1
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Paul T, Ha T, Myong S. Regeneration of PEG slide for multiple rounds of single-molecule measurements. Biophys J 2021; 120:1788-1799. [PMID: 33675764 DOI: 10.1016/j.bpj.2021.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022] Open
Abstract
Single-molecule fluorescence detection of protein and other biomolecules requires a polyethylene glycol (PEG)-passivated surface. Individual channels on a PEG-passivated slide are typically used only a few times, limiting the number of experiments per slide. Here, we report several strategies for regenerating PEG surfaces for multiple rounds of experiments. First, we show regeneration of DNA- or RNA-tethered surfaces by washing out the bound protein by 0.1% sodium dodecyl sulfate, which is significantly more effective than 6 M urea, 6 M GdmCl, or 100 μM proteinase K. Strikingly, 10 consecutive experiments in five different systems produced indistinguishable results both in molecule count and protein activity. Second, duplexed DNA unwound by helicase or denatured by 50 mM NaOH was reannealed with a complementary strand to regenerate the duplexed substrate with an exceptionally high recovery rate. Third, the biotin-PEG layer was regenerated by using 7 M NaOH to strip off NeutrAvidin, which can be reapplied for additional experiments. We demonstrate five cycles of regenerating antibody immobilized surface by which three different protein activity was measured. Altogether, our methods represent reliable and reproducible yet simple and rapid strategies that will enhance the efficiency of single-molecule experiments.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, Maryland
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois.
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2
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Li B, Cao Y, Westhof E, Miao Z. Advances in RNA 3D Structure Modeling Using Experimental Data. Front Genet 2020; 11:574485. [PMID: 33193680 PMCID: PMC7649352 DOI: 10.3389/fgene.2020.574485] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/02/2020] [Indexed: 12/26/2022] Open
Abstract
RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA structures using x-ray crystallography is both laborious and demands expertise, thus, hindering our comprehension of RNA structural biology. The computational modeling of RNA structure was a milestone in the birth of bioinformatics. Although computational modeling has been greatly improved over the last decade showing many successful cases, the accuracy of such computational modeling is not only length-dependent but also varies according to the complexity of the structure. To increase credibility, various experimental data were integrated into computational modeling. In this review, we summarize the experiments that can be integrated into RNA structure modeling as well as the computational methods based on these experimental data. We also demonstrate how computational modeling can help the experimental determination of RNA structure. We highlight the recent advances in computational modeling which can offer reliable structure models using high-throughput experimental data.
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Affiliation(s)
- Bing Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Eric Westhof
- Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
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3
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Zhao M, Steffen FD, Börner R, Schaffer MF, Sigel RKO, Freisinger E. Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy. Nucleic Acids Res 2019; 46:e13. [PMID: 29136199 PMCID: PMC5814972 DOI: 10.1093/nar/gkx1100] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/21/2017] [Indexed: 02/07/2023] Open
Abstract
Labeling of long RNA molecules in a site-specific yet generally applicable manner is integral to many spectroscopic applications. Here we present a novel covalent labeling approach that is site-specific and scalable to long intricately folded RNAs. In this approach, a custom-designed DNA strand that hybridizes to the RNA guides a reactive group to target a preselected adenine residue. The functionalized nucleotide along with the concomitantly oxidized 3'-terminus can subsequently be conjugated to two different fluorophores via bio-orthogonal chemistry. We validate this modular labeling platform using a regulatory RNA of 275 nucleotides, the btuB riboswitch of Escherichia coli, demonstrate its general applicability by modifying a base within a duplex, and show its site-selectivity in targeting a pair of adjacent adenines. Native folding and function of the RNA is confirmed on the single-molecule level by using FRET as a sensor to visualize and characterize the conformational equilibrium of the riboswitch upon binding of its cofactor adenosylcobalamin. The presented labeling strategy overcomes size and site constraints that have hampered routine production of labeled RNA that are beyond 200 nt in length.
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Affiliation(s)
- Meng Zhao
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Fabio D Steffen
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Richard Börner
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | | | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
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4
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Baker KA, Lamichhane R, Lamichhane T, Rueda D, Cunningham PR. Protein-RNA Dynamics in the Central Junction Control 30S Ribosome Assembly. J Mol Biol 2016; 428:3615-31. [PMID: 27192112 DOI: 10.1016/j.jmb.2016.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/02/2016] [Accepted: 05/07/2016] [Indexed: 11/18/2022]
Abstract
Interactions between ribosomal proteins (rproteins) and ribosomal RNA (rRNA) facilitate the formation of functional ribosomes. S15 is a central domain primary binding protein that has been shown to trigger a cascade of conformational changes in 16S rRNA, forming the functional structure of the central domain. Previous biochemical and structural studies in vitro have revealed that S15 binds a three-way junction of helices 20, 21, and 22, including nucleotides 652-654 and 752-754. All junction nucleotides except 653 are highly conserved among the Bacteria. To identify functionally important motifs within the junction, we subjected nucleotides 652-654 and 752-754 to saturation mutagenesis and selected and analyzed functional mutants. Only 64 mutants with greater than 10% ribosome function in vivo were isolated. S15 overexpression complemented mutations in the junction loop in each of the partially active mutants, although mutations that produced inactive ribosomes were not complemented by overexpression of S15. Single-molecule Förster or fluorescence resonance energy transfer (smFRET) was used to study the Mg(2+)- and S15-induced conformational dynamics of selected junction mutants. Comparison of the structural dynamics of these mutants with the wild type in the presence and absence of S15 revealed specific sequence and structural motifs in the central junction that are important in ribosome function.
