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Stagno JR, Bhandari YR, Conrad CE, Liu Y, Wang YX. Real-time crystallographic studies of the adenine riboswitch using an X-ray free-electron laser. FEBS J 2017; 284:3374-3380. [PMID: 28504865 DOI: 10.1111/febs.14110] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/27/2017] [Accepted: 05/12/2017] [Indexed: 11/26/2022]
Abstract
Structures of the four reaction states of the adenine riboswitch aptamer domain, including a transient intermediate state were solved by serial femtosecond crystallography. The structures not only demonstrate the use of X-ray free-electron lasers for RNA crystallography but have also proven that transient states can be determined in real time by mix-and-inject crystallography. These results illustrate the structural basis for the ligand-induced conformational changes associated with the molecular 'switch'.
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Affiliation(s)
- Jason R Stagno
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yuba R Bhandari
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Chelsie E Conrad
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yu Liu
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
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2
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Abstract
Nucleic acid crystallization buffers contain a large variety of chemicals fitting specific needs. Among them, anions are often solely considered for pH-regulating purposes and as cationic co-salts while their ability to directly bind to nucleic acid structures is rarely taken into account. Here we review current knowledge related to the use of anions in crystallization buffers along with data on their biological prevalence. Chloride ions are frequently identified in crystal structures but display low cytosolic concentrations. Hence, they are thought to be distant from nucleic acid structures in the cell. Sulfate ions are also frequently identified in crystal structures but their localization in the cell remains elusive. Nevertheless, the characterization of the binding properties of these ions is essential for better interpreting the solvent structure in crystals and consequently, avoiding mislabeling of electron densities. Furthermore, understanding the binding properties of these anions should help to get clues related to their potential effects in crowded cellular environments.
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Affiliation(s)
- Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR 9002 CNRS/Université de Strasbourg, 15, rue René Descartes, Strasbourg Cedex, 67084, France
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3
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Batey RT, Kieft JS. Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data. Methods Mol Biol 2016; 1320:219-32. [PMID: 26227046 DOI: 10.1007/978-1-4939-2763-0_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Solving a novel RNA structure by x-ray crystallography requires a means to obtain initial phase estimates. This is a challenge because many of the tools available for solving protein structures are not available for RNA. We have developed a reliable means to use hexammine cations to address this challenge. The process involves engineering the RNA to introduce a reliable hexammine binding site into the structure, then soaking crystals of these RNAs with an iridium (III) or cobalt (III) compound in a "directed soaking" strategy. Diffraction data obtained from these crystals then can be used in SAD or MAD phasing. In many cases, suitable derivatives can be obtained by soaking the hexammine into RNA crystals that have not been engineered. Considerations for using this method and example protocols are presented.
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Affiliation(s)
- Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 596 UCB, Boulder, CO, 80309, USA,
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4
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Abstract
In recent years a wide variety of RNA molecules regulating fundamental cellular processes has been discovered. Therefore, RNA structure determination is experiencing a boost and many more RNA structures are likely to be determined in the years to come. The broader availability of experimentally determined RNA structures implies that molecular replacement (MR) will be used more and more frequently as a method for phasing future crystallographic structures. In this report we describe various aspects relative to RNA structure determination by MR. First, we describe how to select and create MR search models for nucleic acids. Second, we describe how to perform MR searches on RNA using available crystallographic software. Finally, we describe how to refine and interpret the successful MR solutions. These protocols are applicable to determine novel RNA structures as well as to establish structural-functional relationships on existing RNA structures.
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5
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Mir A, Chen J, Robinson K, Lendy E, Goodman J, Neau D, Golden BL. Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction. Biochemistry 2015; 54:6369-81. [PMID: 26398724 PMCID: PMC4710350 DOI: 10.1021/acs.biochem.5b00824] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer. Metal ions have been implicated in the chemical mechanism, but no interactions between divalent metal ions and the cleavage site have been observed crystallographically. To better understand how this ribozyme functions, we have solved crystal structures of wild-type and G12A mutant ribozymes. We observe a pH-dependent conformational change centered around G12, consistent with this nucleotide becoming deprotonated. Crystallographic and kinetic analysis of the G12A mutant reveals a Zn(2+) specificity switch suggesting a direct interaction between a divalent metal ion and the purine at position 12. The metal ion specificity switch and the pH-rate profile of the G12A mutant suggest that the minor imino tautomer of A12 serves as the general base in the mutant ribozyme. We propose a model in which the hammerhead ribozyme rearranges prior to the cleavage reaction, positioning two divalent metal ions in the process. The first metal ion, positioned near G12, becomes directly coordinated to the O6 keto oxygen, to lower the pKa of the general base and organize the active site. The second metal ion, positioned near G10.1, bridges the N7 of G10.1 and the scissile phosphate and may participate directly in the cleavage reaction.
