51
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Ageely EA, Kartje ZJ, Rohilla KJ, Barkau CL, Gagnon KT. Quadruplex-Flanking Stem Structures Modulate the Stability and Metal Ion Preferences of RNA Mimics of GFP. ACS Chem Biol 2016; 11:2398-406. [PMID: 27467146 DOI: 10.1021/acschembio.6b00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spinach family of RNA aptamers are RNA mimics of green fluorescent protein (GFP) that have previously been designed to address the challenges of imaging RNA inside living cells. However, relatively low levels of free intracellular magnesium limited the practical use of these aptamers. Recent cell-based selections identified the broccoli RNA aptamer, which requires less magnesium for fluorescence, but the basis for magnesium preference remained unclear. Here, we find that the broccoli RNA structure is very similar to that of baby spinach, a truncated version of the spinach aptamer. Differences in stability and metal ion preferences between these two aptamers, and among broccoli mutants, are primarily associated with the sequence and structure of predicted quadruplex-flanking stem structures. Mutation of purine-purine pairs in broccoli at the terminal stem-quadruplex transition caused reversion of broccoli to a higher magnesium dependence. Unique duplex-to-quadruplex transitions in GFP-mimic RNAs likely explain their sensitivity to magnesium for stability and fluorescence. Thus, optimizations designed to improve aptamers should take into consideration the role of metal ions in stabilizing the transitions and interactions between independently folding RNA structural motifs.
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Affiliation(s)
- Eman A. Ageely
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Zachary J. Kartje
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Kushal J. Rohilla
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
| | - Christopher L. Barkau
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
| | - Keith T. Gagnon
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
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52
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Kikuchi N, Kolpashchikov DM. Split Spinach Aptamer for Highly Selective Recognition of DNA and RNA at Ambient Temperatures. Chembiochem 2016; 17:1589-92. [PMID: 27305425 DOI: 10.1002/cbic.201600323] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 12/25/2022]
Abstract
Split spinach aptamer (SSA) probes for fluorescent analysis of nucleic acids were designed and tested. In SSA design, two RNA or RNA/DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for low-fluorescent 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) dye, which resulted in up to a 270-fold increase in fluorescence. The major advantage of the SSA over state-of-the art fluorescent probes is high selectivity: it produces only background fluorescence in the presence of a single-base-mismatched analyte, even at room temperature. SSA is therefore a promising tool for label-free analysis of nucleic acids at ambient temperatures.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.
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53
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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54
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Afonin KA, Viard M, Tedbury P, Bindewald E, Parlea L, Howington M, Valdman M, Johns-Boehme A, Brainerd C, Freed EO, Shapiro BA. The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities. NANO LETTERS 2016; 16:1746-53. [PMID: 26926382 PMCID: PMC6345527 DOI: 10.1021/acs.nanolett.5b04676] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Current work reports the use of single-stranded RNA toeholds of different lengths to promote the reassociation of various RNA-DNA hybrids, which results in activation of multiple split functionalities inside human cells. The process of reassociation is analyzed and followed with a novel computational multistrand secondary structure prediction algorithm and various experiments. All of our previously designed RNA/DNA nanoparticles employed single-stranded DNA toeholds to initiate reassociation. The use of RNA toeholds is advantageous because of the simpler design rules, the shorter toeholds, and the smaller size of the resulting nanoparticles (by up to 120 nucleotides per particle) compared to the same hybrid nanoparticles with single-stranded DNA toeholds. Moreover, the cotranscriptional assemblies result in higher yields for hybrid nanoparticles with ssRNA toeholds.