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MESH Headings
- DNA Mutational Analysis
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Fluorescence Resonance Energy Transfer
- Genetic Complementation Test
- Macromolecular Substances/metabolism
- Magnesium/metabolism
- Models, Biological
- Models, Molecular
- Protein Binding
- Protein Conformation
- Protein Interaction Maps
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small, Bacterial/metabolism
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Affiliation(s)
- Kris Ann Baker
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Rajan Lamichhane
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Tek Lamichhane
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA; Section of Virology, Department of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Single Molecule Imaging Group, MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, UK.
| | - Philip R Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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5
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Hardin JW, Warnasooriya C, Kondo Y, Nagai K, Rueda D. Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET. Nucleic Acids Res 2015; 43:10963-74. [PMID: 26503251 PMCID: PMC4678811 DOI: 10.1093/nar/gkv1011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/24/2015] [Indexed: 11/13/2022] Open
Abstract
In large ribonucleoprotein machines, such as ribosomes and spliceosomes, RNA functions as an assembly scaffold as well as a critical catalytic component. Protein binding to the RNA scaffold can induce structural changes, which in turn modulate subsequent binding of other components. The spliceosomal U4/U6 di-snRNP contains extensively base paired U4 and U6 snRNAs, Snu13, Prp31, Prp3 and Prp4, seven Sm and seven LSm proteins. We have studied successive binding of all protein components to the snRNA duplex during di-snRNP assembly by electrophoretic mobility shift assay and accompanying conformational changes in the U4/U6 RNA 3-way junction by single-molecule FRET. Stems I and II of the duplex were found to co-axially stack in free RNA and function as a rigid scaffold during the entire assembly, but the U4 snRNA 5' stem-loop adopts alternative orientations each stabilized by Prp31 and Prp3/4 binding accounting for altered Prp3/4 binding affinities in presence of Prp31.
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Affiliation(s)
- John W Hardin
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chandani Warnasooriya
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Yasushi Kondo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Rueda
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
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6
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Shaw E, St-Pierre P, McCluskey K, Lafontaine DA, Penedo JC. Using sm-FRET and denaturants to reveal folding landscapes. Methods Enzymol 2015; 549:313-41. [PMID: 25432755 DOI: 10.1016/b978-0-12-801122-5.00014-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
RNA folding studies aim to clarify the relationship among sequence, tridimensional structure, and biological function. In the last decade, the application of single-molecule fluorescence resonance energy transfer (sm-FRET) techniques to investigate RNA structure and folding has revealed the details of conformational changes and timescale of the process leading to the formation of biologically active RNA structures with subnanometer resolution on millisecond timescales. In this review, we initially summarize the first wave of single-molecule FRET-based RNA techniques that focused on analyzing the influence of mono- and divalent metal ions on RNA function, and how these studies have provided very valuable information about folding pathways and the presence of intermediate and low-populated states. Next, we describe a second generation of single-molecule techniques that combine sm-FRET with the use of chemical denaturants as an emerging powerful approach to reveal information about the dynamics and energetics of RNA folding that remains hidden using conventional sm-FRET approaches. The main advantages of using the competing interplay between folding agents such as metal ions and denaturants to observe and manipulate the dynamics of RNA folding and RNA-ligand interactions is discussed in the context of the adenine riboswitch aptamer.
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Affiliation(s)
- Euan Shaw
- SUPA School of Physics and Astronomy, University of St. Andrews, St. Andrews, Fife, United Kingdom
| | - Patrick St-Pierre
- RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Kaley McCluskey
- SUPA School of Physics and Astronomy, University of St. Andrews, St. Andrews, Fife, United Kingdom
| | - Daniel A Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de Sherbrooke, Sherbrooke, Québec, Canada.
| | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St. Andrews, St. Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, United Kingdom.
