51
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Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies. J Mol Model 2017; 23:311. [DOI: 10.1007/s00894-017-3480-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/19/2017] [Indexed: 11/26/2022]
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52
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Chakraborty S, Krishnan Y. A structural map of oncomiR-1 at single-nucleotide resolution. Nucleic Acids Res 2017; 45:9694-9705. [PMID: 28934477 PMCID: PMC5766152 DOI: 10.1093/nar/gkx613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/05/2017] [Indexed: 12/20/2022] Open
Abstract
The miR-17-92a cluster, also known as 'oncomiR-1', is an RNA transcript that plays a pivotal regulatory role in cellular processes, including the cell cycle, proliferation and apoptosis. Its dysregulation underlies the development of several cancers. Oncomir-1 comprises six constituent miRNAs, each processed with different efficiencies as a function of both developmental time and tissue type. The structural mechanisms that regulate such differential processing are unknown, and this has impeded our understanding of the dysregulation of oncomiR-1 in pathophysiology. By probing the sensitivity of each nucleotide in oncomiR-1 to reactive small molecules, we present a secondary structural map of this RNA at single-nucleotide resolution. The secondary structure and solvent accessible regions of oncomiR-1 reveal that most of its primary microRNA domains are suboptimal substrates for Drosha-DGCR8, and therefore resistant to microprocessing. The structure indicates that the binding of trans-acting factors is required to remodel the tertiary organization and unmask cryptic primary microRNA domains to facilitate their processing into pre-microRNAs.
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Affiliation(s)
- Saikat Chakraborty
- National Centre for Biological Sciences-TIFR, Bangalore, Karnataka 560065, India
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.,Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL 60637, USA
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53
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Mukherjee D, Bhattacharyya D. Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation. J Mol Model 2017; 23:300. [DOI: 10.1007/s00894-017-3470-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
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54
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Dawn of the in vivo RNA structurome and interactome. Biochem Soc Trans 2017; 44:1395-1410. [PMID: 27911722 DOI: 10.1042/bst20160075] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/19/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
Abstract
RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure-function relationship on a transcriptomic scale. In this review, molecular tools and NGS methods used for RNA structure probing are presented, novel insights uncovered by RNA structurome and interactome studies are highlighted, and perspectives on current challenges and potential future directions are discussed. A more complete understanding of the RNA structures and interactions in vivo will help illuminate the novel roles of RNA in gene regulation, development, and diseases.
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55
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Urbanek MO, Krzyzosiak WJ. Discriminating RNA variants with single-molecule allele-specific FISH. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:230-241. [DOI: 10.1016/j.mrrev.2016.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
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56
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Glouzon JPS, Perreault JP, Wang S. The super-n-motifs model: a novel alignment-free approach for representing and comparing RNA secondary structures. Bioinformatics 2017; 33:1169-1178. [PMID: 28088762 DOI: 10.1093/bioinformatics/btw773] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 12/13/2022] Open
Abstract
Motivation Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations. The super-n-motifs model computes a vector representation of secondary structures as linear combinations of these motifs. Results We demonstrate the accuracy of our model for comparison of secondary structures from linear and circular RNA while also considering pseudoknot and G4 motifs. We show that the super-n-motifs representation effectively captures the most important structural features of secondary structures, as compared to other representations such as ordered tree, arc-annotated and string representations. Finally, we demonstrate the time efficiency of our model, which is alignment free and capable of performing large-scale comparisons of 10 000 secondary structures with an efficiency up to 4 orders of magnitude faster than existing approaches. Availability and Implementation The super-n-motifs model was implemented in C ++. Source code and Linux binary are freely available at http://jpsglouzon.github.io/supernmotifs/ . Contact Shengrui.Wang@Usherbrooke.ca. Supplementary information Supplementary data are available at Bioinformatics o nline.
