers.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kenta Takada
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yoichiro Tanaka
- Facility for RI Research and Education, Instrumental Analysis Center, Yokohama National University , 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Yoshikazu Nakamura
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo , Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Ribomic Inc. , 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology , Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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14
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Zhou Y, Chi H, Wu Y, Marks RS, Steele TWJ. Organic additives stabilize RNA aptamer binding of malachite green. Talanta 2016; 160:172-182. [PMID: 27591602 DOI: 10.1016/j.talanta.2016.06.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 11/27/2022]
Abstract
Aptamer-ligand binding has been utilized for biological applications due to its specific binding and synthetic nature. However, the applications will be limited if the binding or the ligand is unstable. Malachite green aptamer (MGA) and its labile ligand malachite green (MG) were found to have increasing apparent dissociation constants (Kd) as determined through the first order rate loss of emission intensity of the MGA-MG fluorescent complex. The fluorescent intensity loss was hypothesized to be from the hydrolysis of MG into malachite green carbinol base (MGOH). Random screening organic additives were found to reduce or retain the fluorescence emission and the calculated apparent Kd of MGA-MG binding. The protective effect became more apparent as the percentage of organic additives increased up to 10% v/v. The mechanism behind the organic additive protective effects was primarily from a ~5X increase in first order rate kinetics of MGOH→MG (kMGOH→MG), which significantly changed the equilibrium constant (Keq), favoring the generation of MG, versus MGOH without organic additives. A simple way has been developed to stabilize the apparent Kd of MGA-MG binding over 24h, which may be beneficial in stabilizing other triphenylmethane or carbocation ligand-aptamer interactions that are susceptible to SN1 hydrolysis.
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Affiliation(s)
- Yubin Zhou
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore
| | - Hong Chi
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore
| | - Yuanyuan Wu
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore
| | - Robert S Marks
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore; Department of Biotechnology Engineering, Faculty of Engineering Sciences, Ben Gurion University of the NegevP.O. Box 653Beer Sheva84105Israel
| | - Terry W J Steele
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University50 Nanyang AvenueSingapore639798Singapore.
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15
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Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations. Biophys J 2016; 107:2962-2971. [PMID: 25517161 DOI: 10.1016/j.bpj.2014.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/16/2014] [Accepted: 11/03/2014] [Indexed: 12/12/2022] Open
Abstract
Synthetic riboswitches are versatile tools for the study and manipulation of biological systems. Yet, the underlying mechanisms governing its structural properties and regulation under physiological conditions are poorly studied. We performed spectroscopic and calorimetric experiments to explore the folding kinetics and thermodynamics of the tetracycline-binding aptamer, which can be employed as synthetic riboswitch, in the range of physiological magnesium concentrations. The dissociation constant of the ligand-aptamer complex was found to strongly depend on the magnesium concentration. At physiological magnesium concentrations, tetracycline induces a significant conformational shift from a compact, but heterogeneous intermediate state toward the completely formed set of tertiary interactions defining the regulation-competent structure. Thus, the switching functionality of the tetracycline-binding aptamer appears to include both a conformational rearrangement toward the regulation-competent structure and its thermodynamic stabilization.
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16
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Abstract
Intracellular trafficking and asymmetric localization of RNA molecules within cells are a prevalent process across phyla involved in developmental control and signaling and thus in the determination of cell fate. In addition to intracellular localization, plants support the trafficking of RNA molecules also between cells through plasmodesmata (PD), which has important roles in the cell-to-cell and systemic communication during plant growth and development. Viruses have developed strategies to exploit the underlying plant RNA transport mechanisms for the cell-to-cell and systemic dissemination of infection. In vivo RNA visualization methods have revolutionized the study of RNA dynamics in living cells. However, their application in plants is still in its infancy. To gain insights into the RNA transport mechanisms in plants, we study the localization and transport of Tobacco mosaic virus RNA using MS2 tagging. This technique involves the tagging of the RNA of interest with repeats of an RNA stem-loop (SL) that is derived from the origin of assembly of the bacteriophage MS2 and recruits the MS2 coat protein (MCP). Thus, expression of MCP fused to a fluorescent marker allows the specific visualization of the SL-carrying RNA. Here we describe a detailed protocol for Agrobacterium tumefaciens-mediated transient expression and in vivo visualization of MS2-tagged mRNAs in Nicotiana benthamiana leaves.
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Affiliation(s)
- E J Peña
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata CONICET, Fac. Cs. Exactas, U.N.L.P., La Plata, Argentina
| | - M Heinlein
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France.
