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Isothermal Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes. Methods Mol Biol 2016; 1320:127-43. [PMID: 26227041 DOI: 10.1007/978-1-4939-2763-0_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The success rate of nucleic acids/ligands co-crystallization can be significantly improved by performing preliminary biophysical analyses. Among suitable biophysical approaches, isothermal titration calorimetry (ITC) is certainly a method of choice. ITC can be used in a wide range of experimental conditions to monitor in real time the formation of the RNA- or DNA-ligand complex, with the advantage of providing in addition the complete binding profile of the interaction. Following the ITC experiment, the complex is ready to be concentrated for crystallization trials. This chapter describes a detailed experimental protocol for using ITC as a tool for monitoring RNA/small molecule binding, followed by co-crystallization.
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Bouchard P, Legault P. A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme. RNA (NEW YORK, N.Y.) 2014; 20:1451-64. [PMID: 25051972 PMCID: PMC4138328 DOI: 10.1261/rna.046144.114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/03/2014] [Indexed: 05/20/2023]
Abstract
Kissing loops are tertiary structure elements that often play key roles in functional RNAs. In the Neurospora VS ribozyme, a kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain is known to play an important role in substrate recognition. In addition, this I/V kissing-loop interaction is associated with a helix shift in SLI that activates the substrate for catalysis. To better understand the role of this kissing-loop interaction in substrate recognition and activation by the VS ribozyme, we performed a thermodynamic characterization by isothermal titration calorimetry using isolated SLI and SLV stem-loops. We demonstrate that preshifted SLI variants have higher affinity for SLV than shiftable SLI variants, with an energetic cost of 1.8-3 kcal/mol for the helix shift in SLI. The affinity of the preshifted SLI for SLV is remarkably high, the interaction being more stable by 7-8 kcal/mol than predicted for a comparable duplex containing three Watson-Crick base pairs. The structural basis of this remarkable stability is discussed in light of previous NMR studies. Comparative thermodynamic studies reveal that kissing-loop complexes containing 6-7 Watson-Crick base pairs are as stable as predicted from comparable RNA duplexes; however, those with 2-3 Watson-Crick base pairs are more stable than predicted. Interestingly, the stability of SLI/ribozyme complexes is similar to that of SLI/SLV complexes. Thus, the I/V kissing loop interaction represents the predominant energetic contribution to substrate recognition by the trans-cleaving VS ribozyme.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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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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4
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Lévesque D, Reymond C, Perreault JP. Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme. PLoS One 2012; 7:e40309. [PMID: 22768274 PMCID: PMC3386971 DOI: 10.1371/journal.pone.0040309] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/04/2012] [Indexed: 01/09/2023] Open
Abstract
The HDV ribozyme’s folding pathway is, by far, the most complex folding
pathway elucidated to date for a small ribozyme. It includes 6 different steps
that have been shown to occur before the chemical cleavage. It is likely that
other steps remain to be discovered. One of the most critical of these unknown
steps is the formation of the trans Watson-Crick GU base
pair within loop III. The U23 and G28 nucleotides that
form this base pair are perfectly conserved in all natural variants of the
HDV ribozyme, and therefore are considered as being part of the signature
of HDV-like ribozymes. Both the formation and the transformation of this base
pair have been studied mainly by crystal structure and by molecular dynamic
simulations. In order to obtain physical support for the formation of this
base pair in solution, a set of experiments, including direct mutagenesis,
the site-specific substitution of chemical groups, kinetic studies, chemical
probing and magnesium-induced cleavage, were performed with the specific goal
of characterizing this trans Watson-Crick GU base pair in
an antigenomic HDV ribozyme. Both U23 and G28 can be
substituted for nucleotides that likely preserve some of the H-bond interactions
present before and after the cleavage step. The formation of the more stable trans
Watson-Crick base pair is shown to be a post-cleavage event, while a possibly
weaker trans Watson-Crick/Hoogsteen interaction seems to
form before the cleavage step. The formation of this unusually stable post-cleavage
base pair may act as a driving force on the chemical cleavage by favouring
the formation of a more stable ground state of the product-ribozyme complex.
To our knowledge, this represents the first demonstration of a potential stabilising
role of a post-cleavage conformational switch event in a ribozyme-catalyzed
reaction.
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Affiliation(s)
- Dominique Lévesque
- Département de Biochimie, Faculté
de Médecine et des Sciences de la Santé, Université de
Sherbrooke, Sherbrooke, Québec, Canada
| | - Cédric Reymond
- Département de Biochimie, Faculté
de Médecine et des Sciences de la Santé, Université de
Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Département de Biochimie, Faculté
de Médecine et des Sciences de la Santé, Université de
Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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5
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Silencing of amyloid precursor protein expression using a new engineered delta ribozyme. Int J Alzheimers Dis 2012; 2012:947147. [PMID: 22482079 PMCID: PMC3296272 DOI: 10.1155/2012/947147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 11/01/2011] [Indexed: 11/17/2022] Open
Abstract
Alzheimer's disease (AD) etiological studies suggest that an elevation in amyloid-β peptides (Aβ) level contributes to aggregations of the peptide and subsequent development of the disease. The major constituent of these amyloid peptides is the 1 to 40–42 residue peptide (Aβ40−42) derived from amyloid protein precursor (APP). Most likely, reducing Aβ levels in the brain may block both its aggregation and neurotoxicity and would be beneficial for patients with AD. Among the several possible ways to lower Aβ accumulation in the cells, we have selectively chosen to target the primary step in the Aβ cascade, namely, to reduce APP gene expression. Toward this end, we engineered specific SOFA-HDV ribozymes, a new generation of catalytic RNA tools, to decrease APP mRNA levels. Additionally, we demonstrated that APP-ribozymes are effective at decreasing APP mRNA and protein levels as well as Aβ levels in neuronal cells. Our results could lay the groundwork for a new protective treatment for AD.