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Affiliation(s)
- Jean-Pierre Séhi Glouzon
- Department of Computer Science, Faculty of Science, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada.,RNA Group, Department of Biochemistry, Faculty of Medicine and Health Sciences, Applied Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Jean-Pierre Perreault
- RNA Group, Department of Biochemistry, Faculty of Medicine and Health Sciences, Applied Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Shengrui Wang
- Department of Computer Science, Faculty of Science, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
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57
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D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P. Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops. RNA (NEW YORK, N.Y.) 2017; 23:259-269. [PMID: 27999116 PMCID: PMC5311481 DOI: 10.1261/rna.059097.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023]
Abstract
When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its "natural" fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion may occur for loops with UNCG sequences, for instance within tRNA anticodon loops. Hence, we show that some structured tetranucleotide sequences starting with G or U can adopt either of these folds. The underlying structural basis that defines these two fold types is the mutually exclusive stacking of a backbone oxygen on either the first (in GNRA) or the last nucleobase (in UNCG), generating an oxygen-π contact. We thereby propose to refrain from using sequences to distinguish between loop conformations. Instead, we suggest using descriptors such as U-turn (for "GNRA-type" folds) and a newly described Z-turn (for "UNCG-type" folds). Because tetraloops adopt for the largest part only two (inter)convertible turns, we are better able to interpret from a structural perspective loop interchangeability occurring in ribosomes and viral RNA. In this respect, we propose a general view on the inclination for a given sequence to adopt (or not) a specific fold. We also suggest how long-noncoding RNAs may adopt discrete but transient structures, which are therefore hard to predict.
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Affiliation(s)
- Luigi D'Ascenzo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Filip Leonarski
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Quentin Vicens
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Pascal Auffinger
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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58
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Nik Kamarudin NAA, Mohammed NA, Mustaffa KMF. Aptamer Technology: Adjunct Therapy for Malaria. Biomedicines 2017; 5:biomedicines5010001. [PMID: 28536344 PMCID: PMC5423489 DOI: 10.3390/biomedicines5010001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/08/2016] [Accepted: 12/16/2016] [Indexed: 02/07/2023] Open
Abstract
Malaria is a life-threatening parasitic infection occurring in the endemic areas, primarily in children under the age of five, pregnant women, and patients with human immunodeficiency virus and acquired immunodeficiency syndrome (HIV)/(AIDS) as well as non-immune individuals. The cytoadherence of infected erythrocytes (IEs) to the host endothelial surface receptor is a known factor that contributes to the increased prevalence of severe malaria cases due to the accumulation of IEs, mainly in the brain and other vital organs. Therefore, further study is needed to discover a new potential anti-adhesive drug to treat severe malaria thus reducing its mortality rate. In this review, we discuss how the aptamer technology could be applied in the development of a new adjunct therapy for current malaria treatment.
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Affiliation(s)
- Nik Abdul Aziz Nik Kamarudin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, 16150 Kelantan, Malaysia.
| | - Nurul Adila Mohammed
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, 16150 Kelantan, Malaysia.
| | - Khairul Mohd Fadzli Mustaffa
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, 16150 Kelantan, Malaysia.
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59
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Maiti S, Bhattacharyya D. Stacking interactions involving non-Watson–Crick basepairs: dispersion corrected density functional theory studies. Phys Chem Chem Phys 2017; 19:28718-28730. [DOI: 10.1039/c7cp04904h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking interactions between a non Watson–Crick G:A S:HT basepair and C:G basepair is predicted in terms of roll, twist and slide basepair step parameters using DFT-D augmented with coarse-grain energy penalty for sugar–phosphate backbone.
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Affiliation(s)
- Satyabrata Maiti
- Computational Science Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
- Homi Bhaba National Institute
| | - Dhananjay Bhattacharyya
- Computational Science Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
- Homi Bhaba National Institute
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60
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Reiss CW, Xiong Y, Strobel SA. Structural Basis for Ligand Binding to the Guanidine-I Riboswitch. Structure 2016; 25:195-202. [PMID: 28017522 DOI: 10.1016/j.str.2016.11.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/11/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022]
Abstract
The guanidine-I riboswitch is a conserved RNA element with approximately 2,000 known examples across four phyla of bacteria. It exists upstream of nitrogen metabolism and multidrug resistance transporter genes and alters expression through the specific recognition of a free guanidinium cation. Here we report the structure of a guanidine riboswitch aptamer from Sulfobacillus acidophilus at 2.7 Å resolution. Helices P1, P1a, P1b, and P2 form a coaxial stack that acts as a scaffold for ligand binding. A previously unidentified P3 helix docks into P1a to form the guanidinium binding pocket, which is completely enclosed. Every functional group of the ligand is recognized through hydrogen bonding to guanine bases and phosphate oxygens. Guanidinium binding is further stabilized through cation-π interactions with guanine bases. This allows the riboswitch to recognize guanidinium while excluding other bacterial metabolites with a guanidino group, including the amino acid arginine.
