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Akhter S, Tang Z, Wang J, Haboro M, Holmstrom ED, Wang J, Miao Y. Mechanism of Ligand Binding to Theophylline RNA Aptamer. J Chem Inf Model 2024; 64:1017-1029. [PMID: 38226603 PMCID: PMC11058067 DOI: 10.1021/acs.jcim.3c01454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Studying RNA-ligand interactions and quantifying their binding thermodynamics and kinetics are of particular relevance in the field of drug discovery. Here, we combined biochemical binding assays and accelerated molecular simulations to investigate ligand binding and dissociation in RNA using the theophylline-binding RNA as a model system. All-atom simulations using a Ligand Gaussian accelerated Molecular Dynamics method (LiGaMD) have captured repetitive binding and dissociation of theophylline and caffeine to RNA. Theophylline's binding free energy and kinetic rate constants align with our experimental data, while caffeine's binding affinity is over 10,000 times weaker, and its kinetics could not be determined. LiGaMD simulations allowed us to identify distinct low-energy conformations and multiple ligand binding pathways to RNA. Simulations revealed a "conformational selection" mechanism for ligand binding to the flexible RNA aptamer, which provides important mechanistic insights into ligand binding to the theophylline-binding model. Our findings suggest that compound docking using a structural ensemble of representative RNA conformations would be necessary for structure-based drug design of flexible RNA.
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Affiliation(s)
- Sana Akhter
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Zhichao Tang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Jinan Wang
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Mercy Haboro
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Erik D Holmstrom
- Department of Molecular Biosciences and Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Yinglong Miao
- Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
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2
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Kaiser C, Vogel M, Appel B, Weigand J, Müller S, Suess B, Wachtveitl J. Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering. J Mol Biol 2023; 435:168253. [PMID: 37640152 DOI: 10.1016/j.jmb.2023.168253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Engineering in vitro selected RNA aptamers into in vivo functional riboswitches represents a long-standing challenge in molecular biology. The highly specific aptamer domain of the riboswitch undergoes a conformational adjustment in response to ligand sensing, which in turn exerts the regulatory function. Besides essential factors like structural complexity and ligand binding kinetics, the active role of magnesium ions in stabilizing RNA tertiary structures and assisting in ligand binding can be a vital criterion. We present spectroscopic studies on the magnesium ion-driven folding of the Tetracycline binding aptamer. Using fluorescent labels, the aptamer pre-folding and subsequent ligand binding is monitored by magnesium titration experiments and time-resolved stopped-flow measurements. A minimum concentration of 0.5 mM magnesium is required to fold into a magnesium ion-stabilized binding-competent state with a preformed binding pocket. Tetracycline binding causes a pronounced conformational change that results in the establishment of the triple helix core motif, and that further propagates towards the closing stem. By a dynamic acquisition of magnesium ions, a kink motif is formed at the intersection of the triple helix and closing stem regions. This ultimately entails a stabilization of the closing stem which is discussed as a key element in the regulatory function of the Tetracycline aptamer.
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Affiliation(s)
- Christoph Kaiser
- Institute for Physical and Theoretical Chemistry, Goethe University, Frankfurt/Main, Max-von-Laue Str. 9, D-60438, Germany.
| | - Marc Vogel
- Department of Biology, Technical University Darmstadt, Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany
| | - Bettina Appel
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Julia Weigand
- Department of Biology, Technical University Darmstadt, Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Marbacher Weg 6, D-35037, Germany. https://twitter.com/WachtveitlLab
| | - Sabine Müller
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Centre for Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany.
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University, Frankfurt/Main, Max-von-Laue Str. 9, D-60438, Germany.
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3
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Lunelli L, Germanis M, Vanzetti L, Potrich C. Different Strategies for the Microfluidic Purification of Antibiotics from Food: A Comparative Study. BIOSENSORS 2023; 13:325. [PMID: 36979536 PMCID: PMC10046095 DOI: 10.3390/bios13030325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/17/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
The presence of residual antibiotics in food is increasingly emerging as a worrying risk for human health both for the possible direct toxicity and for the development of antibiotic-resistant bacteria. In the context of food safety, new methods based on microfluidics could offer better performance, providing improved rapidity, portability and sustainability, being more cost effective and easy to use. Here, a microfluidic method based on the use of magnetic microbeads specifically functionalized and inserted in polymeric microchambers is proposed. The microbeads are functionalized either with aptamers, antibodies or small functional groups able to interact with specific antibiotics. The setup of these different strategies as well as the performance of the different functionalizations are carefully evaluated and compared. The most promising results are obtained employing the functionalization with aptamers, which are able not only to capture and release almost all tetracycline present in the initial sample but also to deliver an enriched and simplified solution of antibiotic. These solutions of purified antibiotics are particularly suitable for further analyses, for example, with innovative methods, such as label-free detection. On the contrary, the on-chip process based on antibodies could capture only partially the antibiotics, as well as the protocol based on beads functionalized with small groups specific for sulfonamides. Therefore, the on-chip purification with aptamers combined with new portable detection systems opens new possibilities for the development of sensors in the field of food safety.
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Affiliation(s)
- Lorenzo Lunelli
- Bruno Kessler Foundation, Center for Sensors & Devices, Via Sommarive 18, 38123 Trento, Italy
- National Research Council, Institute of Biophysics, Via alla Cascata 56/C, 38123 Trento, Italy
| | - Martina Germanis
- Bruno Kessler Foundation, Center for Sensors & Devices, Via Sommarive 18, 38123 Trento, Italy
- FTH Srl (Femtorays), Via Solteri 38, 38121 Trento, Italy
| | - Lia Vanzetti
- Bruno Kessler Foundation, Center for Sensors & Devices, Via Sommarive 18, 38123 Trento, Italy
| | - Cristina Potrich
- Bruno Kessler Foundation, Center for Sensors & Devices, Via Sommarive 18, 38123 Trento, Italy
- National Research Council, Institute of Biophysics, Via alla Cascata 56/C, 38123 Trento, Italy
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4
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Abstract
There is growing interest in therapeutic intervention that targets disease-relevant RNAs using small molecules. While there have been some successes in RNA-targeted small-molecule discovery, a deeper understanding of structure-activity relationships in pursuing these targets has remained elusive. One of the best-studied tertiary-structured RNAs is the theophylline aptamer, which binds theophylline with high affinity and selectivity. Although not a drug target, this aptamer has had many applications, especially pertaining to genetic control circuits. Heretofore, no compound has been shown to bind the theophylline aptamer with greater affinity than theophylline itself. However, by carrying out a high-throughput screen of low-molecular-weight compounds, several unique hits were identified that are chemically distinct from theophylline and bind with up to 340-fold greater affinity. Multiple atomic-resolution X-ray crystal structures were determined to investigate the binding mode of theophylline and four of the best hits. These structures reveal both the rigidity of the theophylline aptamer binding pocket and the opportunity for other ligands to bind more tightly in this pocket by forming additional hydrogen-bonding interactions. These results give encouragement that the same approaches to drug discovery that have been applied so successfully to proteins can also be applied to RNAs.
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R O'Steen M, M Kolpashchikov D. A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer. SENSORS AND ACTUATORS REPORTS 2022; 4:100125. [PMID: 36373144 PMCID: PMC9635949 DOI: 10.1016/j.snr.2022.100125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/30/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Multiplex assays often rely on expensive sensors incorporating covalently linked fluorescent dyes. Herein, we developed a self-assembling aptamer-based multiplex assay. This multiplex approach utilizes a previously established split aptamer sensor in conjugation with a novel split aptamer sensor based upon a malachite green DNA aptamer. This system was capable of simultaneous fluorescent detection of two SARS COVID-19-related sequences in one sample with individual sensors that possesses a limit of detection (LOD) in the low nM range. Optimization of the Split Malachite Green (SMG) sensor yielded a minimized aptamer construct, Mini-MG, capable of inducing fluorescence of malachite green in both a DNA hairpin and sensor format.