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7
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Perez-Gonzalez DC, Penedo JC. Single-Molecule Strategies for DNA and RNA Diagnostics. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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8
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Trojanowski P, Plötner J, Grünewald C, Graupner FF, Slavov C, Reuss AJ, Braun M, Engels JW, Wachtveitl J. Photo-physical properties of 2-(1-ethynylpyrene)-adenosine: influence of hydrogen bonding on excited state properties. Phys Chem Chem Phys 2014; 16:13875-88. [PMID: 24894337 DOI: 10.1039/c4cp01148a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photo-physical properties of 2-(1-ethynylpyrene)-adenosine (PyA), a fluorescent probe for RNA dynamics, were examined by solvation studies. The excited-state dynamics display the influence of the vicinity on the spectral features. Combining improved transient absorption and streak camera measurements along with a new analysis method provide a detailed molecular picture of the photophysics. After intramolecular vibrational energy redistribution (IVR), two distinct states are observed. Solvent class (protic/aprotic) and permittivity strongly affect the properties of these states and their population ratio. As a result their emission spectrum is altered, while the fluorescence quantum yield and the overall lifetime remain nearly unchanged. Consequently, the hitherto existing model of the photophysics is herein refined and extended. The findings can serve as basis for improving the information content of measurements with PyA as a label in RNA.
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Affiliation(s)
- P Trojanowski
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt/Main, Germany.
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9
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Paudel B, Rueda D. RNA folding dynamics using laser-assisted single-molecule refolding. Methods Mol Biol 2014; 1086:289-307. [PMID: 24136611 DOI: 10.1007/978-1-62703-667-2_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
RNA folding pathways can be complex and even include kinetic traps or misfolded intermediates that can be slow to resolve. Characterizing these pathways is critical to understanding how RNA molecules acquire their biological function. We have previously developed a novel approach to help characterize such misfolded intermediates. Laser-assisted single-molecule refolding (LASR) is a powerful technique that combines temperature-jump (T-jump) kinetics with single-molecule detection. In a typical LASR experiment, the temperature is rapidly increased and conformational dynamics are characterized, in real-time, at the single-molecule level using single-molecule fluorescence resonance energy transfer (smFRET). Here, we provide detailed protocols for performing LASR experiments including sample preparation, temperature calibration, and data analysis.
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Affiliation(s)
- Bishnu Paudel
- Department of Medicine, Section of Virology, Imperial College, London, UK
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10
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Alemán E, de Silva C, Patrick EM, Musier-Forsyth K, Rueda D. Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle. J Phys Chem Lett 2014; 5:777-781. [PMID: 24803990 PMCID: PMC3985717 DOI: 10.1021/jz4025832] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/06/2014] [Indexed: 05/25/2023]
Abstract
Fluorescent nucleotide analogues, such as 2-aminopurine (2AP) and pyrrolo-C (PyC), have been extensively used to study nucleic acid local conformational dynamics in bulk experiments. Here we present a proof-of-principle approach using 2AP and PyC fluorescence at the single-molecule level. Our data show that ssDNA, dsDNA, or RNA containing both 2AP and PyC can be monitored using single-molecule fluorescence and a click chemistry immobilization method. We demonstrate that this approach can be used to monitor DNA and RNA in real time. This is the first reported assay using fluorescent nucleotide analogs at the single-molecule level. We anticipate that single 2AP or PyC fluorescence will have numerous applications in studies of DNA and RNA, including protein-induced base-flipping dynamics in protein-nucleic acid complexes.
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Affiliation(s)
- Elvin
A. Alemán
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Chamaree de Silva
- Department
of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Eric M. Patrick
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Karin Musier-Forsyth
- Department
of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - David Rueda
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
- Department of Medicine, Section of
Virology and Single Molecule Imaging Group,
MRC Clinical Sciences Center, Imperial College, Du Cane Road, London W12 0NN, United
Kingdom
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11
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Karunatilaka KS, Rueda D. Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex. RNA (NEW YORK, N.Y.) 2014; 20:16-23. [PMID: 24243115 PMCID: PMC3866641 DOI: 10.1261/rna.041806.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The spliceosome catalyzes precursor-mRNA splicing in all eukaryotes. It consists of over 100 proteins and five small nuclear RNAs (snRNAs), including U2 and U6 snRNAs, which are essential for catalysis. Human and yeast snRNAs share structural similarities despite the fact that human snRNAs contain numerous post-transcriptional modifications. Although functions for these modifications have been proposed, their exact roles are still not well understood. To help elucidate these roles in pre-mRNA splicing, we have used single-molecule fluorescence to characterize the effect of several post-transcriptional modifications in U2 snRNA on the conformation and dynamics of the U2-U6 complex in vitro. Consistent with yeast, the human U2-U6 complex reveals the presence of a magnesium-dependent dynamic equilibrium among three conformations. Interestingly, our data show that modifications in human U2 stem I modulate the dynamic equilibrium of the U2-U6 complex by stabilizing the four-helix structure. However, the small magnitude of this effect suggests that post-transcriptional modifications in human snRNAs may have a primary role in the mediation of specific RNA-protein interactions in vivo.