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Affiliation(s)
- Caroline W Reiss
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yong Xiong
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Scott A Strobel
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
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61
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Choi SJ, Ban C. Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition. Sci Rep 2016; 6:34998. [PMID: 27725738 PMCID: PMC5057103 DOI: 10.1038/srep34998] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/22/2016] [Indexed: 02/07/2023] Open
Abstract
Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base-phosphate zipper, and DNA G·G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s.
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Affiliation(s)
- Sung-Jin Choi
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
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62
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Secondary structure model of the naked segment 7 influenza A virus genomic RNA. Biochem J 2016; 473:4327-4348. [PMID: 27694388 DOI: 10.1042/bcj20160651] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/25/2016] [Accepted: 09/30/2016] [Indexed: 11/17/2022]
Abstract
The influenza A virus (IAV) genome comprises eight negative-sense viral (v)RNA segments. The seventh segment of the genome encodes two essential viral proteins and is specifically packaged alongside the other seven vRNAs. To gain insights into the possible roles of RNA structure both within and without virions, a secondary structure model of a naked (protein-free) segment 7 vRNA (vRNA7) has been determined using chemical mapping and thermodynamic energy minimization. The proposed structure model was validated using microarray mapping, RNase H cleavage and comparative sequence analysis. Additionally, the detailed structures of three vRNA7 fragment constructs - comprising independently folded subdomains - were determined. Much of the proposed vRNA7 structure is preserved between IAV strains, suggesting their importance in the influenza replication cycle. Possible structure rearrangements, which allow or preclude long-range RNA interactions, are also proposed.
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63
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Parlea L, Bindewald E, Sharan R, Bartlett N, Moriarty D, Oliver J, Afonin KA, Shapiro BA. Ring Catalog: A resource for designing self-assembling RNA nanostructures. Methods 2016; 103:128-37. [PMID: 27090005 PMCID: PMC6319925 DOI: 10.1016/j.ymeth.2016.04.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/14/2016] [Accepted: 04/14/2016] [Indexed: 01/02/2023] Open
Abstract
Designing self-assembling RNA ring structures based on known 3D structural elements connected via linker helices is a challenging task due to the immense number of motif combinations, many of which do not lead to ring-closure. We describe an in silico solution to this design problem by combinatorial assembly of RNA 3-way junctions, bulges, and kissing loops, and tabulating the cases that lead to ring formation. The solutions found are made available in the form of a web-accessible Ring Catalog. As an example of a potential use of this resource, we chose a predicted RNA square structure consisting of five RNA strands and demonstrate experimentally that the self-assembly of those five strands leads to the formation of a square-like complex. This is a demonstration of a novel "design by catalog" approach to RNA nano-structure generation. The URL https://rnajunction.ncifcrf.gov/ringdb can be used to access the resource.
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Affiliation(s)
- Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Rishabh Sharan
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Nathan Bartlett
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Daniel Moriarty
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Jerome Oliver
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Bruce A Shapiro
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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64
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Bermejo GA, Clore GM, Schwieters CD. Improving NMR Structures of RNA. Structure 2016; 24:806-815. [PMID: 27066747 DOI: 10.1016/j.str.2016.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 01/27/2023]
Abstract
Here, we show that modern solution nuclear magnetic resonance (NMR) structures of RNA exhibit more steric clashes and conformational ambiguities than their crystallographic X-ray counterparts. To tackle these issues, we developed RNA-ff1, a new force field for structure calculation with Xplor-NIH. Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force field and the original structures associated with the experimental data. In addition, with smaller base-pair step rises in helical stems, RNA-ff1 structures enjoy more favorable base stacking. Finally, structural accuracy improves in the majority of cases, as supported by complete residual dipolar coupling cross-validation. Thus, the reported advances show great promise in bridging the quality gap that separates NMR and X-ray structures of RNA.