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Affiliation(s)
- Martin R O'Steen
- Chemistry Department, University of Central Florida, Orlando, FL, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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6
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Sester C, McCone JA, Sen A, Vorster I, Harvey JE, Hodgkiss JM. Unravelling the binding mode of a methamphetamine aptamer: a spectroscopic and calorimetric investigation. Biophys J 2022; 121:2193-2205. [PMID: 35474264 DOI: 10.1016/j.bpj.2022.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/10/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid aptamers are bio-molecular recognition agents that bind to their targets with high specificity and affinity, and hold promise in a range of biosensor and therapeutic applications. In the case of small molecule targets, their small size and limited number of functional groups constitute challenges for their detection by aptamer-based biosensors because bio-recognition events may both be weak and produce poorly transduced signals. The binding affinity is principally used to characterize aptamer-ligand interactions; however a structural understanding of bio-recognition is arguably more valuable in order to design a strong response in biosensor applications. Using a combination of nuclear magnetic resonance, circular dichroism, and isothermal titration calorimetry, we propose a binding model for a new methamphetamine aptamer and determine the main interactions driving complex formation. These measurements reveal only modest structural changes to the aptamer upon binding and are consistent with a conformational selection binding model. The aptamer-methamphetamine complex formation was observed to be entropically driven, apparently involving hydrophobic and electrostatic interactions. Taken together, our results exemplify a means of elucidating small molecule-aptamer binding interactions, which may be decisive in the development of aptasensors and therapeutics, and may contribute to a deeper understanding of interactions driving aptamer selection.
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Affiliation(s)
- Clement Sester
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington PO Box 600, Wellington 6040, New Zealand; School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6040, New Zealand
| | - Jordan Aj McCone
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Anindita Sen
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington PO Box 600, Wellington 6040, New Zealand; School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6040, New Zealand
| | - Ian Vorster
- School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6040, New Zealand
| | - Joanne E Harvey
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Justin M Hodgkiss
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington PO Box 600, Wellington 6040, New Zealand; School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington 6040, New Zealand.
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Billet B, Chovelon B, Fiore E, Faure P, Ravelet C, Peyrin E. Detection of small molecules by fluorescence intensity using single dye labeled aptamers and quencher transition metal ions. Biosens Bioelectron 2022; 205:114091. [PMID: 35217256 DOI: 10.1016/j.bios.2022.114091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022]
Abstract
We describe herein an aptamer-based sensing approach that signal the presence of small-molecule targets when fluorescent DNA probes are challenged with the Ni2+ or Co2+ quencher metal ions. Functional oligonucleotides targeting L-tyrosinamide (L-Tym), adenosine (Ade) or cocaine (Coc) were end-labeled by the Texas-Red fluorophore. A fluorescence quenching occurred upon association of these transition metal ions with the free conjugates. The formation of the target-probe complex, by the way of variations in the overall binding of quencher metal ions along the DNA strands, led to a partial restoration (for the Ade and Coc systems) or a further attenuation (for the L-Tym system) of the fluorescence intensity. The absolute signal gain varied from 40 to 180% depending on the target-probe pair investigated. The approach was also used to detect the compound Ade in a spiked biological matrix in 1 min or less. The transition metal ion-based quenching strategy is characterized by its very simple implementation, low cost, and rapid signaling.
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Affiliation(s)
- Blandine Billet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
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8
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Kaiser C, Schneider J, Groher F, Suess B, Wachtveitl J. What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials. Nucleic Acids Res 2021; 49:3661-3671. [PMID: 33772594 PMCID: PMC8053125 DOI: 10.1093/nar/gkab166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/25/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
Among the many in vitro-selected aptamers derived from SELEX protocols, only a small fraction has the potential to be applied for synthetic riboswitch engineering. Here, we present a comparative study of the binding properties of three different aptamers that bind to ciprofloxacin with similar KD values, yet only two of them can be applied as riboswitches. We used the inherent ligand fluorescence that is quenched upon binding as the reporter signal in fluorescence titration and in time-resolved stopped-flow experiments. Thus, we were able to demonstrate differences in the binding kinetics of regulating and non-regulating aptamers. All aptamers studied underwent a two-step binding mechanism that suggests an initial association step followed by a reorganization of the aptamer to accommodate the ligand. We show that increasing regulatory potential is correlated with a decreasing back-reaction rate of the second binding step, thus resulting in a virtually irreversible last binding step of regulating aptamers. We suggest that a highly favoured structural adaption of the RNA to the ligand during the final binding step is essential for turning an aptamer into a riboswitch. In addition, our results provide an explanation for the fact that so few aptamers with regulating capacity have been found to date. Based on our data, we propose an adjustment of the selection protocol for efficient riboswitch detection.
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Affiliation(s)
- Christoph Kaiser
- Institute for Physical and Theoretical Chemistry, Goethe-Universität Frankfurt, Max-von-Laue-Straße 8, D-60438 Frankfurt am Main, Germany
| | - Jeannine Schneider
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-Universität Frankfurt, Max-von-Laue-Straße 8, D-60438 Frankfurt am Main, Germany
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9
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A malachite green light-up aptasensor for the detection of theophylline. Talanta 2021; 232:122417. [PMID: 34074405 DOI: 10.1016/j.talanta.2021.122417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022]
Abstract
Biosensors are of interest for the quantitative detection of small molecules (metabolites, drugs and contaminants for instance). To this end, fluorescence is a widely used technique that is easily associated to aptamers. Light-up aptamers constitute a particular class of oligonucleotides that, specifically induce fluorescence emission when binding to cognate fluorogenic ligands such as malachite green (MG). We engineered a dual aptasensor for theophylline (Th) based on the combination of switching hairpin aptamers specific for MG on the one hand and for Th on the other hand, hence their names: malaswitch (Msw) and theoswitch (Thsw). The two aptaswitches form a loop-loop or kissing Msw-Thsw complex only in the presence of theophylline, allowing binding of MG, subsequently generating a fluorescent signal. The combination of the best Msw and Thsw variants, MswG12 and Thsw19.1, results in a 20-fold fluorescence enhancement of MG at saturating theophylline concentration. This aptasensor discriminates between theophylline and its analogues caffeine and theobromine. Kissing aptaswitches derived from light-up aptamers constitute a novel sensing device.
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10
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Ender A, Etzel M, Hammer S, Findeiß S, Stadler P, Mörl M. Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch. Nucleic Acids Res 2021; 49:1784-1800. [PMID: 33469651 PMCID: PMC7897497 DOI: 10.1093/nar/gkaa1282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022] Open
Abstract
We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Maja Etzel
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Stefan Hammer
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Peter Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Science, Inselstr. 22, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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11
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Klein J, Buffin-Meyer B, Boizard F, Moussaoui N, Lescat O, Breuil B, Fedou C, Feuillet G, Casemayou A, Neau E, Hindryckx A, Decatte L, Levtchenko E, Raaijmakers A, Vayssière C, Goua V, Lucas C, Perrotin F, Cloarec S, Benachi A, Manca-Pellissier MC, Delmas HL, Bessenay L, Le Vaillant C, Allain-Launay E, Gondry J, Boudailliez B, Simon E, Prieur F, Lavocat MP, Saliou AH, De Parscau L, Bidat L, Noel C, Floch C, Bourdat-Michel G, Favre R, Weingertner AS, Oury JF, Baudouin V, Bory JP, Pietrement C, Fiorenza M, Massardier J, Kessler S, Lounis N, Auriol FC, Marcorelles P, Collardeau-Frachon S, Zürbig P, Mischak H, Magalhães P, Batut J, Blader P, Saulnier Blache JS, Bascands JL, Schaefer F, Decramer S, Schanstra JP. Amniotic fluid peptides predict postnatal kidney survival in developmental kidney disease. Kidney Int 2020; 99:737-749. [PMID: 32750455 DOI: 10.1016/j.kint.2020.06.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 12/16/2022]
Abstract
Although a rare disease, bilateral congenital anomalies of the kidney and urinary tract (CAKUT) are the leading cause of end stage kidney disease in children. Ultrasound-based prenatal prediction of postnatal kidney survival in CAKUT pregnancies is far from accurate. To improve prediction, we conducted a prospective multicenter peptidome analysis of amniotic fluid spanning 140 evaluable fetuses with CAKUT. We identified a signature of 98 endogenous amniotic fluid peptides, mainly composed of fragments from extracellular matrix proteins and from the actin binding protein thymosin-β4. The peptide signature predicted postnatal kidney outcome with an area under the curve of 0.96 in the holdout validation set of patients with CAKUT with definite endpoint data. Additionally, this peptide signature was validated in a geographically independent sub-cohort of 12 patients (area under the curve 1.00) and displayed high specificity in non-CAKUT pregnancies (82 and 94% in 22 healthy fetuses and in 47 fetuses with congenital cytomegalovirus infection respectively). Change in amniotic fluid thymosin-β4 abundance was confirmed with ELISA. Knockout of thymosin-β4 in zebrafish altered proximal and distal tubule pronephros growth suggesting a possible role of thymosin β4 in fetal kidney development. Thus, recognition of the 98-peptide signature in amniotic fluid during diagnostic workup of prenatally detected fetuses with CAKUT can provide a long-sought evidence base for accurate management of the CAKUT disorder that is currently unavailable.