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Affiliation(s)
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, United Kingdom
- Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, London W12 0NN, United Kingdom
- Corresponding authorE-mail
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12
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König SLB, Liyanage PS, Sigel RKO, Rueda D. Helicase-mediated changes in RNA structure at the single-molecule level. RNA Biol 2013; 10:133-48. [PMID: 23353571 DOI: 10.4161/rna.23507] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA helicases are a diverse group of RNA-dependent ATPases known to play a large number of biological roles inside the cell, such as RNA unwinding, remodeling, export and degradation. Understanding how helicases mediate changes in RNA structure is therefore of fundamental interest. The advent of single-molecule spectroscopic techniques has unveiled with unprecedented detail the interplay of RNA helicases with their substrates. In this review, we describe the characterization of helicase-RNA interactions by single-molecule approaches. State-of-the-art techniques are presented, followed by a discussion of recent advancements in this exciting field.
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13
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Cardo L, Karunatilaka KS, Rueda D, Sigel RKO. Single molecule FRET characterization of large ribozyme folding. Methods Mol Biol 2012; 848:227-51. [PMID: 22315073 DOI: 10.1007/978-1-61779-545-9_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A procedure to investigate the folding of group II intron by single molecule Fluorescence Resonance Energy Transfer (smFRET) using total internal reflection fluorescence microscopy (TIRFM) is described in this chapter. Using our previous studies on the folding and dynamics of a large ribozyme in the presence of metal ions (i.e., Mg(2+) and Ca(2+)) and/or the DEAD-box protein Mss116 as an example, we here describe step-by-step procedures to perform experiments. smFRET allows the investigation of individual molecules, thus, providing kinetic and mechanistic information hidden in ensemble averaged experiments.
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Affiliation(s)
- Lucia Cardo
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
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14
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Lamichhane R, Solem A, Black W, Rueda D. Single-molecule FRET of protein-nucleic acid and protein-protein complexes: surface passivation and immobilization. Methods 2010; 52:192-200. [PMID: 20554047 PMCID: PMC3321382 DOI: 10.1016/j.ymeth.2010.06.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Indexed: 11/23/2022] Open
Abstract
Single-molecule fluorescence spectroscopy reveals the real time dynamics that occur during biomolecular interactions that would otherwise be hidden by the ensemble average. It also removes the requirement to synchronize reactions, thus providing a very intuitive approach to study kinetics of biological systems. Surface immobilization is commonly used to increase observation times to the minute time scale, but it can be detrimental if the sample interacts non-specifically with the surface. Here, we review detailed protocols to prevent such interactions by passivating the surface or by trapping the molecules inside surface immobilized lipid vesicles. Finally, we discuss recent examples where these methods were applied to study the dynamics of important cellular processes at the single-molecule level.
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Affiliation(s)
- Rajan Lamichhane
- Department of Chemistry, Wayne State University, Detroit MI 48202
| | - Amanda Solem
- Department of Chemistry, Wayne State University, Detroit MI 48202
| | - Will Black
- Department of Chemistry, Wayne State University, Detroit MI 48202
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit MI 48202
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15
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Wiebe NJP, Meyer IM. TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures. PLoS Comput Biol 2010; 6:e1000823. [PMID: 20589081 PMCID: PMC2891591 DOI: 10.1371/journal.pcbi.1000823] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2009] [Accepted: 05/19/2010] [Indexed: 12/20/2022] Open
Abstract
The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular environment. Many non-coding genes exert their function via an RNA structure which starts emerging while the RNA sequence is being transcribed from the genome. The resulting folding pathway is known to depend on a variety of features such as the transcription speed, the concentration of various ions and the binding of proteins and other molecules. Not all of these influences can be adequately captured by the existing computational methods which try to replicate what happens in vivo. So far, it has been challenging to experimentally investigate co-transcriptional folding pathways in vivo and only little data from in vitro experiments exists. In order to investigate if functionally similar RNA sequences from different organisms fold in a similar way, we have developed a new computational method, called Transat, which does not require the detailed computational modeling of the cellular environment. We show in a comprehensive analysis that our method is capable of detecting known structural features and provide evidence that structural features of the in vivo folding pathways have been conserved for several biologically interesting classes of RNA sequences.
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Affiliation(s)
- Nicholas J. P. Wiebe
- Centre for High-Throughput Biology & Department of Computer Science and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Irmtraud M. Meyer
- Centre for High-Throughput Biology & Department of Computer Science and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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16
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Wachowius F, Höbartner C. Chemical RNA modifications for studies of RNA structure and dynamics. Chembiochem 2010; 11:469-80. [PMID: 20135663 DOI: 10.1002/cbic.200900697] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Falk Wachowius
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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