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Affiliation(s)
- Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA.
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65
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Gelinas AD, Davies DR, Janjic N. Embracing proteins: structural themes in aptamer-protein complexes. Curr Opin Struct Biol 2016; 36:122-32. [PMID: 26919170 DOI: 10.1016/j.sbi.2016.01.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 01/17/2023]
Abstract
Understanding the structural rules that govern specific, high-affinity binding characteristic of aptamer-protein interactions is important in view of the increasing use of aptamers across many applications. From the modest number of 16 aptamer-protein structures currently available, trends are emerging. The flexible phosphodiester backbone allows folding into precise three-dimensional structures using known nucleic acid motifs as scaffolds that orient specific functional groups for target recognition. Still, completely novel motifs essential for structure and function are found in modified aptamers with diversity-enhancing side chains. Aptamers and antibodies, two classes of macromolecules used as affinity reagents with entirely different backbones and composition, recognize protein epitopes of similar size and with comparably high shape complementarity.
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Affiliation(s)
- Amy D Gelinas
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, United States
| | - Douglas R Davies
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, United States.
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66
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Crucial steps to life: From chemical reactions to code using agents. Biosystems 2016; 140:49-57. [DOI: 10.1016/j.biosystems.2015.12.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/05/2015] [Accepted: 12/07/2015] [Indexed: 01/21/2023]
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67
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RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure. PLoS One 2015; 10:e0139900. [PMID: 26509713 PMCID: PMC4624896 DOI: 10.1371/journal.pone.0139900] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 08/17/2015] [Indexed: 01/09/2023] Open
Abstract
Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D module prediction tools and apply them on a 13-way vertebrate sequence-based alignment. We find that RNA 3D modules predicted by metaRNAmodules and JAR3D are significantly enriched in the screened windows compared to their shuffled counterparts. The initially estimated FDR of 47.0% is lowered to below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence.
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68
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Rybarczyk A, Szostak N, Antczak M, Zok T, Popenda M, Adamiak R, Blazewicz J, Szachniuk M. New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinformatics 2015; 16:276. [PMID: 26329823 PMCID: PMC4557229 DOI: 10.1186/s12859-015-0718-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 08/24/2015] [Indexed: 11/19/2022] Open
Abstract
Background The function of RNA is strongly dependent on its structure, so an appropriate recognition of this structure, on every level of organization, is of great importance. One particular concern is the assessment of base-base interactions, described as the secondary structure, the knowledge of which greatly facilitates an interpretation of RNA function and allows for structure analysis on the tertiary level. The RNA secondary structure can be predicted from a sequence using in silico methods often adjusted with experimental data, or assessed from 3D structure atom coordinates. Computational approaches typically consider only canonical, Watson-Crick and wobble base pairs. Handling of non-canonical interactions, important for a full description of RNA structure, is still very difficult. Results We introduce our novel approach to assessing an extended RNA secondary structure, which characterizes both canonical and non-canonical base pairs, along with their type classification. It is based on predicting the RNA 3D structure from a user-provided sequence or a secondary structure that only describes canonical base pairs, and then deriving the extended secondary structure from atom coordinates. In our example implementation, this was achieved by integrating the functionality of two fully automated, high fidelity methods in a computational pipeline: RNAComposer for the 3D RNA structure prediction and RNApdbee for base-pair annotation. Conclusions The presented methodology ties together existing applications for RNA 3D structure prediction and base-pair annotation. The example performance, applying RNAComposer and RNApdbee, reveals better accuracy in non-canonical base pair assessment than the compared methods that directly predict RNA secondary structure. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0718-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnieszka Rybarczyk
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Natalia Szostak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
| | - Maciej Antczak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,European Center for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
| | - Ryszard Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,European Center for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Marta Szachniuk
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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Zahran M, Sevim Bayrak C, Elmetwaly S, Schlick T. RAG-3D: a search tool for RNA 3D substructures. Nucleic Acids Res 2015; 43:9474-88. [PMID: 26304547 PMCID: PMC4627073 DOI: 10.1093/nar/gkv823] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/03/2015] [Indexed: 01/23/2023] Open
Abstract
To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.