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17
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Yang J, Donolato M, Pinto A, Bosco FG, Hwu ET, Chen CH, Alstrøm TS, Lee GH, Schäfer T, Vavassori P, Boisen A, Lin Q, Hansen MF. Blu-ray based optomagnetic aptasensor for detection of small molecules. Biosens Bioelectron 2015; 75:396-403. [PMID: 26342583 DOI: 10.1016/j.bios.2015.08.062] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
This paper describes an aptamer-based optomagnetic biosensor for detection of a small molecule based on target binding-induced inhibition of magnetic nanoparticle (MNP) clustering. For the detection of a target small molecule, two mutually exclusive binding reactions (aptamer-target binding and aptamer-DNA linker hybridization) are designed. An aptamer specific to the target and a DNA linker complementary to a part of the aptamer sequence are immobilized onto separate MNPs. Hybridization of the DNA linker and the aptamer induces formation of MNP clusters. The target-to-aptamer binding on MNPs prior to the addition of linker-functionalized MNPs significantly hinders the hybridization reaction, thus reducing the degree of MNP clustering. The clustering state, which is thus related to the target concentration, is then quantitatively determined by an optomagnetic readout technique that provides the hydrodynamic size distribution of MNPs and their clusters. A commercial Blu-ray optical pickup unit is used for optical signal acquisition, which enables the establishment of a low-cost and miniaturized biosensing platform. Experimental results show that the degree of MNP clustering correlates well with the concentration of a target small molecule, adenosine triphosphate (ATP) in this work, in the range between 10µM and 10mM. This successful proof-of-concept indicates that our optomagnetic aptasensor can be further developed as a low-cost biosensing platform for detection of small molecule biomarkers in an out-of-lab setting.
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Affiliation(s)
- Jaeyoung Yang
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark; Department of Mechanical Engineering, Columbia University, New York, NY 10027, United States
| | - Marco Donolato
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - Alessandro Pinto
- POLYMAT, University of the Basque Country UPV/EHU, 20018 Donostia-San Sebastián, Spain
| | - Filippo Giacomo Bosco
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - En-Te Hwu
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Ching-Hsiu Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Tommy Sonne Alstrøm
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - Gwan-Hyoung Lee
- Department of Materials Science and Engineering, Yonsei University, Seoul 120-749, Republic of Korea
| | - Thomas Schäfer
- POLYMAT, University of the Basque Country UPV/EHU, 20018 Donostia-San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Paolo Vavassori
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain; CIC nanoGUNE Consolider, 20018 Donostia-San Sebastián, Spain
| | - Anja Boisen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, United States.
| | - Mikkel Fougt Hansen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark.
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18
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Fiore E, Dausse E, Dubouchaud H, Peyrin E, Ravelet C. Ultrafast capillary electrophoresis isolation of DNA aptamer for the PCR amplification-based small analyte sensing. Front Chem 2015; 3:49. [PMID: 26322305 PMCID: PMC4533002 DOI: 10.3389/fchem.2015.00049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/27/2015] [Indexed: 01/14/2023] Open
Abstract
Here, we report a new homogeneous DNA amplification-based aptamer assay for small analyte sensing. The aptamer of adenosine chosen as the model analyte was split into two fragments able to assemble in the presence of target. Primers were introduced at extremities of one fragment in order to generate the amplifiable DNA component. The amount of amplifiable fragment was quantifiable by Real-Time Polymerase Chain Reaction (RT-PCR) amplification and directly reliable on adenosine concentration. This approach combines the very high separation efficiency and the homogeneous format (without immobilization) of capillary electrophoresis (CE) and the sensitivity of real time PCR amplification. An ultrafast isolation of target-bound split aptamer (60 s) was developed by designing a CE input/ouput scheme. Such method was successfully applied to the determination of adenosine with a LOD of 1 μM.
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Affiliation(s)
- Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Eric Dausse
- Laboratoire ARNA, Institut National de la Santé et de la Recherche Médicale U869, Université Bordeaux Bordeaux, France
| | - Hervé Dubouchaud
- Laboratoire de Bioénergétique Fondamentale et Appliquée, Institut National de la Santé et de la Recherche Médicale U1055, University Grenoble Alpes Grenoble, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
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19
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Patra M, Mukhopadhyay C, Chakrabarti A. Malachite green interacts with the membrane skeletal protein, spectrin. RSC Adv 2015. [DOI: 10.1039/c5ra15488j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Energy minimized complex of MG with the self association domain of spectrin.