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Affiliation(s)
- Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Bénédicte Buffin-Meyer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Franck Boizard
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Nabila Moussaoui
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Ophélie Lescat
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Benjamin Breuil
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Camille Fedou
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Guylène Feuillet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Audrey Casemayou
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Eric Neau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - An Hindryckx
- Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium
| | - Luc Decatte
- Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium
| | - Elena Levtchenko
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Anke Raaijmakers
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Christophe Vayssière
- Université Toulouse III Paul-Sabatier, Toulouse, France; Department of Obstetrics and Gynecology, Paule de Viguier Hospital, CHU Toulouse, Toulouse, France; INSERM, UMR1027, Toulouse, France
| | - Valérie Goua
- Prenatal Diagnosis Unit, Poitiers University Hospital, Poitiers, France
| | | | - Franck Perrotin
- Department of Obstetrics, Gynecology and Fetal Medicine, University Hospital of Tours, Tours, France; INSERM, U1253, "Imaging and Brain," François-Rabelais University of Tours, Tours, France
| | - Sylvie Cloarec
- Reference Center for Rare Kidney Diseases, Pediatric Nephrology Service, CHRU Clocheville, Tours, France
| | - Alexandra Benachi
- Gynecology-Obstetric Service, AP-HP, Hôpital Antoine Béclère, Université Paris-Sud, Clamart, France
| | - Marie-Christine Manca-Pellissier
- Center for Prenatal Diagnosis, Timone Children's Hospital, Assistance Publique Hopitaux de Marseille, Aix-Marseille Université, Marseille, France
| | | | - Lucie Bessenay
- Pediatric Service, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Emma Allain-Launay
- Pediatric Nephrology Service, Hôpital Mère-Enfants, CHU Nantes, Nantes, France
| | - Jean Gondry
- Department of Obstetrics and Gynecology, University Hospital of Amiens, Amiens, France; INSERM, U1105, Picardie Jules Verne University, CHU Amiens, Amiens, France
| | | | - Elisabeth Simon
- Prenatal Diagnosis, Fondation Lenval, CHU de Nice, Nice, France
| | - Fabienne Prieur
- Clinical Genetics Service, CHU de Saint-Etienne, Saint-Etienne, France
| | - Marie-Pierre Lavocat
- Department of Pediatrics, Hôpital Nord, CHU de Saint Etienne, Saint Etienne, France
| | - Anne-Hélène Saliou
- Multidisciplinary Center for Prenatal Diagnosis, CHRU de Brest, Brest, France
| | - Loic De Parscau
- Department of Pediatrics and Medical Genetics, CHRU Morvan, Brest, France
| | - Laurent Bidat
- Gynecology-Obstetrics Service, Centre Hospitalier René Dubos, Pontoise, France
| | - Catherine Noel
- Gynecology-Obstetrics Service, Centre Hospitalier René Dubos, Pontoise, France
| | - Corinne Floch
- Pediatric Service, Hôpital Louis Mourier, Colombes, France
| | | | - Romain Favre
- Ultrasound and Foetal Medicine Service of the Department of Gynecology and Obstetrics, Hôpitaux Universitaires de Strasbourg, CMCO, Schiltigheim, France
| | - Anne-Sophie Weingertner
- Ultrasound and Foetal Medicine Service of the Department of Gynecology and Obstetrics, Hôpitaux Universitaires de Strasbourg, CMCO, Schiltigheim, France
| | - Jean-François Oury
- Gynecology-Obstetrics Service, Hôpital Universitaire Robert Debré, APHP, Paris, France
| | - Véronique Baudouin
- Pediatric Nephrology Service, Hôpital Universitaire Robert-Debré, APHP, Paris, France
| | - Jean-Paul Bory
- Service de Gynécologie-Obstétrique, Maternité Alix-de-Champagne, CHU de Reims, Reims, France
| | | | - Maryse Fiorenza
- Gynecology-Obstetrics Service, l'Hôpital Mère Enfant de Limoges, Limoges, France
| | - Jérôme Massardier
- Gynecology-Obstetrics Service, Hospices Civils de Lyon, Hôpital Femme Mère Enfant, Bron, France
| | | | - Nadia Lounis
- Pediatric Clinical Research Unit, Clinical Research Center Toulouse, Hôpital des Enfants, Toulouse, France
| | - Françoise Conte Auriol
- Pediatric Clinical Research Unit, Clinical Research Center Toulouse, Hôpital des Enfants, Toulouse, France
| | - Pascale Marcorelles
- Department of Pathology, EA 4685, Neuronal Epithelium Interaction Laboratory, Université de Bretagne Occidentale Brest, France
| | - Sophie Collardeau-Frachon
- Department of Pathology, Children and Mother's Hospital, Groupement Hospitalier Est, CHU de Lyon-Bron, France
| | - Petra Zürbig
- Mosaiques Diagnostics and Therapeutics, Hannover, Germany
| | - Harald Mischak
- Mosaiques Diagnostics and Therapeutics, Hannover, Germany; Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Pedro Magalhães
- Mosaiques Diagnostics and Therapeutics, Hannover, Germany; Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | - Julie Batut
- Center for Developmental Biology (UMR5547) and Center for Integrative Biology (FR 3743), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Patrick Blader
- Center for Developmental Biology (UMR5547) and Center for Integrative Biology (FR 3743), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Jean-Sebastien Saulnier Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | - Franz Schaefer
- Division of Pediatric Nephrology, Heidelberg University Center for Pediatrics and Adolescent Medicine, Heidelberg, Germany
| | - Stéphane Decramer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France; Pediatric Nephrology Service, Hôpital des Enfants, CHU Toulouse, Toulouse, France; Reference Center for Rare Renal Diseases of the Southwest (SORARE), Toulouse, France.
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France.
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12
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Kato S, Ono T, Minagawa H, Horii K, Shiratori I, Waga I, Ito K, Aoki T. FSBC: fast string-based clustering for HT-SELEX data. BMC Bioinformatics 2020; 21:263. [PMID: 32580745 PMCID: PMC7313139 DOI: 10.1186/s12859-020-03607-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 06/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The combination of systematic evolution of ligands by exponential enrichment (SELEX) and deep sequencing is termed high-throughput (HT)-SELEX, which enables searching aptamer candidates from a massive amount of oligonucleotide sequences. A clustering method is an important procedure to identify sequence groups including aptamer candidates for evaluation with experimental analysis. In general, aptamer includes a specific target binding region, which is necessary for binding to the target molecules. The length of the target binding region varies depending on the target molecules and/or binding styles. Currently available clustering methods for HT-SELEX only estimate clusters based on the similarity of full-length sequences or limited length of motifs as target binding regions. Hence, a clustering method considering the target binding region with different lengths is required. Moreover, to handle such huge data and to save sequencing cost, a clustering method with fast calculation from a single round of HT-SELEX data, not multiple rounds, is also preferred. RESULTS We developed fast string-based clustering (FSBC) for HT-SELEX data. FSBC was designed to estimate clusters by searching various lengths of over-represented strings as target binding regions. FSBC was also designed for fast calculation with search space reduction from a single round, typically the final round, of HT-SELEX data considering imbalanced nucleobases of the aptamer selection process. The calculation time and clustering accuracy of FSBC were compared with those of four conventional clustering methods, FASTAptamer, AptaCluster, APTANI, and AptaTRACE, using HT-SELEX data (>15 million oligonucleotide sequences). FSBC, AptaCluster, and AptaTRACE could complete the clustering for all sequence data, and FSBC and AptaTRACE performed higher clustering accuracy. FSBC showed the highest clustering accuracy and had the second fastest calculation speed among all methods compared. CONCLUSION FSBC is applicable to a large HT-SELEX dataset, which can facilitate the accurate identification of groups including aptamer candidates. AVAILABILITY OF DATA AND MATERIALS FSBC is available at http://www.aoki.ecei.tohoku.ac.jp/fsbc/.