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6
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Boodram SN, Johnson PE. Finding the path in an RNA folding landscape. Structure 2011; 18:1550-1. [PMID: 21134633 DOI: 10.1016/j.str.2010.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this issue of Structure, Reymond et al. (2010) combine molecular and computational biology approaches to provide structural details for intermediates in the folding pathway of the hepatitis delta virus ribozyme.
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Affiliation(s)
- Sherry N Boodram
- Department of Chemistry, York University, Toronto, ON M3J1P3, Canada
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7
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Reymond C, Lévesque D, Bisaillon M, Perreault JP. Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme. Structure 2011; 18:1608-16. [PMID: 21134640 DOI: 10.1016/j.str.2010.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 09/13/2010] [Accepted: 09/17/2010] [Indexed: 01/23/2023]
Abstract
Both the role and the interacting partners of an RNA molecule can change depending on its tertiary structure. Consequently, it is important to be able to accurately predict the complete folding pathway of an RNA molecule. The hepatitis delta virus (HDV) ribozyme is a small catalytic RNA with the greatest number of folding intermediates making it the model of choice with which to address this problem. The tertiary structures of the known putative intermediates along the folding pathway of the HDV ribozyme were predicted using the Macromolecular Conformations Symbolic programming (MC-Sym) software. The structures obtained by this method received physical support from Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE). The analysis of these structures elucidated several features of the HDV ribozyme. In addition, this report represents an application for MC-Sym that permits progression one step further toward the computer prediction of an RNA molecule-folding pathway.
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Affiliation(s)
- Cédric Reymond
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec J1H5N4, Canada
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8
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Falconer RJ, Collins BM. Survey of the year 2009: applications of isothermal titration calorimetry. J Mol Recognit 2010; 24:1-16. [DOI: 10.1002/jmr.1073] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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9
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Fiore JL, Kraemer B, Koberling F, Edmann R, Nesbitt DJ. Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop-receptor tertiary interaction. Biochemistry 2010; 48:2550-8. [PMID: 19186984 DOI: 10.1021/bi8019788] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA folding thermodynamics are crucial for structure prediction, which requires characterization of both enthalpic and entropic contributions of tertiary motifs to conformational stability. We explore the temperature dependence of RNA folding due to the ubiquitous GAAA tetraloop-receptor docking interaction, exploiting immobilized and freely diffusing single-molecule fluorescence resonance energy transfer (smFRET) methods. The equilibrium constant for intramolecular docking is obtained as a function of temperature (T = 21-47 degrees C), from which a van't Hoff analysis yields the enthalpy (DeltaH degrees) and entropy (DeltaS degrees) of docking. Tetraloop-receptor docking is significantly exothermic and entropically unfavorable in 1 mM MgCl(2) and 100 mM NaCl, with excellent agreement between immobilized (DeltaH degrees = -17.4 +/- 1.6 kcal/mol, and DeltaS degrees = -56.2 +/- 5.4 cal mol(-1) K(-1)) and freely diffusing (DeltaH degrees = -17.2 +/- 1.6 kcal/mol, and DeltaS degrees = -55.9 +/- 5.2 cal mol(-1) K(-1)) species. Kinetic heterogeneity in the tetraloop-receptor construct is unaffected over the temperature range investigated, indicating a large energy barrier for interconversion between the actively docking and nondocking subpopulations. Formation of the tetraloop-receptor interaction can account for approximately 60% of the DeltaH degrees and DeltaS degrees of P4-P6 domain folding in the Tetrahymena ribozyme, suggesting that it may act as a thermodynamic clamp for the domain. Comparison of the isolated tetraloop-receptor and other tertiary folding thermodynamics supports a theme that enthalpy- versus entropy-driven folding is determined by the number of hydrogen bonding and base stacking interactions.
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Affiliation(s)
- Julie L Fiore
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309-0440, USA
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Reymond C, Beaudoin JD, Perreault JP. Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cell Mol Life Sci 2009; 66:3937-50. [PMID: 19718544 PMCID: PMC2777235 DOI: 10.1007/s00018-009-0124-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 01/12/2023]
Abstract
RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today's knowledge in the field.
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Affiliation(s)
- Cedric Reymond
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
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11
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Feig AL. Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry. Methods Enzymol 2009; 468:409-22. [PMID: 20946780 DOI: 10.1016/s0076-6879(09)68019-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Isothermal Titration Calorimetry (ITC) provides a sensitive and accurate means by which to study the thermodynamics of RNA folding, RNA binding to small molecules, and RNA-protein interactions. The advent of extremely sensitive instrumentation and the increasing availability of ITC in shared facilities have made it increasingly valuable as a tool for RNA biochemistry. As an isothermal measurement, it allows analysis at a defined temperature, distinguishing it from thermal melting approaches (UV melting and differential scanning calorimetry, for instance) that provide thermodynamic information specific to the melting temperature. Residual structures at low temperature in the unfolded state and heat capacity changes lead to potential differences between thermodynamic values measured by ITC and those derived from melting studies. This article describes how ITC can be put to use in the study of RNA biochemistry.
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Affiliation(s)
- Andrew L Feig
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
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