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Affiliation(s)
- Mai Zahran
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, NY 11201, USA
| | | | - Shereef Elmetwaly
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, NY 10003, USA Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
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70
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Čech P, Hoksza D, Svozil D. MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinformatics 2015; 16:253. [PMID: 26264783 PMCID: PMC4531852 DOI: 10.1186/s12859-015-0696-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/05/2015] [Indexed: 12/03/2022] Open
Abstract
Background Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. Results In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. Conclusion To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
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Affiliation(s)
- Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic
| | - David Hoksza
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic. .,Department of Software Engineering, Faculty of Mathematics and Physics, Charles University in Prague, Malostranské nám. 25, CZ-118 00, Prague, Czech Republic.
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic.
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71
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Hoksza D, Svozil D. Multiple 3D RNA Structure Superposition Using Neighbor Joining. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:520-530. [PMID: 26357263 DOI: 10.1109/tcbb.2014.2351810] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER-a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.
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Giambaşu GM, York DM, Case DA. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. RNA (NEW YORK, N.Y.) 2015; 21:963-74. [PMID: 25805858 PMCID: PMC4408802 DOI: 10.1261/rna.047357.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/17/2015] [Indexed: 05/16/2023]
Abstract
RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements.
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Affiliation(s)
- George M Giambaşu
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Darrin M York
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - David A Case
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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73
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Mondal M, Mukherjee S, Halder S, Bhattacharyya D. Stacking geometry for non-canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion-corrected DFT-D study. Biopolymers 2015; 103:328-38. [DOI: 10.1002/bip.22616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/01/2015] [Accepted: 01/08/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Manas Mondal
- Computational Science Division; Saha Institute of Nuclear Physics; 1/AF Bidhannagar Kolkata 700064 India
| | - Sanchita Mukherjee
- Computational Science Division; Saha Institute of Nuclear Physics; 1/AF Bidhannagar Kolkata 700064 India
| | - Sukanya Halder
- Computational Science Division; Saha Institute of Nuclear Physics; 1/AF Bidhannagar Kolkata 700064 India
| | - Dhananjay Bhattacharyya
- Computational Science Division; Saha Institute of Nuclear Physics; 1/AF Bidhannagar Kolkata 700064 India
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Zhong C, Zhang S. RNAMotifScanX: a graph alignment approach for RNA structural motif identification. RNA (NEW YORK, N.Y.) 2015; 21:333-346. [PMID: 25595715 PMCID: PMC4338331 DOI: 10.1261/rna.044891.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 11/28/2014] [Indexed: 06/04/2023]
Abstract
RNA structural motifs are recurrent three-dimensional (3D) components found in the RNA architecture. These RNA structural motifs play important structural or functional roles and usually exhibit highly conserved 3D geometries and base-interaction patterns. Analysis of the RNA 3D structures and elucidation of their molecular functions heavily rely on efficient and accurate identification of these motifs. However, efficient RNA structural motif search tools are lacking due to the high complexity of these motifs. In this work, we present RNAMotifScanX, a motif search tool based on a base-interaction graph alignment algorithm. This novel algorithm enables automatic identification of both partially and fully matched motif instances. RNAMotifScanX considers noncanonical base-pairing interactions, base-stacking interactions, and sequence conservation of the motifs, which leads to significantly improved sensitivity and specificity as compared with other state-of-the-art search tools. RNAMotifScanX also adopts a carefully designed branch-and-bound technique, which enables ultra-fast search of large kink-turn motifs against a 23S rRNA. The software package RNAMotifScanX is implemented using GNU C++, and is freely available from http://genome.ucf.edu/RNAMotifScanX.