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Affiliation(s)
- Shintaro Kato
- NEC Solution Innovators, Ltd, 1-18-7 Shinkiba, Koto-ku, Tokyo, 136-8627, Japan. .,Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai-shi, Miyagi, 980-8579, Japan.
| | - Takayoshi Ono
- Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai-shi, Miyagi, 980-8579, Japan
| | - Hirotaka Minagawa
- NEC Solution Innovators, Ltd, 1-18-7 Shinkiba, Koto-ku, Tokyo, 136-8627, Japan
| | - Katsunori Horii
- NEC Solution Innovators, Ltd, 1-18-7 Shinkiba, Koto-ku, Tokyo, 136-8627, Japan
| | - Ikuo Shiratori
- NEC Solution Innovators, Ltd, 1-18-7 Shinkiba, Koto-ku, Tokyo, 136-8627, Japan
| | - Iwao Waga
- NEC Solution Innovators, Ltd, 1-18-7 Shinkiba, Koto-ku, Tokyo, 136-8627, Japan
| | - Koichi Ito
- Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai-shi, Miyagi, 980-8579, Japan
| | - Takafumi Aoki
- Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai-shi, Miyagi, 980-8579, Japan
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13
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Tanida Y, Matsuura A. Alchemical free energy calculations via metadynamics: Application to the theophylline-RNA aptamer complex. J Comput Chem 2020; 41:1804-1819. [PMID: 32449538 DOI: 10.1002/jcc.26221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/03/2020] [Accepted: 04/26/2020] [Indexed: 11/08/2022]
Abstract
We propose a computational workflow for robust and accurate prediction of both binding poses and their affinities at early stage in designing drug candidates. Small, rigid ligands with few intramolecular degrees of freedom, for example, fragment-like molecules, have multiple binding poses, even at a single binding site, and their affinities are often close to each other. We explore various structures of ligand binding to a target through metadynamics using a small number of collective variables, followed by reweighting to obtain the atomic coordinates. After identifying each binding pose by cluster analysis, we perform alchemical free energy calculations on each structure to obtain the overall value. We applied this protocol in computing free energy of binding for the theophylline-RNA aptamer complex. Of the six (meta)stable structures found, the most favorable binding structure is consistent with the structure obtained by NMR. The overall free energy of binding reproduces the experimental values very well.
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14
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Kiggins C, Skinner A, Resendiz MJE. 7,8-Dihydro-8-oxoguanosine Lesions Inhibit the Theophylline Aptamer or Change Its Selectivity. Chembiochem 2020; 21:1347-1355. [PMID: 31845489 PMCID: PMC7297664 DOI: 10.1002/cbic.201900684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Indexed: 12/15/2022]
Abstract
Aptamers are attractive constructs due to their high affinity/selectivity towards a target. Here 7,8-dihydro-8-oxoguanosine (8-oxoG) has been used, due in part to its unique H-bonding capabilities (Watson-Crick or Hoogsteen), to expand the "RNA alphabet". Its impact on the theophylline RNA aptamer was explored by modifying its binding pocket at positions G11, G25, or G26. Structural probing, with RNases A and T1 , showed that modification at G11 leads to a drastic structural change, whereas the G25-/G26-modified analogues exhibited cleavage patterns similar to that of the canonical construct. The recognition properties towards three xanthine derivatives were then explored through thermophoresis. Modifying the aptamer at position G11 led to binding inhibition. Modification at G25, however, changed the selectivity towards theobromine (Kd ≈160 μm), with a poor affinity for theophylline (Kd >1.5 mm) being observed. Overall, 8-oxoG can have an impact on the structures of aptamers in a position-dependent manner, leading to altered target selectivity.
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Affiliation(s)
- Courtney Kiggins
- Present address: Department of ChemistryU.S. Air Force Academy2355 Fairchild DriveUSAF AcademyColorado SpringsCO80840USA
| | - Austin Skinner
- Department of ChemistryUniversity of Colorado Denver1151 Arapahoe Street, Science Building Room 4145DenverCO80204USA
| | - Marino J. E. Resendiz
- Department of ChemistryUniversity of Colorado Denver1151 Arapahoe Street, Science Building Room 4145DenverCO80204USA
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15
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Wrist A, Sun W, Summers RM. The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research. ACS Synth Biol 2020; 9:682-697. [PMID: 32142605 DOI: 10.1021/acssynbio.9b00475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The theophylline aptamer was isolated from an oligonucleotide library in 1994. Since that time, the aptamer has found wide utility, particularly in synthetic biology, cellular engineering, and diagnostic applications. The primary application of the theophylline aptamer is in the construction and characterization of synthetic riboswitches for regulation of gene expression. These riboswitches have been used to control cellular motility, regulate carbon metabolism, construct logic gates, screen for mutant enzymes, and control apoptosis. Other applications of the theophylline aptamer in cellular engineering include regulation of RNA interference and genome editing through CRISPR systems. Here we describe the uses of the theophylline aptamer for cellular engineering over the past 25 years. In so doing, we also highlight important synthetic biology applications to control gene expression in a ligand-dependent manner.
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Affiliation(s)
- Alexandra Wrist
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Wanqi Sun
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ryan M. Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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16
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Wong RS, Chen YY, Smolke CD. Regulation of T cell proliferation with drug-responsive microRNA switches. Nucleic Acids Res 2019; 46:1541-1552. [PMID: 29244152 PMCID: PMC5815133 DOI: 10.1093/nar/gkx1228] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/30/2017] [Indexed: 11/21/2022] Open
Abstract
As molecular and cellular therapies advance in the clinic, the role of genetic regulation is becoming increasingly important for controlling therapeutic potency and safety. The emerging field of mammalian synthetic biology provides promising tools for the construction of regulatory platforms that can intervene with endogenous pathways and control cell behavior. Recent work has highlighted the development of synthetic biological systems that integrate sensing of molecular signals to regulated therapeutic function in various disease settings. However, the toxicity and limited dosing of currently available molecular inducers have largely inhibited translation to clinical settings. In this work, we developed synthetic microRNA-based genetic systems that are controlled by the pharmaceutical drug leucovorin, which is readily available and safe for prolonged administration in clinical settings. We designed microRNA switches to target endogenous cytokine receptor subunits (IL-2Rβ and γc) that mediate various signaling pathways in T cells. We demonstrate the function of these control systems by effectively regulating T cell proliferation with the drug input. Each control system produced unique functional responses, and combinatorial targeting of multiple receptor subunits exhibited greater repression of cell growth. This work highlights the potential use of drug-responsive genetic control systems to improve the management and safety of cellular therapeutics.
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Affiliation(s)
- Remus S Wong
- Department of Bioengineering, 443 Via Ortega, MC 4245, Stanford University, Stanford, CA 94305, USA
| | - Yvonne Y Chen
- Department of Chemical and Biomolecular Engineering, 420 Westwood Plaza, Boelter Hall 5531, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Christina D Smolke
- Department of Bioengineering, 443 Via Ortega, MC 4245, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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17
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Birman Y, Khorsand S, Tu E, Mortensen RB, Butko MT. Second-harmonic generation-based methods to detect and characterize ligand-induced RNA conformational changes. Methods 2019; 167:92-104. [PMID: 31116965 DOI: 10.1016/j.ymeth.2019.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/11/2019] [Accepted: 05/15/2019] [Indexed: 10/26/2022] Open
Abstract
Second-harmonic generation (SHG) is a biophysical tool that senses ligand-induced conformational changes in biomolecules. The Biodesy Delta™ has been developed as a high-throughput screening platform to monitor conformational changes in proteins and oligonucleotides by SHG to support drug discovery efforts. This work will outline (1) an overview of this technology, (2) detailed protocols for optimizing screening-ready SHG assays on RNA targets, (3) practical considerations for developing robust and informative SHG measurements, and (4) a case study that demonstrates the application of these recommendations on an RNA target. The previously published theophylline aptamer SHG assay [1] was further optimized to maximize the assay window between the positive control (theophylline) and the negative control (caffeine). Optimization of this assay provides practical considerations for building a robust SHG assay on an RNA target, including testing for specific tethering of the conjugate to the surface as well as testing tool compound response stability, reversibility, and concentration-dependence/affinity. A more robust, better-performing theophylline aptamer SHG assay was achieved that would be more appropriate for conducting a screen.
