101
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Freisinger E, Sigel RK. From nucleotides to ribozymes—A comparison of their metal ion binding properties. Coord Chem Rev 2007. [DOI: 10.1016/j.ccr.2007.03.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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102
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Zhao L, Xia T. Direct revelation of multiple conformations in RNA by femtosecond dynamics. J Am Chem Soc 2007; 129:4118-9. [PMID: 17373794 DOI: 10.1021/ja068391q] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liang Zhao
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75083-0688, USA
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103
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Davis JH, Foster TR, Tonelli M, Butcher SE. Role of metal ions in the tetraloop-receptor complex as analyzed by NMR. RNA (NEW YORK, N.Y.) 2007; 13:76-86. [PMID: 17119098 PMCID: PMC1705752 DOI: 10.1261/rna.268307] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Metal ions are critical for the proper folding of RNA, and the GAAA tetraloop-receptor is necessary for the optimal folding and function of many RNAs. We have used NMR to investigate the role of metal ions in the structure of the tetraloop-receptor in solution. The NMR data indicate native tertiary structure is formed under a wide range of ionic conditions. The lack of conformational adaptation in response to very different ionic conditions argues against a structural role for divalent ions. Nuclear Overhauser effects to cobalt hexammine and paramagnetic relaxation enhancement induced by manganese ions were used to determine the NMR structures of the tetraloop receptor in association with metal ions, providing the first atomic-level view of these interactions in the solution state. Five manganese and two cobalt hexammine ions could be localized to the RNA surface. The locations of the associated metal ions are similar, but not identical to, those of previously determined crystal structures. The sites of association are in general agreement with nonlinear Poisson-Boltzmann calculations of the electrostatic surface, emphasizing the general importance of diffusely associated ions in RNA tertiary structure.
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Affiliation(s)
- Jared H Davis
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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104
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Abstract
New RNA interaction interfaces are reported for designing RNA modules for directional supramolecular self-assembly. The new interfaces are generated from existing ones by inserting C-loops between the interaction motifs that mediate supramolecular assembly. C-Loops are new modular motifs recently identified in crystal structures that increase the helical twist of RNA helices in which they are inserted and thus reduce the distance between pairs of loop or loop-receptor motifs from 11 to 9 base-stacking layers while maintaining correct orientation for binding to cognate interaction interfaces. Binding specificities of C-loop-containing molecules for cognate molecules that also have inserted C-loops were found to range up to 20-fold. Binding affinities for most C-loop-containing molecules were generally equal or higher than those for the parent molecules lacking C-loops.
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Affiliation(s)
- Kirill A Afonin
- Department of Chemistry and Center for Bimolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43402, USA
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105
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Gumbs OH, Padgett RA, Dayie KT. Fluorescence and solution NMR study of the active site of a 160-kDa group II intron ribozyme. RNA (NEW YORK, N.Y.) 2006; 12:1693-707. [PMID: 16894219 PMCID: PMC1557703 DOI: 10.1261/rna.137006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 06/29/2006] [Indexed: 05/11/2023]
Abstract
We have reconstructed the group II intron from Pylaiella littoralis (PL) into a hydrolytic ribozyme, comprising domains 1-3 (D123) connected in cis plus domain 5 (D5) supplied in trans that efficiently cleaves spliced exon substrates. Using a novel gel-based fluorescence assay and nuclear magnetic resonance (NMR) spectroscopy, we monitored the direct binding of D5 to D123, characterized the kinetics of the spliced exon hydrolysis reaction (which is mechanistically analogous to the reverse of the second catalytic step of splicing), and identified the binding surface of D123 on D5. This PL ribozyme acts as an RNA endonuclease even at low monovalent (100 mM KCl) and divalent ion concentrations (1-10 mM MgCl(2)). This is in contrast to other group II intron ribozyme systems that require high levels of salt, making NMR analysis problematic. D5 binds tightly to D123 with a K(d) of 650 +/- 250 nM, a K(m) of approximately 300 nM, and a K(cat) of 0.02 min(-1) under single turnover conditions. Within the approximately 160-kDa D123-D5 binary complex, site-specific binding to D123 leads to dramatic chemical shift perturbation of residues localized to the tetraloop and internal bulge within D5, suggesting a structural switch model for D5-assisted splicing. This minimal ribozyme thus recapitulates the essential features of the reverse of the second catalytic step and represents a well-behaved system for ongoing high-resolution structural work to complement folding and catalytic functional studies.