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Affiliation(s)
- Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida 32816, USA
| | - Shaojie Zhang
- Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida 32816, USA
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Bowater RP, Cobb AM, Pivonkova H, Havran L, Fojta M. Biophysical and electrochemical studies of protein–nucleic acid interactions. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-014-1405-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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76
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Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations. Biophys J 2014; 106:447-58. [PMID: 24461020 DOI: 10.1016/j.bpj.2013.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/23/2013] [Accepted: 12/03/2013] [Indexed: 01/31/2023] Open
Abstract
RNA junctions are common secondary structural elements present in a wide range of RNA species. They play crucial roles in directing the overall folding of RNA molecules as well as in a variety of biological functions. In particular, there has been great interest in the dynamics of RNA junctions, including conformational pathways of fully base-paired 4-way (4H) RNA junctions. In such constructs, all nucleotides participate in one of the four double-stranded stem regions, with no connecting loops. Dynamical aspects of these 4H RNAs are interesting because frequent interchanges between parallel and antiparallel conformations are thought to occur without binding of other factors. Gel electrophoresis and single-molecule fluorescence resonance energy transfer experiments have suggested two possible pathways: one involves a helical rearrangement via disruption of coaxial stacking, and the other occurs by a rotation between the helical axes of coaxially stacked conformers. Employing molecular dynamics simulations, we explore this conformational variability in a 4H junction derived from domain 3 of the foot-and-mouth disease virus internal ribosome entry site (IRES); this junction contains highly conserved motifs for RNA-RNA and RNA-protein interactions, important for IRES activity. Our simulations capture transitions of the 4H junction between parallel and antiparallel conformations. The interconversion is virtually barrier-free and occurs via a rotation between the axes of coaxially stacked helices with a transient perpendicular intermediate. We characterize this transition, with various interhelical orientations, by pseudodihedral angle and interhelical distance measures. The high flexibility of the junction, as also demonstrated experimentally, is suitable for IRES activity. Because foot-and-mouth disease virus IRES structure depends on long-range interactions involving domain 3, the perpendicular intermediate, which maintains coaxial stacking of helices and thereby consensus primary and secondary structure information, may be beneficial for guiding the overall organization of the RNA system in domain 3.
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Mehdizadeh Aghdam E, Barzegar A, Hejazi MS. Evolutionary Origin and Conserved Structural Building Blocks of Riboswitches and Ribosomal RNAs: Riboswitches as Probable Target Sites for Aminoglycosides Interaction. Adv Pharm Bull 2014; 4:225-35. [PMID: 24754005 DOI: 10.5681/apb.2014.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 11/24/2013] [Accepted: 11/26/2013] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Riboswitches, as noncoding RNA sequences, control gene expression through direct ligand binding. Sporadic reports on the structural relation of riboswitches with ribosomal RNAs (rRNA), raises an interest in possible similarity between riboswitches and rRNAs evolutionary origins. Since aminoglycoside antibiotics affect microbial cells through binding to functional sites of the bacterial rRNA, finding any conformational and functional relation between riboswitches/rRNAs is utmost important in both of medicinal and basic research. METHODS Analysis of the riboswitches structures were carried out using bioinformatics and computational tools. The possible functional similarity of riboswitches with rRNAs was evaluated based on the affinity of paromomycin antibiotic (targeting "A site" of 16S rRNA) to riboswitches via docking method. RESULTS There was high structural similarity between riboswitches and rRNAs, but not any particular sequence based similarity between them was found. The building blocks including "hairpin loop containing UUU", "peptidyl transferase center conserved hairpin A loop"," helix 45" and "S2 (G8) hairpin" as high identical rRNA motifs were detected in all kinds of riboswitches. Surprisingly, binding energies of paromomycin with different riboswitches are considerably better than the binding energy of paromomycin with "16S rRNA A site". Therefore the high affinity of paromomycin to bind riboswitches in comparison with rRNA "A site" suggests a new insight about riboswitches as possible targets for aminoglycoside antibiotics. CONCLUSION These findings are considered as a possible supporting evidence for evolutionary origin of riboswitches/rRNAs and also their role in the exertion of antibiotics effects to design new drugs based on the concomitant effects via rRNA/riboswitches.