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Affiliation(s)
- Kirill A. Afonin
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Philip Tedbury
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Marshall Howington
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Melissa Valdman
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Alizah Johns-Boehme
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Cara Brainerd
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Eric O. Freed
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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55
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Aw SS, Tang MX, Teo YN, Cohen SM. A conformation-induced fluorescence method for microRNA detection. Nucleic Acids Res 2016; 44:e92. [PMID: 26951376 PMCID: PMC4889923 DOI: 10.1093/nar/gkw108] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 02/12/2016] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs play important roles in a large variety of biological systems and processes through their regulation of target mRNA expression, and show promise as clinical biomarkers. However, their small size presents challenges for tagging or direct detection. Innovation in techniques to sense and quantify microRNAs may aid research into novel aspects of microRNA biology and contribute to the development of diagnostics. By introducing an additional stem loop into the fluorescent RNA Spinach and altering its 3' and 5' ends, we have generated a new RNA, Pandan, that functions as the basis for a microRNA sensor. Pandan contains two sequence-variable stem loops that encode complementary sequence for a target microRNA of interest. In its sensor form, it requires the binding of a target microRNA in order to reconstitute the RNA scaffold for fluorophore binding and fluorescence. Binding of the target microRNA resulted in large changes in fluorescence intensity. The median fold change in fluorescence observed for the sensors tested was ∼50-fold. Pandan RNA sensors exhibit good signal-to-noise ratios, and can detect their target microRNAs within complex RNA mixtures.
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Affiliation(s)
- Sherry S Aw
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Melissa Xm Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Yin Nah Teo
- Molecular Engineering Laboratory, Biomolecular Sciences Institutes, A*STAR, 61 Biopolis Drive, 138673, Singapore Division of Chemistry and Biological Chemistry, SPMS, Nanyang Technological University, 637371, Singapore
| | - Stephen M Cohen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore Department of Cellular and Molecular Medicine,University of Copenhagen, Blegdamsvej 3, Copenhagen 2200 N, Denmark
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56
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Ausländer S, Fuchs D, Hürlemann S, Ausländer D, Fussenegger M. Engineering a ribozyme cleavage-induced split fluorescent aptamer complementation assay. Nucleic Acids Res 2016; 44:e94. [PMID: 26939886 PMCID: PMC4889925 DOI: 10.1093/nar/gkw117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/16/2016] [Indexed: 12/19/2022] Open
Abstract
Hammerhead ribozymes are self-cleaving RNA molecules capable of regulating gene expression in living cells. Their cleavage performance is strongly influenced by intra-molecular loop–loop interactions, a feature not readily accessible through modern prediction algorithms. Ribozyme engineering and efficient implementation of ribozyme-based genetic switches requires detailed knowledge of individual self-cleavage performances. By rational design, we devised fluorescent aptamer-ribozyme RNA architectures that allow for the real-time measurement of ribozyme self-cleavage activity in vitro. The engineered nucleic acid molecules implement a split Spinach aptamer sequence that is made accessible for strand displacement upon ribozyme self-cleavage, thereby complementing the fluorescent Spinach aptamer. This fully RNA-based ribozyme performance assay correlates ribozyme cleavage activity with Spinach fluorescence to provide a rapid and straightforward technology for the validation of loop–loop interactions in hammerhead ribozymes.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - David Fuchs
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Samuel Hürlemann
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058 Basel, Switzerland Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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57
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Autour A, Westhof E, Ryckelynck M. iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications. Nucleic Acids Res 2016; 44:2491-500. [PMID: 26932363 PMCID: PMC4824111 DOI: 10.1093/nar/gkw083] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/01/2016] [Indexed: 01/03/2023] Open
Abstract
Using random mutagenesis and high throughput screening by microfluidic-assisted In Vitro Compartmentalization, we report the isolation of an order of magnitude times brighter mutants of the light-up RNA aptamers Spinach that are far less salt-sensitive and with a much higher thermal stability than the parent molecule. Further engineering gave iSpinach, a molecule with folding and fluorescence properties surpassing those of all currently known aptamer based on the fluorogenic co-factor 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI). We illustrate the potential of iSpinach in a new sensitive and high throughput-compatible fluorogenic assay that measures co-transcriptionally the catalytic constant (kcat) of a model ribozyme.