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Affiliation(s)
- Yuliya Birman
- Biodesy, Inc., South San Francisco 94080, United States
| | - Sina Khorsand
- Biodesy, Inc., South San Francisco 94080, United States
| | - Erick Tu
- Biodesy, Inc., South San Francisco 94080, United States
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18
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Kocaaga B, Kurkcuoglu O, Tatlier M, Batirel S, Guner FS. Low‐methoxyl pectin–zeolite hydrogels controlling drug release promote
in vitro
wound healing. J Appl Polym Sci 2019. [DOI: 10.1002/app.47640] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Banu Kocaaga
- Department of Chemical EngineeringIstanbul Technical University, Maslak 34469 Istanbul Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical EngineeringIstanbul Technical University, Maslak 34469 Istanbul Turkey
| | - Melkon Tatlier
- Department of Chemical EngineeringIstanbul Technical University, Maslak 34469 Istanbul Turkey
| | - Saime Batirel
- Department of Medical Biochemistry, School of MedicineMarmara University, Maltepe 34854 Istanbul Turkey
| | - F. Seniha Guner
- Department of Chemical EngineeringIstanbul Technical University, Maslak 34469 Istanbul Turkey
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19
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Cai S, Yan J, Xiong H, Liu Y, Peng D, Liu Z. Investigations on the interface of nucleic acid aptamers and binding targets. Analyst 2019; 143:5317-5338. [PMID: 30357118 DOI: 10.1039/c8an01467a] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA of 20-100 nucleotides in length that have attracted substantial scientific interest due to their ability to specifically bind to target molecules via the formation of three-dimensional structures. Compared to traditional protein antibodies, aptamers have several advantages, such as their small size, high binding affinity, specificity, flexible structure, being chemical synthesizable and modifiable, good biocompatibility, high stability and low immunogenicity, which all contribute to their widely applications in the biomedical field. To date, much progress has been made in the study and applications of aptamers, however, detailed information on how aptamers bind to their targets is still scarce. Over the past few decades, many methods have been introduced to investigate the aptamer-target binding process, such as measuring the main kinetic or thermodynamic parameters, detecting the structural changes of the binding complexes, etc. Apart from traditional physicochemical methods, various types of molecular docking programs have been applied to simulate the aptamer-target interactions, while these simulations also have limitations. To facilitate the further research on the interactions, herein, we provide a brief review to illustrate the recent advances in the study of aptamer-target interactions. We summarize the binding targets of aptamers, such as small molecules, macromolecules, and even cells. Their binding constants (KD) are also summarized. Methods to probe the aptamer-target binding process, such as surface plasmon resonance (SPR), circular dichroism spectroscopy (CD), isothermal titration calorimetry (ITC), footprinting assay, truncation and mutation assay, nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography and molecular docking simulation are indicated. The binding forces mediating the aptamer-target interactions, such as hydrogen bonding, electrostatic interaction, the hydrophobic effect, π-π stacking and van der Waals forces are summarized. The challenges and future perspectives are also discussed.
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Affiliation(s)
- Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, PR China.
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20
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Kashida S, Saito H. Design of Ligand-Controlled Genetic Switches Based on RNA Interference. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Shunnichi Kashida
- Center for iPS Cell Research and Application, Kyoto University; Department of Life Science Frontiers; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
- Ecole Normale Supérieure, UMR 8640 CNRS-ENS-UPMC Pasteur; Department of Chemistry; 24 rue Lhomond Paris 75005 France
| | - Hirohide Saito
- Center for iPS Cell Research and Application, Kyoto University; Department of Life Science Frontiers; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
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21
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Dou N, Yu S, Ye X, Yang D, Li Y, Gao Y. Aberrant overexpression of ADAR1 promotes gastric cancer progression by activating mTOR/p70S6K signaling. Oncotarget 2018; 7:86161-86173. [PMID: 27863387 PMCID: PMC5349904 DOI: 10.18632/oncotarget.13354] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/08/2016] [Indexed: 12/24/2022] Open
Abstract
ADAR1, one of adenosine deaminases acting on RNA, modulates RNA transcripts through converting adenosine (A) to inosine (I) by deamination. Emerging evidence has implicated that ADAR1 plays an important role in a few of human cancers, however, its expression and physiological significance in gastric cancer remain undefined. In the present study, we demonstrated that ADAR1 was frequently overexpressed in gastric cancer samples by quantitative real-time PCR analysis. In a gastric cancer tissue microarray, ADAR1 staining was closely correlated with tumor stage (P < 0.001) and N classification (P < 0.001). Functional analysis indicated that ADAR1 overexpression promoted cell proliferation and migration in vitro, whereas ADAR1 knockdown resulted in an opposite phenotypes. Furthermore, ADAR1 knockdown also inhibited tumorigenicity and lung metastasis potential of gastric cancer cells in nude mice models. Mechanistically, ADAR1 expression had a significant effect on phosphorylation level of mTOR, p70S kinase, and S6 ribosomal protein, implying its involvement in the regulation of mTOR signaling pathway. We conclude that ADAR1 contributes to gastric cancer development and progression via activating mTOR/p70S6K/S6 ribosomal protein signaling axis. Our findings suggest that ADAR1 may be a valuable biomarker for GC diagnosis and prognosis and may represent a new novel therapeutic opportunities.
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Affiliation(s)
- Ning Dou
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Shijun Yu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaojuan Ye
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Dong Yang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
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22
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Butko MT, Moree B, Mortensen RB, Salafsky J. Detection of Ligand-Induced Conformational Changes in Oligonucleotides by Second-Harmonic Generation at a Supported Lipid Bilayer Interface. Anal Chem 2016; 88:10482-10489. [PMID: 27696827 DOI: 10.1021/acs.analchem.6b02498] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There is a high demand for characterizing oligonucleotide structural changes associated with binding interactions as well as identifying novel binders that modulate their structure and function. In this study, second-harmonic generation (SHG) was used to study RNA and DNA oligonucleotide conformational changes associated with ligand binding. For this purpose, we developed an avidin-based biotin capture surface based on a supported lipid bilayer membrane. The technique was applied to two well-characterized aptamers, both of which undergo conformational changes upon binding either a protein or a small molecule ligand. In both cases, SHG was able to resolve conformational changes in these oligonucleotides sensitively and specifically, in solution and in real time, using nanogram amounts of material. In addition, we developed a competition assay for the oligonucleotides between the specific ligands and known, nonspecific binders, and we demonstrated that intercalators and minor groove binders affect the conformation of the DNA and RNA oligonucleotides in different ways upon binding and subsequently block specific ligand binding in all cases. Our work demonstrates the broad potential of SHG for studying oligonucleotides and their conformational changes upon interaction with ligands. As SHG offers a powerful, high-throughput screening approach, our results here also open an important new avenue for identifying novel chemical probes or sequence-targeted drugs that disrupt or modulate DNA or RNA structure and function.
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Affiliation(s)
- Margaret T Butko
- Biodesy, Inc. , 384 Oyster Point Boulevard, Suite No. 8, South San Francisco, California 94080, United States
| | - Ben Moree
- Biodesy, Inc. , 384 Oyster Point Boulevard, Suite No. 8, South San Francisco, California 94080, United States
| | - Richard B Mortensen
- Biodesy, Inc. , 384 Oyster Point Boulevard, Suite No. 8, South San Francisco, California 94080, United States
| | - Joshua Salafsky
- Biodesy, Inc. , 384 Oyster Point Boulevard, Suite No. 8, South San Francisco, California 94080, United States
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23
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Agustin E, Asare Okai PN, Khan I, Miller MR, Wang R, Sheng J, Royzen M. A fast click-slow release strategy towards the HPLC-free synthesis of RNA. Chem Commun (Camb) 2016; 52:1405-8. [PMID: 26619912 DOI: 10.1039/c5cc05392g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general strategy for purification of oligonucleotides synthesized by solid phase synthesis is described. It is based on a recently developed concept involving a bio-orthogonal inverse electron demand Diels-Alder reaction between trans-cyclooctene and tetrazine, termed 'click-to-release'. The strategy has been applied towards the synthesis and purification of a model hairpin RNA strand, as well as a 34 nt long aptamer.
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Affiliation(s)
- E Agustin
- Department of Chemistry, SUNY, University at Albany, 1400 Washington Avenue, Albany, NY 1222, USA.
| | - P N Asare Okai
- Department of Chemistry, SUNY, University at Albany, 1400 Washington Avenue, Albany, NY 1222, USA.
| | - I Khan
- Department of Chemistry, SUNY, University at Albany, 1400 Washington Avenue, Albany, NY 1222, USA.
| | - M R Miller
- Department of Chemistry, SUNY, University at Albany, 1400 Washington Avenue, Albany, NY 1222, USA.
| | - R Wang
- Department of Chemistry, SUNY, University at Albany, 1400 Washington Avenue, Albany, NY 1222, USA.
| | - J Sheng
- Department of Chemistry, SUNY, University at Albany, 1400 Washington Avenue, Albany, NY 1222, USA.
| | - M Royzen
- Department of Chemistry, SUNY, University at Albany, 1400 Washington Avenue, Albany, NY 1222, USA.