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Affiliation(s)
- Orlando H Gumbs
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
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106
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Badorrek CS, Gherghe CM, Weeks KM. Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization. Proc Natl Acad Sci U S A 2006; 103:13640-5. [PMID: 16945907 PMCID: PMC1564256 DOI: 10.1073/pnas.0606156103] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Retroviruses selectively package two copies of their RNA genomes in the context of a large excess of nongenomic RNA. Specific packaging of genomic RNA is achieved, in part, by recognizing RNAs that form a poorly understood dimeric structure at their 5' ends. We identify, quantify the stability of, and use extensive experimental constraints to calculate a 3D model for a tertiary structure domain that mediates specific interactions between RNA genomes in a gamma retrovirus. In an initial interaction, two stem-loop structures from one RNA form highly stringent cross-strand loop-loop base pairs with the same structures on a second genomic RNA. Upon subsequent folding to the final dimer state, these intergenomic RNA interactions convert to a high affinity and compact tertiary structure, stabilized by interdigitated interactions between U-shaped RNA units. This retroviral conformational switch model illustrates how two-step formation of an RNA tertiary structure yields a stringent molecular recognition event at early assembly steps that can be converted to the stable RNA architecture likely packaged into nascent virions.
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Affiliation(s)
| | - Costin M. Gherghe
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
- *To whom correspondence should be addressed. E-mail:
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107
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Abstract
Three-dimensional structure determination of small proteins and oligonucleotides by solution NMR is established. With the development of novel NMR and labeling techniques, structure determination is now feasible for proteins with a molecular mass of up to approximately 100 kDa and RNAs of up to 35 kDa. Beyond these molecular masses special techniques and approaches are required for applying NMR as a multiprobe method for structural investigations of proteins and RNAs. It is the aim of this review to summarize the NMR techniques and approaches available to advance the molecular mass limit of NMR both for proteins (up to 1 MDa) and RNAs (up to 100 kDa). Physical pictures of the novel techniques, their experimental applications, as well as labeling and assignment strategies are discussed and accompanied by future perspectives.
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Affiliation(s)
- Andreas G Tzakos
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom
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108
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Jaeger L, Chworos A. The architectonics of programmable RNA and DNA nanostructures. Curr Opin Struct Biol 2006; 16:531-43. [PMID: 16843653 DOI: 10.1016/j.sbi.2006.07.001] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 06/14/2006] [Accepted: 07/04/2006] [Indexed: 11/30/2022]
Abstract
The past several years have witnessed the emergence of a new world of nucleic-acid-based architectures with highly predictable and programmable self-assembly properties. For almost two decades, DNA has been the primary material for nucleic acid nanoconstruction. More recently, the dramatic increase in RNA structural information led to the development of RNA architectonics, the scientific study of the principles of RNA architecture with the aim of constructing RNA nanostructures of any arbitrary size and shape. The remarkable modularity and the distinct but complementary nature of RNA and DNA nanomaterials are revealed by the various self-assembly strategies that aim to achieve control of the arrangement of matter at a nanoscale level.
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Affiliation(s)
- Luc Jaeger
- Department of Chemistry and Biochemistry, Material Research Laboratory, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
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109
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Wu B, Petersen M, Girard F, Tessari M, Wijmenga SS. Prediction of molecular alignment of nucleic acids in aligned media. JOURNAL OF BIOMOLECULAR NMR 2006; 35:103-15. [PMID: 16718586 DOI: 10.1007/s10858-006-9004-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 03/04/2006] [Accepted: 03/14/2006] [Indexed: 05/09/2023]
Abstract
We demonstrate--using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined--that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request.