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Affiliation(s)
- Aamir Mir
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ji Chen
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kyle Robinson
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Emma Lendy
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jaclyn Goodman
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - David Neau
- Department of Chemistry and Chemical Biology, Cornell University, Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Barbara L. Golden
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States,Corresponding Author: Telephone: (765) 496-6165;
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6
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Mooers BHM. Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing. Methods Mol Biol 2015; 1240:191-216. [PMID: 25352146 DOI: 10.1007/978-1-4939-1896-6_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Head-to-head fusions of two identical double-stranded fragments of RNA can be designed to self-assemble from a single RNA species and form a double-stranded helix with a twofold rotation axis relating the two strands. These symmetrical RNA molecules are more likely to crystallize without end-on-end statistical packing disorder because the two halves of the molecule are identical. This approach can be used to study many fragments of double-stranded RNA or many isolated helical domains from large single-stranded RNAs that may not yet be amenable to high-resolution studies by crystallography or NMR. We used fusion RNAs to study one (the U-helix) of three functional domains formed when guide RNA binds to its cognate pre-edited mRNA from the trypanosome RNA editing system. The U-helix forms when the 3' oligo(U) tail of the guide RNA (gRNA) binds to the purine-rich, pre-edited mRNA upstream from the current RNA editing site. Fusion RNAs 16-and 32-base pairs in length formed crystals that gave diffraction to 1.37 and 1.05 Å respectively. We provide the composition of a fusion RNA crystallization screen and describe the X-ray data collection, structure determination, and refinement of the crystal structures of fusion RNAs.
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Affiliation(s)
- Blaine H M Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 975 NE 10th St., Stanton L. Young Biomedical Research Center Rm. 466, Oklahoma City, OK, 73104-5419, USA,
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7
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Veeraraghavan N, Ganguly A, Chen JH, Bevilacqua PC, Hammes-Schiffer S, Golden BL. Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry 2011; 50:2672-82. [PMID: 21348498 PMCID: PMC3068245 DOI: 10.1021/bi2000164] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The hepatitis delta virus (HDV) ribozyme uses both metal ion and nucleobase catalysis in its cleavage mechanism. A reverse G·U wobble was observed in a recent crystal structure of the precleaved state. This unusual base pair positions a Mg(2+) ion to participate in catalysis. Herein, we used molecular dynamics (MD) and X-ray crystallography to characterize the conformation and metal binding characteristics of this base pair in product and precleaved forms. Beginning with a crystal structure of the product form, we observed formation of the reverse G·U wobble during MD trajectories. We also demonstrated that this base pair is compatible with the diffraction data for the product-bound state. During MD trajectories of the product form, Na(+) ions interacted with the reverse G·U wobble in the RNA active site, and a Mg(2+) ion, introduced in certain trajectories, remained bound at this site. Beginning with a crystal structure of the precleaved form, the reverse G·U wobble with bound Mg(2+) remained intact during MD simulations. When we removed Mg(2+) from the starting precleaved structure, Na(+) ions interacted with the reverse G·U wobble. In support of the computational results, we observed competition between Na(+) and Mg(2+) in the precleaved ribozyme crystallographically. Nonlinear Poisson-Boltzmann calculations revealed a negatively charged patch near the reverse G·U wobble. This anionic pocket likely serves to bind metal ions and to help shift the pK(a) of the catalytic nucleobase, C75. Thus, the reverse G·U wobble motif serves to organize two catalytic elements, a metal ion and catalytic nucleobase, within the active site of the HDV ribozyme.
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Affiliation(s)
- Narayanan Veeraraghavan
- Huck Institutes of Life Sciences, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Abir Ganguly
- Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jui-Hui Chen
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Philip C. Bevilacqua
- Huck Institutes of Life Sciences, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
| | - Barbara L. Golden
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
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8
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Hagihara M, Yoneda K, Yabuuchi H, Okuno Y, Nakatani K. A reverse transcriptase stop assay revealed diverse quadruplex formations in UTRs in mRNA. Bioorg Med Chem Lett 2010; 20:2350-3. [PMID: 20206514 DOI: 10.1016/j.bmcl.2010.01.158] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/21/2010] [Accepted: 01/25/2010] [Indexed: 11/19/2022]
Abstract
Here, we developed a reverse transcriptase based method (RTase stop assay) to characterize quadruplex formations in guanine-rich RNAs with high sensitivity and specificity. By using the RTase stop assay, we also revealed a plausible structural polymorphism in biologically important RNAs. The RTase stop assay would provide helpful insight into RNA quadruplex structures and functions, together with other analytical methods, including various footprinting techniques.