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Affiliation(s)
- Alexis Autour
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
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58
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Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T. Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. Sci Rep 2015; 5:17295. [PMID: 26612428 PMCID: PMC4661537 DOI: 10.1038/srep17295] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/15/2015] [Indexed: 12/24/2022] Open
Abstract
Live cell RNA imaging using genetically encoded fluorescent labels is an important tool for monitoring RNA activities. A recently reported RNA aptamer-fluorogen system, the Spinach, in which an RNA aptamer binds and induces the fluorescence of a GFP-like 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) ligand, can be readily tagged to the RNA of interest. Although the aptamer-fluorogen system is sufficient for imaging highly abundant non-coding RNAs (tRNAs, rRNAs, etc.), it performs poorly for mRNA imaging due to low brightness. In addition, whether the aptamer-fluorogen system may perturb the native RNA characteristics has not been systematically characterized at the levels of RNA transcription, translation and degradation. To increase the brightness of these aptamer-fluorogen systems, we constructed and tested tandem arrays containing multiple Spinach aptamers (8-64 aptamer repeats). Such arrays enhanced the brightness of the tagged mRNA molecules by up to ~17 fold in living cells. Strong laser excitation with pulsed illumination further increased the imaging sensitivity of Spinach array-tagged RNAs. Moreover, transcriptional fusion to the Spinach array did not affect mRNA transcription, translation or degradation, indicating that aptamer arrays might be a generalizable labeling method for high-performance and low-perturbation live cell RNA imaging.
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Affiliation(s)
- Jichuan Zhang
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jingyi Fei
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Benjamin J. Leslie
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
| | - Kyu Young Han
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
| | - Thomas E. Kuhlman
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
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59
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Peters G, Coussement P, Maertens J, Lammertyn J, De Mey M. Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice. Biotechnol Adv 2015; 33:1829-44. [PMID: 26514597 DOI: 10.1016/j.biotechadv.2015.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
Synthetic biology, in close concert with systems biology, is revolutionizing the field of metabolic engineering by providing novel tools and technologies to rationally, in a standardized way, reroute metabolism with a view to optimally converting renewable resources into a broad range of bio-products, bio-materials and bio-energy. Increasingly, these novel synthetic biology tools are exploiting the extensive programmable nature of RNA, vis-à-vis DNA- and protein-based devices, to rationally design standardized, composable, and orthogonal parts, which can be scaled and tuned promptly and at will. This review gives an extensive overview of the recently developed parts and tools for i) modulating gene expression ii) building genetic circuits iii) detecting molecules, iv) reporting cellular processes and v) building RNA nanostructures. These parts and tools are becoming necessary armamentarium for contemporary metabolic engineering. Furthermore, the design criteria, technological challenges, and recent metabolic engineering success stories of the use of RNA devices are highlighted. Finally, the future trends in transforming metabolism through RNA engineering are critically evaluated and summarized.
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Affiliation(s)
- Gert Peters
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Pieter Coussement
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jeroen Lammertyn
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, 3001 Louvain, Belgium
| | - Marjan De Mey
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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60
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Ketterer S, Fuchs D, Weber W, Meier M. Systematic reconstruction of binding and stability landscapes of the fluorogenic aptamer spinach. Nucleic Acids Res 2015; 43:9564-72. [PMID: 26400180 PMCID: PMC4627091 DOI: 10.1093/nar/gkv944] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/10/2015] [Indexed: 01/08/2023] Open
Abstract
Fluorogenic RNAs that are based on the complex formed by 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) derivatives and the RNA aptamer named Spinach were used to engineer a new generation of in vitro and in vivo sensors for bioanalytics. With the resolved crystal structure of the RNA/small molecule complex, the engineering map becomes available, but comprehensive information regarding the thermodynamic profile of the molecule is missing. Here, we reconstructed the full thermodynamic binding and stability landscapes between DFHBI and a truncated sequence of first-generation Spinach. For this purpose, we established a systematic screening procedure for single- and double-point mutations on a microfluidic large-scale integrated chip platform for 87-nt long RNAs. The thermodynamic profile with single base resolution was used to engineer an improved fluorogenic spinach generation via a directed rather than evolutional approach.