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Affiliation(s)
- Malay Patra
- Chemistry Department
- University of Calcutta
- Kolkata 700009
- India
| | | | - Abhijit Chakrabarti
- Crystallography & Molecular Biology Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
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20
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Filonov GS, Moon JD, Svensen N, Jaffrey SR. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J Am Chem Soc 2014; 136:16299-308. [PMID: 25337688 PMCID: PMC4244833 DOI: 10.1021/ja508478x] [Citation(s) in RCA: 479] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Genetically
encoded fluorescent ribonucleic acids (RNAs) have diverse
applications, including imaging RNA trafficking and as a component
of RNA-based sensors that exhibit fluorescence upon binding small
molecules in live cells. These RNAs include the Spinach and Spinach2
aptamers, which bind and activate the fluorescence of fluorophores
similar to that found in green fluorescent protein. Although additional
highly fluorescent RNA–fluorophore complexes would extend the
utility of this technology, the identification of novel RNA–fluorophore
complexes is difficult. Current approaches select aptamers on the
basis of their ability to bind fluorophores, even though fluorophore
binding alone is not sufficient to activate fluorescence. Additionally,
aptamers require extensive mutagenesis to efficiently fold and exhibit
fluorescence in living cells. Here we describe a platform for rapid
generation of highly fluorescent RNA–fluorophore complexes
that are optimized for function in cells. This procedure involves
selection of aptamers on the basis of their binding to fluorophores,
coupled with fluorescence-activated cell sorting (FACS) of millions
of aptamers expressed in Escherichia coli. Promising
aptamers are then further optimized using a FACS-based directed evolution
approach. Using this approach, we identified several novel aptamers,
including a 49-nt aptamer, Broccoli. Broccoli binds and activates
the fluorescence of (Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one. Broccoli shows
robust folding and green fluorescence in cells, and increased fluorescence
relative to Spinach2. This reflects, in part, improved folding in
the presence of low cytosolic magnesium concentrations. Thus, this
novel fluorescence-based selection approach simplifies the generation
of aptamers that are optimized for expression and performance in living
cells.
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Affiliation(s)
- Grigory S Filonov
- Department of Pharmacology, Weill Cornell Medical College , New York, New York 10065, United States
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21
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Chang AL, McKeague M, Liang JC, Smolke CD. Kinetic and equilibrium binding characterization of aptamers to small molecules using a label-free, sensitive, and scalable platform. Anal Chem 2014; 86:3273-8. [PMID: 24548121 PMCID: PMC3983011 DOI: 10.1021/ac5001527] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Nucleic
acid aptamers function as versatile sensing and targeting
agents for analytical, diagnostic, therapeutic, and gene-regulatory
applications, but their limited characterization and functional validation
have hindered their broader implementation. We report the development
of a surface plasmon resonance-based platform for rapid characterization
of kinetic and equilibrium binding properties of aptamers to small
molecules. Our system is label-free and scalable and enables analysis
of different aptamer–target pairs and binding conditions with
the same platform. This method demonstrates improved sensitivity,
flexibility, and stability compared to other aptamer characterization
methods. We validated our assay against previously reported aptamer
affinity and kinetic measurements and further characterized a diverse
panel of 12 small molecule-binding RNA and DNA aptamers. We report
the first kinetic characterization for six of these aptamers and affinity
characterization of two others. This work is the first example of
direct comparison of in vitro selected and natural aptamers using
consistent characterization conditions, thus providing insight into
the influence of environmental conditions on aptamer binding kinetics
and affinities, indicating different possible regulatory strategies
used by natural aptamers, and identifying potential in vitro selection
strategies to improve resulting binding affinities.
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Affiliation(s)
- Andrew L Chang
- Department of Chemistry, Stanford University , Stanford, CA 94305, United States
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22
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Song W, Strack RL, Svensen N, Jaffrey SR. Plug-and-play fluorophores extend the spectral properties of Spinach. J Am Chem Soc 2014; 136:1198-201. [PMID: 24393009 PMCID: PMC3929357 DOI: 10.1021/ja410819x] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Spinach
and Spinach2 are RNA aptamers that can be used for the
genetic encoding of fluorescent RNA. Spinach2 binds and activates
the fluorescence of (Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one (DFHBI), allowing
the dynamic localizations of Spinach2-tagged RNAs to be imaged in
live cells. The spectral properties of Spinach2 are limited by DFHBI,
which produces fluorescence that is bluish-green and is not optimized
for filters commonly used in fluorescence microscopes. Here we characterize
the structural features that are required for fluorophore binding
to Spinach2 and describe novel fluorophores that bind and are switched
to a fluorescent state by Spinach2. These diverse Spinach2–fluorophore
complexes exhibit fluorescence that is more compatible with existing
microscopy filter sets and allows Spinach2-tagged constructs to be
imaged with either GFP or YFP filter cubes. Thus, these “plug-and-play”
fluorophores allow the spectral properties of Spinach2 to be altered
on the basis of the specific spectral needs of the experiment.
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Affiliation(s)
- Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University , New York, New York 10065, United States
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