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Affiliation(s)
- Masaki Hagihara
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan
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9
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Gong B, Chen JH, Yajima R, Chen Y, Chase E, Chadalavada DM, Golden BL, Carey PR, Bevilacqua PC. Raman crystallography of RNA. Methods 2009; 49:101-11. [PMID: 19409996 PMCID: PMC2753759 DOI: 10.1016/j.ymeth.2009.04.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 04/21/2009] [Accepted: 04/23/2009] [Indexed: 01/30/2023] Open
Abstract
Raman crystallography is the application of Raman spectroscopy to single crystals. This technique has been applied to a variety of protein molecules where it has provided unique information about biopolymer folding, substrate binding, and catalysis. Here, we describe the application of Raman crystallography to functional RNA molecules. RNA represents unique opportunities and challenges for Raman crystallography. One issue that confounds studies of RNA is its tendency to adopt multiple non-functional folds. Raman crystallography has the advantage that it isolates a single state of the RNA within the crystal and can evaluate its fold, metal ion binding properties (ligand identity, stoichiometry, and affinity), proton binding properties (identity, stoichiometry, and affinity), and catalytic potential. In particular, base-specific stretches can be identified and then associated with the binding of metal ions and protons. Because measurements are carried out in the hanging drop at ambient, rather than cryo, conditions and because RNA crystals tend to be approximately 70% solvent, RNA dynamics and conformational changes become experimentally accessible. This review focuses on experimental setup and procedures, acquisition and interpretation of Raman data, and determination of physicochemical properties of the RNA. Raman crystallographic and solution biochemical experiments on the HDV RNA enzyme are summarized and found to be in excellent agreement. Remarkably, characterization of the crystalline state has proven to help rather than hinder functional characterization of functional RNA, most likely because the tendency of RNA to fold heterogeneously is limited in a crystalline environment. Future applications of Raman crystallography to RNA are briefly discussed.
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Affiliation(s)
- Bo Gong
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Jui-Hui Chen
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Rieko Yajima
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Yuanyuan Chen
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Elaine Chase
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Durga M. Chadalavada
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Barbara L. Golden
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Paul R. Carey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Philip C. Bevilacqua
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
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10
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Spitale RC, Wedekind JE. Exploring ribozyme conformational changes with X-ray crystallography. Methods 2009; 49:87-100. [PMID: 19559088 PMCID: PMC2782588 DOI: 10.1016/j.ymeth.2009.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 05/28/2009] [Accepted: 06/05/2009] [Indexed: 11/18/2022] Open
Abstract
Relating three-dimensional fold to function is a central challenge in RNA structural biology. Toward this goal, X-ray crystallography has long been considered the "gold standard" for structure determinations at atomic resolution, although NMR spectroscopy has become a powerhouse in this arena as well. In the area of dynamics, NMR remains the dominant technique to probe the magnitude and timescales of molecular motion. Although the latter area remains largely unassailable by conventional crystallographic methods, inroads have been made on proteins using Laue radiation on timescales of ms to ns. Proposed 'fourth generation' radiation sources, such as free-electron X-ray lasers, promise ps- to fs-timescale resolution, and credible evidence is emerging that supports the feasibility of single molecule imaging. At present however, the preponderance of RNA structural information has been derived from timescale and motion insensitive crystallographic techniques. Importantly, developments in computing, automation and high-flux synchrotron sources have propelled the rapidity of 'conventional' RNA crystal structure determinations to timeframes of hours once a suitable set of phases is obtained. With a sufficient number of crystal structures, it is possible to create a structural ensemble that can provide insight into global and local molecular motion characteristics that are relevant to biological function. Here we describe techniques to explore conformational changes in the hairpin ribozyme, a representative non-protein-coding RNA catalyst. The approaches discussed include: (i) construct choice and design using prior knowledge to improve X-ray diffraction; (ii) recognition of long-range conformational changes and (iii) use of single-base or single-atom changes to create ensembles. The methods are broadly applicable to other RNA systems.