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Affiliation(s)
- Simon Ketterer
- Microfluidic and Biological Engineering, Department of Microsystems Engineering - IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany Centre for Biological Signalling Studies - BIOSS, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - David Fuchs
- Microfluidic and Biological Engineering, Department of Microsystems Engineering - IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany Centre for Biological Signalling Studies - BIOSS, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Wilfried Weber
- Centre for Biological Signalling Studies - BIOSS, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Matthias Meier
- Microfluidic and Biological Engineering, Department of Microsystems Engineering - IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany Centre for Biological Signalling Studies - BIOSS, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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61
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Tsvetkova IB, Yi G, Yi Y, Kao CC, Dragnea BG. Segmented GFP-like aptamer probes for functional imaging of viral genome trafficking. Virus Res 2015; 210:291-7. [PMID: 26325297 DOI: 10.1016/j.virusres.2015.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/25/2015] [Accepted: 08/28/2015] [Indexed: 01/21/2023]
Abstract
Recently developed GFP-like RNA aptamers harbor a few unique potential benefits for in vivo RNA imaging applications, including co-packaging of viral genomes. Here we examine them in the context of co-packaging of RNA strands during virion assembly and trafficking. The approach is applicable both in vitro and in vivo, thus bridging an existing methodological gap. We have found that splitting the aptamer sequence in the loop region into two separate parts allows for subsequent self-assembly into a functional unit, which preserves the dye-binding pocket. In presence of the dye, virus-like particles encapsulating segmented GFP-like aptamers provided bright fluorescence emission and showed negligible bleaching due to continuous chromophore exchange: two desirable characteristics for real-time in vivo single particle studies requiring a broader dynamic range than currently available. Proof-of-principle in vivo imaging experiments confirmed detectability of aptamer-loaded virus-like particles in barley root cells even in presence of significant autofluorescence background.
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Affiliation(s)
- Irina B Tsvetkova
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
| | - Guanghui Yi
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, USA
| | - Yi Yi
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Cheng C Kao
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, USA
| | - Bogdan G Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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62
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Fiore E, Dausse E, Dubouchaud H, Peyrin E, Ravelet C. Ultrafast capillary electrophoresis isolation of DNA aptamer for the PCR amplification-based small analyte sensing. Front Chem 2015; 3:49. [PMID: 26322305 PMCID: PMC4533002 DOI: 10.3389/fchem.2015.00049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/27/2015] [Indexed: 01/14/2023] Open
Abstract
Here, we report a new homogeneous DNA amplification-based aptamer assay for small analyte sensing. The aptamer of adenosine chosen as the model analyte was split into two fragments able to assemble in the presence of target. Primers were introduced at extremities of one fragment in order to generate the amplifiable DNA component. The amount of amplifiable fragment was quantifiable by Real-Time Polymerase Chain Reaction (RT-PCR) amplification and directly reliable on adenosine concentration. This approach combines the very high separation efficiency and the homogeneous format (without immobilization) of capillary electrophoresis (CE) and the sensitivity of real time PCR amplification. An ultrafast isolation of target-bound split aptamer (60 s) was developed by designing a CE input/ouput scheme. Such method was successfully applied to the determination of adenosine with a LOD of 1 μM.
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Affiliation(s)
- Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Eric Dausse
- Laboratoire ARNA, Institut National de la Santé et de la Recherche Médicale U869, Université Bordeaux Bordeaux, France
| | - Hervé Dubouchaud
- Laboratoire de Bioénergétique Fondamentale et Appliquée, Institut National de la Santé et de la Recherche Médicale U1055, University Grenoble Alpes Grenoble, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
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63
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Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, Ferré-D’Amaré AR. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol 2014; 21:658-63. [PMID: 25026079 PMCID: PMC4143336 DOI: 10.1038/nsmb.2865] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 07/07/2014] [Indexed: 12/22/2022]
Abstract
GFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in vitro-evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live-cell, real-time imaging of biological RNAs without resorting to large RNA-binding protein-GFP fusions. To elucidate the molecular basis of Spinach fluorescence, we solved the cocrystal structure of Spinach bound to its cognate exogenous chromophore, showing that Spinach activates the small molecule by immobilizing it between a base triple, a G-quadruplex and an unpaired G. Mutational and NMR analyses indicate that the G-quadruplex is essential for Spinach fluorescence, is also present in other fluorogenic RNAs and may represent a general strategy for RNAs to induce fluorescence of chromophores. The structure guided the design of a miniaturized 'Baby Spinach', and it provides a foundation for structure-driven design and tuning of fluorescent RNAs.
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Affiliation(s)
| | - Michael C. Chen
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Wenjiao Song
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY
| | - Rita L. Strack
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY
| | - Andrea Thorn
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, NY
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