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Affiliation(s)
- Elnaz Mehdizadeh Aghdam
- Drug Applied Research Center and Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran. ; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Drug Applied Research Center and Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran. ; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
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Grigg JC, Ke A. Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure 2013; 21:2025-32. [PMID: 24095061 PMCID: PMC3879790 DOI: 10.1016/j.str.2013.09.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/01/2013] [Accepted: 09/03/2013] [Indexed: 01/07/2023]
Abstract
T box riboswitches are cis-acting RNA elements that bind to tRNA and sense its aminoacylation state to influence gene expression. Here, we present the 3.2 Å resolution X-ray crystal structures of the T box Stem I-tRNA complex and tRNA, in isolation. T box Stem I forms an arched conformation with extensive intermolecular contacts to two key points of tRNA, the anticodon and D/T-loops. Free and complexed tRNA exist in significantly different conformations, with the contacts stabilizing flexible D/T-loops and a rearrangement of the D-loop. Using a designed T box RNA/tRNA system, we demonstrate that the T box riboswitch monitors the length and orientation of two essential contacts. Length or orientation mismatches engineered into the T box riboswitch and tRNA disrupt the complex, whereas simultaneous insertion of full helical turns realigns the interfaces and restores interaction between artificially elongated T box riboswitch and tRNA molecules.
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Affiliation(s)
- Jason C. Grigg
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA,Correspondence:
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments. Nucleic Acids Res 2013; 41:9999-10009. [PMID: 24005040 PMCID: PMC3905863 DOI: 10.1093/nar/gkt795] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Recent progress in predicting RNA structure is moving towards filling the ‘gap’ in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm.
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Affiliation(s)
- Corinna Theis
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark, Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
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81
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Shen Y, Wong HS, Zhang S, Zhang L. RNA structural motif recognition based on least-squares distance. RNA (NEW YORK, N.Y.) 2013; 19:1183-1191. [PMID: 23887146 PMCID: PMC3753925 DOI: 10.1261/rna.037648.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 06/13/2013] [Indexed: 06/02/2023]
Abstract
RNA structural motifs are recurrent structural elements occurring in RNA molecules. RNA structural motif recognition aims to find RNA substructures that are similar to a query motif, and it is important for RNA structure analysis and RNA function prediction. In view of this, we propose a new method known as RNA Structural Motif Recognition based on Least-Squares distance (LS-RSMR) to effectively recognize RNA structural motifs. A test set consisting of five types of RNA structural motifs occurring in Escherichia coli ribosomal RNA is compiled by us. Experiments are conducted for recognizing these five types of motifs. The experimental results fully reveal the superiority of the proposed LS-RSMR compared with four other state-of-the-art methods.
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Affiliation(s)
- Ying Shen
- School of Software Engineering, Tongji University, Shanghai 200092, China
| | - Hau-San Wong
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Shaohong Zhang
- Department of Computer Science, Guangzhou University, Guangzhou 510006, China
| | - Lin Zhang
- School of Software Engineering, Tongji University, Shanghai 200092, China
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Abstract
Nearly two decades after Westhof and Michel first proposed that RNA tetraloops may interact with distal helices, tetraloop–receptor interactions have been recognized as ubiquitous elements of RNA tertiary structure. The unique architecture of GNRA tetraloops (N=any nucleotide, R=purine) enables interaction with a variety of receptors, e.g., helical minor grooves and asymmetric internal loops. The most common example of the latter is the GAAA tetraloop–11 nt tetraloop receptor motif. Biophysical characterization of this motif provided evidence for the modularity of RNA structure, with applications spanning improved crystallization methods to RNA tectonics. In this review, we identify and compare types of GNRA tetraloop–receptor interactions. Then we explore the abundance of structural, kinetic, and thermodynamic information on the frequently occurring and most widely studied GAAA tetraloop–11 nt receptor motif. Studies of this interaction have revealed powerful paradigms for structural assembly of RNA, as well as providing new insights into the roles of cations, transition states and protein chaperones in RNA folding pathways. However, further research will clearly be necessary to characterize other tetraloop–receptor and long-range tertiary binding interactions in detail – an important milestone in the quantitative prediction of free energy landscapes for RNA folding.
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Halder S, Bhattacharyya D. RNA structure and dynamics: a base pairing perspective. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:264-83. [PMID: 23891726 DOI: 10.1016/j.pbiomolbio.2013.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022]
Abstract
RNA is now known to possess various structural, regulatory and enzymatic functions for survival of cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different parts of the RNA chain. In addition to the canonical Watson-Crick or wobble base pairs, several non-canonical base pairs are found to be crucial to the structural organization of RNA molecules. They appear within different structural motifs and are found to stabilize the molecule through long-range intra-molecular interactions between basic structural motifs like double helices and loops. These base pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non-canonical base pairs are as stable as the canonical Watson-Crick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy.