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Affiliation(s)
- Robert C. Spitale
- Department of Chemistry, Biological Chemistry Cluster, RC Box 270216, Rochester, NY 14627-0216
| | - Joseph E. Wedekind
- Department of Biochemistry & Biophysics, 601 Elmwood Avenue Box 712, Rochester New York 14642
- Department of Chemistry, Biological Chemistry Cluster, RC Box 270216, Rochester, NY 14627-0216
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11
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Crystallographic studies of DNA and RNA. Methods 2009; 47:168-76. [DOI: 10.1016/j.ymeth.2008.09.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 09/10/2008] [Indexed: 11/23/2022] Open
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12
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Edwards AL, Garst AD, Batey RT. Determining structures of RNA aptamers and riboswitches by X-ray crystallography. Methods Mol Biol 2009; 535:135-63. [PMID: 19377976 DOI: 10.1007/978-1-59745-557-2_9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structural biology plays a central role in gaining a full understanding of the myriad roles of RNA in biology. In recent years, innovative approaches in RNA purification and crystallographic methods have lead to the visualization of an increasing number of unique structures, providing new insights into its function at the atomic level. This article presents general protocols which have streamlined the process of obtaining a homogeneous sample of properly folded and active RNA in high concentrations that crystallizes well in the presence of a suitable heavy-atom for phasing. Of particular importance are approaches toward RNA crystallography that include exploring "construct space" as opposed to "condition space". Moreover, development of a highly flexible method for experimentally phasing RNA crystals may open the door to a relatively simple means of solving these structures.
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Affiliation(s)
- Andrea L Edwards
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
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13
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Key labeling technologies to tackle sizeable problems in RNA structural biology. Int J Mol Sci 2008; 9:1214-1240. [PMID: 19325801 PMCID: PMC2635727 DOI: 10.3390/ijms9071214] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 06/06/2008] [Accepted: 07/14/2008] [Indexed: 01/09/2023] Open
Abstract
The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is vital for the proper functioning of RNAs. Consequently, RNA structure and dynamics necessarily determine their biological function. In the post-genomic era, it is clear that RNAs comprise a larger proportion (>50%) of the transcribed genome compared to proteins (< or =2%). Yet the determination of the 3D structures of RNAs lags considerably behind those of proteins and to date there are even fewer investigations of dynamics in RNAs compared to proteins. Site specific incorporation of various structural and dynamic probes into nucleic acids would likely transform RNA structural biology. Therefore, various methods for introducing probes for structural, functional, and biotechnological applications are critically assessed here. These probes include stable isotopes such as (2)H, (13)C, (15)N, and (19)F. Incorporation of these probes using improved RNA ligation strategies promises to change the landscape of structural biology of supramacromolecules probed by biophysical tools such as nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and Raman spectroscopy. Finally, some of the structural and dynamic problems that can be addressed using these technological advances are outlined.
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14
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Tijerina P, Mohr S, Russell R. DMS footprinting of structured RNAs and RNA-protein complexes. Nat Protoc 2008; 2:2608-23. [PMID: 17948004 DOI: 10.1038/nprot.2007.380] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a protocol in which dimethyl sulfate (DMS) modification of the base-pairing faces of unpaired adenosine and cytidine nucleotides is used for structural analysis of RNAs and RNA-protein complexes (RNPs). The protocol is optimized for RNAs of small to moderate size (< or = 500 nt). The RNA or RNP is first exposed to DMS under conditions that promote formation of the folded structure or complex, as well as 'control' conditions that do not allow folding or complex formation. The positions and extents of modification are then determined by primer extension, polyacrylamide gel electrophoresis and quantitative analysis. From changes in the extent of modification upon folding or protein binding (appearance of a 'footprint'), it is possible to detect local changes in the secondary and tertiary structure of RNA, as well as the formation of RNA-protein contacts. This protocol takes 1.5-3 d to complete, depending on the type of analysis used.
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Affiliation(s)
- Pilar Tijerina
- Department of Chemistry and Biochemistry and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
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15
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Keel AY, Rambo RP, Batey RT, Kieft JS. A general strategy to solve the phase problem in RNA crystallography. Structure 2007; 15:761-72. [PMID: 17637337 PMCID: PMC1995091 DOI: 10.1016/j.str.2007.06.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 06/12/2007] [Accepted: 06/15/2007] [Indexed: 10/23/2022]
Abstract
X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding heavy-atom derivatives to obtain high-quality experimental phase information. Existing techniques have drawbacks, limiting the rate at which important new structures are solved. To address this, we have developed a reliable means to localize heavy atoms specifically to virtually any RNA. By solving the crystal structures of thirteen variants of the G*U wobble pair cation binding motif, we have identified a version that when inserted into an RNA helix introduces a high-occupancy cation binding site suitable for phasing. This "directed soaking" strategy can be integrated fully into existing RNA crystallography methods, potentially increasing the rate at which important structures are solved and facilitating routine solving of structures using Cu-Kalpha radiation. This method already has been used to solve several crystal structures.
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Affiliation(s)
- Amanda Y. Keel
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO, 80045
| | - Robert P. Rambo
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720
| | - Robert T. Batey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309-0215
| | - Jeffrey S. Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO, 80045
- *to whom correspondence should be addressed: , Phone: 303-724-3257, Fax: 303-724-3215
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