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Lin YH, Chang KY. Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator. Nucleic Acids Res 2016; 44:9005-9015. [PMID: 27521370 PMCID: PMC5062990 DOI: 10.1093/nar/gkw718] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/03/2016] [Indexed: 12/18/2022] Open
Abstract
Metabolite-responsive RNA pseudoknots derived from prokaryotic riboswitches have been shown to stimulate −1 programmed ribosomal frameshifting (PRF), suggesting −1 PRF as a promising gene expression platform to extend riboswitch applications in higher eukaryotes. However, its general application has been hampered by difficulty in identifying a specific ligand-responsive pseudoknot that also functions as a ligand-dependent -1 PRF stimulator. We addressed this problem by using the −1 PRF stimulation pseudoknot of SARS-CoV (SARS-PK) to build a ligand-dependent −1 PRF stimulator. In particular, the extra stem of SARS-PK was replaced by an RNA aptamer of theophylline and designed to couple theophylline binding with the stimulation of −1 PRF. Conformational and functional analyses indicate that the engineered theophylline-responsive RNA functions as a mammalian riboswitch with robust theophylline-dependent −1 PRF stimulation activity in a stable human 293T cell-line. Thus, RNA–ligand interaction repertoire provided by in vitro selection becomes accessible to ligand-specific −1 PRF stimulator engineering using SARS-PK as the scaffold for synthetic biology application.
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Affiliation(s)
- Ya-Hui Lin
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
| | - Kung-Yao Chang
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung, 402 Taiwan
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25
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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: 26] [Impact Index Per Article: 3.3] [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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26
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Souard F, Perrier S, Noël V, Fave C, Fiore E, Peyrin E, Garcia J, Vanhaverbeke C. Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling. Chemistry 2015; 21:15740-8. [PMID: 26356596 DOI: 10.1002/chem.201501527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
Abstract
Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.
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Affiliation(s)
- Florence Souard
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
| | - Sandrine Perrier
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Emmanuelle Fiore
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Eric Peyrin
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Julian Garcia
- DCM, Université Grenoble Alpes, Grenoble, 38000 (France).,DCM, CNRS, Grenoble, 38000 (France)
| | - Cécile Vanhaverbeke
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
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Lee SW, Oh MK. A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae. Metab Eng 2015; 28:143-150. [DOI: 10.1016/j.ymben.2015.01.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 12/27/2014] [Accepted: 01/07/2015] [Indexed: 01/08/2023]
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28
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Hsu HT, Lin YH, Chang KY. Synergetic regulation of translational reading-frame switch by ligand-responsive RNAs in mammalian cells. Nucleic Acids Res 2014; 42:14070-82. [PMID: 25414357 PMCID: PMC4267651 DOI: 10.1093/nar/gku1233] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Distinct translational initiation mechanisms between prokaryotes and eukaryotes limit the exploitation of prokaryotic riboswitch repertoire for regulatory RNA circuit construction in mammalian application. Here, we explored programmed ribosomal frameshifting (PRF) as the regulatory gene expression platform for engineered ligand-responsive RNA devices in higher eukaryotes. Regulation was enabled by designed ligand-dependent conformational rearrangements of the two cis-acting RNA motifs of opposite activity in -1 PRF. Particularly, RNA elements responsive to trans-acting ligands can be tailored to modify co-translational RNA refolding dynamics of a hairpin upstream of frameshifting site to achieve reversible and adjustable -1 PRF attenuating activity. Combined with a ligand-responsive stimulator, synthetic RNA devices for synergetic translational-elongation control of gene expression can be constructed. Due to the similarity between co-transcriptional RNA hairpin folding and co-translational RNA hairpin refolding, the RNA-responsive ligand repertoire provided in prokaryotic systems thus becomes accessible to gene-regulatory circuit construction for synthetic biology application in mammalian cells.
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Affiliation(s)
- Hsiu-Ting Hsu
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
| | - Ya-Hui Lin
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
| | - Kung-Yao Chang
- Institute of Biochemistry, National Chung-Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
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29
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Magnetic microparticle-based SELEX process for the identification of highly specific aptamers of heart marker--brain natriuretic peptide. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1338-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Endoh T, Sugimoto N. Aptamer-based universal fluorometric sensors based on allosteric modulation of RNA-peptide interactions. ChemMedChem 2014; 9:2045-8. [PMID: 24990122 DOI: 10.1002/cmdc.201402151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 12/21/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides that serve as molecular recognition units. Aptamers targeting a range of biologically relevant molecules have been developed using selection methods and functional aptamer domains, called riboswitches, are found in natural genomic sequences. Aptamers can be used as starting points for the design of biosensors for diagnostic applications. In this study, we demonstrate a simple strategy to detect binding of an apamer to its target molecule via a fluorometric signal resulting from allosteric suppression of an RNA-peptide interaction. The broad applicability was demonstrated by detection of seven different target molecules-one drug, two antibiotics, and four natural metabolites. This strategy will enable the construction of universal biosensors for various target molecules.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan, University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047 (Japan)
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Wu J, Zhu Y, Xue F, Mei Z, Yao L, Wang X, Zheng L, Liu J, Liu G, Peng C, Chen W. Recent trends in SELEX technique and its application to food safety monitoring. Mikrochim Acta 2014; 181:479-491. [PMID: 25419005 DOI: 10.1007/s00604-013-1156-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The method referred to as "systemic evolution of ligands by exponential enrichment" (SELEX) was introduced in 1990 and ever since has become an important tool for the identification and screening of aptamers. Such nucleic acids can recognize and bind to their corresponding targets (analytes) with high selectivity and affinity, and aptamers therefore have become attractive alternatives to traditional antibodies not the least because they are much more stable. Meanwhile, they have found numerous applications in different fields including food quality and safety monitoring. This review first gives an introduction into the selection process and to the evolution of SELEX, then covers applications of aptamers in the surveillance of food safety (with subsections on absorptiometric, electrochemical, fluorescent and other methods), and then gives conclusions and perspectives. The SELEX method excels by its features of in vitro, high throughput and ease of operation. This review contains 86 references.
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Affiliation(s)
- Jingjing Wu
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Yingyue Zhu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, People's Republic of China
| | - Feng Xue
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Zhanlong Mei
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Li Yao
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Xin Wang
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Lei Zheng
- School of Medical Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Jian Liu
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Guodong Liu
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Chifang Peng
- School Food Science & Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wei Chen
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
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32
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Bonneau E, Legault P. NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions. Biochemistry 2014; 53:579-90. [PMID: 24364590 PMCID: PMC3906864 DOI: 10.1021/bi401484a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metal cations represent key elements of RNA structure and function. In the Neurospora VS ribozyme, metal cations play diverse roles; they are important for substrate recognition, formation of the active site, and shifting the pKa's of two key nucleobases that contribute to the general acid-base mechanism. Recently, we determined the NMR structure of the A730 loop of the VS ribozyme active site (SLVI) that contributes the general acid (A756) in the enzymatic mechanism of the cleavage reaction. Our studies showed that magnesium (Mg(2+)) ions are essential to stabilize the formation of the S-turn motif within the A730 loop that exposes the A756 nucleobase for catalysis. In this article, we extend these NMR investigations by precisely mapping the Mg(2+)-ion binding sites using manganese-induced paramagnetic relaxation enhancement and cadmium-induced chemical-shift perturbation of phosphorothioate RNAs. These experiments identify five Mg(2+)-ion binding sites within SLVI. Four Mg(2+) ions in SLVI are associated with known RNA structural motifs, including the G-U wobble pair and the GNRA tetraloop, and our studies reveal novel insights about Mg(2+) ion binding to these RNA motifs. Interestingly, one Mg(2+) ion is specifically associated with the S-turn motif, confirming its structural role in the folding of the A730 loop. This Mg(2+) ion is likely important for formation of the active site and may play an indirect role in catalysis.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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Li X, Song J, Wang Y, Cheng T. Cyclically amplified fluorescent detection of theophylline and thiamine pyrophosphate by coupling self-cleaving RNA ribozyme with endonuclease. Anal Chim Acta 2013; 797:95-101. [DOI: 10.1016/j.aca.2013.08.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 01/10/2023]
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Carter JR, Balaraman V, Kucharski CA, Fraser TS, Fraser MJ. A novel dengue virus detection method that couples DNAzyme and gold nanoparticle approaches. Virol J 2013; 10:201. [PMID: 23809208 PMCID: PMC3765938 DOI: 10.1186/1743-422x-10-201] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/08/2013] [Indexed: 11/15/2022] Open
Abstract
Background Recent epidemics of dengue viruses (DENV) coupled with new outbreaks on the horizon have renewed the demand for novel detection methods that have the ability to identify this viral pathogen prior to the manifestation of symptoms. The ability to detect DENV in a timely manner is essential for rapid recovery from disease symptoms. A modified lab-derived 10-23 DNAzyme tethered to gold nanoparticles provides a powerful tool for the detection of viruses, such as DENV. Results We examined the effectiveness of coupling DNAzyme (DDZ) activation to the salt-induced aggregation of gold nanoparticles (AuNP) to detect dengue virus (DENV) progeny in mosquito cells. A DNAzyme was designed to recognize the 5’ cyclization sequence (5’ CS) that is conserved among all DENV, and conjugated to AuNPs. DDZ-AuNP has demonstrated the ability to detect the genomic RNA of our model dengue strain, DENV-2 NGC, isolated from infected Aedes albopictus C6/36 cells. These targeting events lead to the rapid aggregation of AuNPs, resulting in a red to clear color transition of the reaction mixes, and thus positive detection of the DENV RNA genome. The inclusion of SDS in the reaction mixture permitted the detection of DENV directly from cell culture supernatants without additional sample processing. Specificity assays demonstrated detection is DENV-specific, while sensitivity assays confirm detection at levels of 1 × 101 TCID50 units. These results demonstrate DDZ-AuNP effectively detects DENV genomes in a sequence specific manner and at concentrations that are practical for field use. Conclusions We have developed an effective detection assay using DNAzyme catalysis coupled with AuNP aggregation for the detection of DENV genomes in a sequence specific manner. Full development of our novel DDZ-AuNP detection method will provide a practical, rapid, and low cost alternative for the detection of DENV in mosquito cells and tissues, and possibly infected patient serum, in a matter of minutes with little to no specialized training required.