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Affiliation(s)
- Bin Wu
- Laboratory of Physical Chemistry-Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6225ED, Nijmegen, The Netherlands
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110
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Downey CD, Fiore JL, Stoddard CD, Hodak JH, Nesbitt DJ, Pardi A. Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker. Biochemistry 2006; 45:3664-73. [PMID: 16533049 PMCID: PMC2735227 DOI: 10.1021/bi0520941] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The GAAA tetraloop-receptor motif is a commonly occurring tertiary interaction in RNA. This motif usually occurs in combination with other tertiary interactions in complex RNA structures. Thus, it is difficult to measure directly the contribution that a single GAAA tetraloop-receptor interaction makes to the folding properties of a RNA. To investigate the kinetics and thermodynamics for the isolated interaction, a GAAA tetraloop domain and receptor domain were connected by a single-stranded A(7) linker. Fluorescence resonance energy transfer (FRET) experiments were used to probe intramolecular docking of the GAAA tetraloop and receptor. Docking was induced using a variety of metal ions, where the charge of the ion was the most important factor in determining the concentration of the ion required to promote docking {[Co(NH(3))(6)(3+)] << [Ca(2+)], [Mg(2+)], [Mn(2+)] << [Na(+)], [K(+)]}. Analysis of metal ion cooperativity yielded Hill coefficients of approximately 2 for Na(+)- or K(+)-dependent docking versus approximately 1 for the divalent ions and Co(NH(3))(6)(3+). Ensemble stopped-flow FRET kinetic measurements yielded an apparent activation energy of 12.7 kcal/mol for GAAA tetraloop-receptor docking. RNA constructs with U(7) and A(14) single-stranded linkers were investigated by single-molecule and ensemble FRET techniques to determine how linker length and composition affect docking. These studies showed that the single-stranded region functions primarily as a flexible tether. Inhibition of docking by oligonucleotides complementary to the linker was also investigated. The influence of flexible versus rigid linkers on GAAA tetraloop-receptor docking is discussed.
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Affiliation(s)
| | | | | | | | | | - Arthur Pardi
- To whom correspondence should be addressed. E-mail: , Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, CO 80309. Phone (303) 492-6263. Fax (303) 492-2439
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111
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Abstract
Fundamental control over supra-molecular self-assembly for organization of matter on the nano-scale is a major objective of nanoscience and nanotechnology. 'RNA tectonics' is the design of modular RNA units, called tectoRNAs, that can be programmed to self-assemble into novel nano- and meso-scopic architectures of desired size and shape. We report the three-dimensional design of tectoRNAs incorporating modular 4-way junction (4WJ) motifs, hairpin loops and their cognate loop-receptors to create extended, programmable interaction interfaces. Specific and directional RNA-RNA interactions at these interfaces enable conformational, topological and orientational control of tectoRNA self-assembly. The interacting motifs are precisely positioned within the helical arms of the 4WJ to program assembly from only one helical stacking conformation of the 4WJ. TectoRNAs programmed to assemble with orientational compensation produce micrometer-scale RNA filaments through supra-molecular equilibrium polymerization. As visualized by transmission electron microscopy, these RNA filaments resemble actin filaments from the protein world. This work emphasizes the potential of RNA as a scaffold for designing and engineering new controllable biomaterials mimicking modern cytoskeletal proteins.
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Affiliation(s)
- Lorena Nasalean
- Department of Chemistry, Bowling Green State UniversityOH 43402, USA
- Center for Biomolecular Sciences, Bowling Green State UniversityOH 43402, USA
| | - Stéphanie Baudrey
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, Material Research Laboratory, University of CaliforniaSanta Barbara, CA 93106-9510, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State UniversityOH 43402, USA
- Center for Biomolecular Sciences, Bowling Green State UniversityOH 43402, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, Material Research Laboratory, University of CaliforniaSanta Barbara, CA 93106-9510, USA
- To whom correspondence should be addressed. Tel: +1 805 893 3628; Fax: +1 805 893 4210;
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