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Affiliation(s)
- James R Carter
- Department of Biological Sciences, Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
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35
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Conidi A, van den Berghe V, Huylebroeck D. Aptamers and their potential to selectively target aspects of EGF, Wnt/β-catenin and TGFβ-smad family signaling. Int J Mol Sci 2013; 14:6690-719. [PMID: 23531534 PMCID: PMC3645661 DOI: 10.3390/ijms14046690] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/05/2013] [Accepted: 03/12/2013] [Indexed: 02/07/2023] Open
Abstract
The smooth identification and low-cost production of highly specific agents that interfere with signaling cascades by targeting an active domain in surface receptors, cytoplasmic and nuclear effector proteins, remain important challenges in biomedical research. We propose that peptide aptamers can provide a very useful and new alternative for interfering with protein–protein interactions in intracellular signal transduction cascades, including those emanating from activated receptors for growth factors. By their targeting of short, linear motif type of interactions, peptide aptamers have joined nucleic acid aptamers for use in signaling studies because of their ease of production, their stability, their high specificity and affinity for individual target proteins, and their use in high-throughput screening protocols. Furthermore, they are entering clinical trials for treatment of several complex, pathological conditions. Here, we present a brief survey of the use of aptamers in signaling pathways, in particular of polypeptide growth factors, starting with the published as well as potential applications of aptamers targeting Epidermal Growth Factor Receptor signaling. We then discuss the opportunities for using aptamers in other complex pathways, including Wnt/β-catenin, and focus on Transforming Growth Factor-β/Smad family signaling.
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Affiliation(s)
- Andrea Conidi
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Campus Gasthuisberg, Building Ond & Nav4 p.o.box 812, room 05.313, Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium.
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36
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Endoh T, Sugimoto N. Selection of RNAs for constructing "Lighting-UP" biomolecular switches in response to specific small molecules. PLoS One 2013; 8:e60222. [PMID: 23555931 PMCID: PMC3608610 DOI: 10.1371/journal.pone.0060222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/22/2013] [Indexed: 11/19/2022] Open
Abstract
RNA and protein are potential molecules that can be used to construct functional nanobiomaterials. Recent findings on riboswitches emphasize on the dominative function of RNAs in regulating protein functions through allosteric interactions between RNA and protein. In this study, we demonstrate a simple strategy to obtain RNAs that have a switching ability with respect to protein function in response to specific target molecules. RNA aptamers specific for small ligands and a trans-activation-responsive (TAR)-RNA were connected by random RNA sequences. RNAs that were allosterically bound to a trans-activator of transcription (Tat)-peptide in response to ligands were selected by repeated negative and positive selection in the absence and presence of the ligands, respectively. The selected RNAs interacted with artificially engineered Renilla Luciferase, in which the Tat-peptide was inserted within the Luciferase, in the presence of the specific ligand and triggered the “Lighting-UP” switch of the engineered Luciferase.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
- * E-mail:
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37
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Penchovsky R. Computational Design and Biosensor Applications of Small Molecule-Sensing Allosteric Ribozymes. Biomacromolecules 2013; 14:1240-9. [DOI: 10.1021/bm400299a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Robert Penchovsky
- Department of Genetics, Faculty
of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tzankov Boulevard, 1164 Sofia, Bulgaria
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Yoshida Y, Waga I, Horii K. Quantitative and sensitive protein detection strategies based on aptamers. Proteomics Clin Appl 2012; 6:574-80. [PMID: 22996907 DOI: 10.1002/prca.201200037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/01/2012] [Accepted: 08/03/2012] [Indexed: 01/24/2023]
Abstract
Aptamers are functional oligonucleotides of single-stranded RNA or DNA that can selectively recognize their targets with high affinity. Hence, they have been widely developed for analytical, diagnostic, and therapeutic applications. In this review, we have summarized recent advances in the development of aptamer-based detection systems. Aptamers can be amplified exponentially by PCR, which is one of the advantages of aptamers over antibodies. Recently, we have developed immuno-aptamers that bind to mouse or rabbit IgG and constructed a novel sensitive detection system based on a conventional ELISA, called the immuno-aptamer PCR assay. In this article, the aptamer-based ready-to-use sensors and another PCR-based aptamer assays are also described; moreover, we have discussed highly sensitive aptamer-based detection systems.
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39
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Jo JJ, Kim JH, Shin JS. Probing translation initiation through ligand binding to the 5' mRNA coding region. Chembiochem 2012; 13:2048-51. [PMID: 22927129 DOI: 10.1002/cbic.201200432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Indexed: 11/08/2022]
Abstract
Secondary structure matters: We have constructed artificial intragenic riboswitches to probe ribosome accessibility to the 5' mRNA coding region at three-base resolution in Escherichia coli. We show that only mRNA folding stability in the +1 to +15 nt region affects the translation process.
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Affiliation(s)
- Joon-Jung Jo
- Department of Biotechnology, Yonsei University, Shinchon-Dong 134, Seoul 120-749, South Korea
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40
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High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab Eng 2012; 14:306-16. [DOI: 10.1016/j.ymben.2012.04.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 04/09/2012] [Accepted: 04/17/2012] [Indexed: 12/25/2022]
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Mascini M, Palchetti I, Tombelli S. Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects. Angew Chem Int Ed Engl 2011; 51:1316-32. [PMID: 22213382 DOI: 10.1002/anie.201006630] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 12/11/2022]
Abstract
In recent years new nucleic acid and protein-based combinatorial molecules have attracted the attention of researchers working in various areas of science, ranging from medicine to analytical chemistry. These molecules, called aptamers, have been proposed as alternatives to antibodies in many different applications. The aim of this Review is to illustrate the peculiarities of these combinatorial molecules which have initially been explored for their importance in molecular medicine, but have enormous potential in other biotechnological fields historically dominated by antibodies, such as bioassays. A description of these molecules is given, and the methods for their selection and production are also summarized. Moreover, critical aspects related to these molecules are discussed.
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Affiliation(s)
- Marco Mascini
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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Mascini M, Palchetti I, Tombelli S. Nucleinsäure- und Peptidaptamere: Grundlagen und bioanalytische Aspekte. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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43
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Lau JL, Baksh MM, Fiedler JD, Brown SD, Kussrow A, Bornhop DJ, Ordoukhanian P, Finn M. Evolution and protein packaging of small-molecule RNA aptamers. ACS NANO 2011; 5:7722-9. [PMID: 21899290 PMCID: PMC3209476 DOI: 10.1021/nn2006927] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A high-affinity RNA aptamer (K(d) = 50 nM) was efficiently identified by SELEX against a heteroaryldihydropyrimidine structure, chosen as a representative drug-like molecule with no cross reactivity with mammalian or bacterial cells. This aptamer, its weaker-binding variants, and a known aptamer against theophylline were each embedded in a longer RNA sequence that was encapsidated inside a virus-like particle by a convenient expression technique. These nucleoprotein particles were shown by backscattering interferometry to bind to the small-molecule ligands with affinities similar to those of the free (nonencapsidated) aptamers. The system therefore comprises a general approach to the production and sequestration of functional RNA molecules, characterized by a convenient label-free analytical technique.
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Affiliation(s)
- Jolene L. Lau
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael M. Baksh
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jason D. Fiedler
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven D. Brown
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amanda Kussrow
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Darryl J. Bornhop
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Phillip Ordoukhanian
- Center for Protein and Nucleic Acid Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - M.G. Finn
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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44
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Sokoloski JE, Godfrey SA, Dombrowski SE, Bevilacqua PC. Prevalence of syn nucleobases in the active sites of functional RNAs. RNA (NEW YORK, N.Y.) 2011; 17:1775-87. [PMID: 21873463 PMCID: PMC3185911 DOI: 10.1261/rna.2759911] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Biological RNAs, like their DNA counterparts, contain helical stretches, which have standard Watson-Crick base pairs in the anti conformation. Most functional RNAs also adopt geometries with far greater complexity such as bulges, loops, and multihelical junctions. Occasionally, nucleobases in these regions populate the syn conformation wherein the base resides close to or over the ribose sugar, which leads to a more compact state. The importance of the syn conformation to RNA function is largely unknown. In this study, we analyze 51 RNAs with tertiary structure, including aptamers, riboswitches, ribozymes, and ribosomal RNAs, for number, location, and properties of syn nucleobases. These RNAs represent the set of nonoverlapping, moderate- to high-resolution structures available at present. We find that syn nucleobases are much more common among purines than pyrimidines, and that they favor C2'-endo-like conformations especially among those nucleobases in the intermediate syn conformation. Strikingly, most syn nucleobases participate in tertiary stacking and base-pairing interactions: Inspection of RNA structures revealed that the majority of the syn nucleobases are in regions assigned to function, with many syn nucleobases interacting directly with a ligand or ribozyme active site. These observations suggest that judicious placement of conformationally restricted nucleotides biased into the syn conformation could enhance RNA folding and catalysis. Such changes could also be useful for locking RNAs into functionally competent folds for use in X-ray crystallography and NMR.
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Affiliation(s)
- Joshua E. Sokoloski
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Stephanie A. Godfrey
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah E. Dombrowski
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C. Bevilacqua
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Corresponding author.E-mail .
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45
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Garst AD, Edwards AL, Batey RT. Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a003533. [PMID: 20943759 DOI: 10.1101/cshperspect.a003533] [Citation(s) in RCA: 243] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A critical feature of the hypothesized RNA world would have been the ability to control chemical processes in response to environmental cues. Riboswitches present themselves as viable candidates for a sophisticated mechanism of regulatory control in RNA-based life. These regulatory elements in the modern world are most commonly found in the 5'-untranslated regions of bacterial mRNAs, directly interacting with metabolites as a means of regulating expression of the coding region via a secondary structural switch. In this review, we focus on recent insights into how these RNAs fold into complex architectures capable of both recognizing a specific small molecule compound and exerting regulatory control over downstream sequences, with an emphasis on transcriptional regulation.
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Affiliation(s)
- Andrew D Garst
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 80309-0215, USA
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46
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Endoh T, Sugimoto N. Gene regulation system with an artificial RNA switch operating in human cells. Chembiochem 2011; 12:1174-8. [PMID: 21538761 DOI: 10.1002/cbic.201100093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
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47
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Babiskin AH, Smolke CD. Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules. Nucleic Acids Res 2011; 39:5299-311. [PMID: 21355039 PMCID: PMC3130268 DOI: 10.1093/nar/gkr090] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The programming of cellular networks to achieve new biological functions depends on the development of genetic tools that link the presence of a molecular signal to gene-regulatory activity. Recently, a set of engineered RNA controllers was described that enabled predictable tuning of gene expression in the yeast Saccharomyces cerevisiae through directed cleavage of transcripts by an RNase III enzyme, Rnt1p. Here, we describe a strategy for building a new class of RNA sensing-actuation devices based on direct integration of RNA aptamers into a region of the Rnt1p hairpin that modulates Rnt1p cleavage rates. We demonstrate that ligand binding to the integrated aptamer domain is associated with a structural change sufficient to inhibit Rnt1p processing. Three tuning strategies based on the incorporation of different functional modules into the Rnt1p switch platform were demonstrated to optimize switch dynamics and ligand responsiveness. We further demonstrated that these tuning modules can be implemented combinatorially in a predictable manner to further improve the regulatory response properties of the switch. The modularity and tunability of the Rnt1p switch platform will allow for rapid optimization and tailoring of this gene control device, thus providing a useful tool for the design of complex genetic networks in yeast.
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Affiliation(s)
- Andrew H Babiskin
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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48
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Desjardins G, Bonneau E, Girard N, Boisbouvier J, Legault P. NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site. Nucleic Acids Res 2011; 39:4427-37. [PMID: 21266483 PMCID: PMC3105416 DOI: 10.1093/nar/gkq1244] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem–loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson–Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme.
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Affiliation(s)
- Geneviève Desjardins
- Département de Biochimie, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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49
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Lee SW, Zhao L, Pardi A, Xia T. Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands. Biochemistry 2010; 49:2943-51. [PMID: 20214401 DOI: 10.1021/bi100106c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
RNAs often exhibit a high degree of conformational dynamics and heterogeneity, leading to a rugged energy landscape. However, the roles of conformational heterogeneity and rapid dynamics in molecular recognition or RNA function have not been extensively elucidated. Ultrafast time-resolved fluorescence spectroscopic experiments were used here to probe picosecond dynamics of the theophylline-binding RNA aptamer. These studies showed that multiple conformations are populated in the free RNA, indicating that this aptamer employs a conformational capture mechanism for ligand binding. The base on residue 27 in an internal loop exists in at least three conformational states in the free RNA, including binding competent and incompetent states that have distinct fluorescence decay signatures indicating different base stacking interactions. Picosecond dynamics were also detected by anisotropy experiments, where these motions indicate additional dynamics for base 27. The picosecond data show that theophylline binding shifts the equilibrium for conformations of base 27 from primarily stacked in the free RNA to mostly unstacked in the RNA-theophylline complex, as observed in the previous NMR structure. In contrast, base 10 in a second internal loop is mostly preorganized in the free RNA, consistent with it being stacked between G11 and G25, as is observed in the bound state. Picosecond dynamics were also measured on a modified aptamer that binds with higher affinity to 3-methylxanthine than theophylline. The modified aptamer shows less heterogeneity in the aptamer-3-methylxanthine complex than what is observed in the theophylline aptamer-theophylline complex.
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Affiliation(s)
- Sang Won Lee
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080-3021, USA
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50
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Freedman H, Huynh LP, Le L, Cheatham TE, Tuszynski JA, Truong TN. Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer. J Phys Chem B 2010; 114:2227-37. [PMID: 20099932 DOI: 10.1021/jp9059664] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To provide more accurate computational estimates of binding free energies in solution from molecular dynamics (MD) simulations, a separate solvation contribution for the binding ligand is determined from a linear response treatment. We use explicit water coordinates for this term and combine with MM-PBSA (molecular mechanics, Poisson-Boltzmann, and surface area contributions) in a new approach (MM-PB/LRA-SA). To assess this method, application to the binding between theophylline and its derivatives to an RNA aptamer was performed and compared with experimental binding affinities. Explicitly solvated MD trajectories were generated with the same parameter set used in the previous work by Gouda et al., who compared the relative binding of these molecules by both the MM-PBSA and thermodynamic integration methods. Substituting the linear response term for the ligand in the MM-PB/LRA-SA approach led to an improvement upon MM-PBSA when compared with experimental and thermodynamic integration results at approximately twice the computational cost. The balance between accuracy and computational expense achieved using this method suggests potential advantages in applying it in the virtual drug-screening process.
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Affiliation(s)
- Holly Freedman
- Department of Experimental Oncology, Room 3336, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada
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