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Affiliation(s)
- Sukanya Halder
- Biophysics division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
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Ishikawa J, Furuta H, Ikawa Y. RNA tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:651-64. [PMID: 23836522 DOI: 10.1002/wrna.1185] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/30/2013] [Accepted: 06/04/2013] [Indexed: 12/24/2022]
Abstract
RNA molecules are versatile biomaterials that act not only as DNA-like genetic materials but also have diverse functions in regulation of cellular biosystems. RNA is capable of regulating gene expression by sequence-specific hybridization. This feature allows the design of RNA-based artificial gene regulators (riboregulators). RNA can also build complex two-dimensional (2D) and 3D nanostructures, which afford protein-like functions and make RNA an attractive material for nanobiotechnology. RNA tectonics is a methodology in RNA nanobiotechnology for the design and construction of RNA nanostructures/nanoobjects through controlled self-assembly of modular RNA units (tectoRNAs). RNA nanostructures designed according to the concept of RNA tectonics are also attractive as tools in synthetic biology, but in vivo RNA tectonics is still in the early stages. This review presents a summary of the achievements of RNA tectonics and its related researches in vitro, and also introduces recent developments that facilitated the use of RNA nanostructures in bacterial cells.
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Affiliation(s)
- Junya Ishikawa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
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85
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Witts RN, Hopson EC, Koballa DE, Van Boening TA, Hopkins NH, Patterson EV, Nagan MC. Backbone-base interactions critical to quantum stabilization of transfer RNA anticodon structure. J Phys Chem B 2013; 117:7489-97. [PMID: 23742318 DOI: 10.1021/jp400084p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transfer RNA (tRNA) anticodons adopt a highly ordered 3'-stack without significant base overlap. Density functional theory at the M06-2X/6-31+G(d,p) level in combination with natural bond orbital analysis was utilized to calculate the intramolecular interactions within the tRNA anticodon that are responsible for stabilizing the stair-stepped conformation. Ten tRNA X-ray crystal structures were obtained from the PDB databank and were trimmed to include only the anticodon bases. Hydrogenic positions were added and optimized for the structures in the stair-stepped conformation. The sugar-phosphate backbone has been retained for these calculations, revealing the role it plays in RNA structural stability. It was found that electrostatic interactions between the sugar-phosphate backbone and the base provide the most stability, rather than the traditionally studied interbase stacking. Base-stacking interactions, though present, were weak and inconsistent. Aqueous solvation was found to have little effect on the intramolecular interactions.
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Affiliation(s)
- Rachel N Witts
- Department of Chemistry, Truman State University, 100 East Normal, Kirksville, Missouri 63501, USA
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Chan CW, Chetnani B, Mondragón A. Structure and function of the T-loop structural motif in noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:507-22. [PMID: 23754657 DOI: 10.1002/wrna.1175] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/10/2013] [Accepted: 04/26/2013] [Indexed: 12/22/2022]
Abstract
The T-loop is a frequently occurring five-nucleotide motif found in the structure of noncoding RNAs where it is commonly assumed to play an important role in stabilizing the tertiary RNA structure by facilitating long-range interactions between different regions of the molecule. T-loops were first identified in tRNA(Phe) and a formal consensus sequence for this motif was formulated and later revised based on analyses of the crystal structures of prokaryotic ribosomal RNAs and RNase P and the corresponding primary sequence of their orthologues. In the past decade, several new structures of large RNA molecules have been added to the RCSB Protein Data Bank, including the eukaryotic ribosome, a self-splicing group II intron, numerous synthetases in complex with their cognate transfer RNAs (tRNAs), transfer-messenger RNA (tmRNA) in complex with SmpB, several riboswitches, and a complex of bacterial RNase P bound to its tRNA substrate. In this review, the search for T-loops is extended to these new RNA molecules based on the previously established structure-based criteria. The review highlights and discusses the function and additional roles of T-loops in four broad categories of RNA molecules, namely tRNAs, ribosomal RNAs (rRNAs), P RNAs, and RNA genetic elements. Additionally, the potential application for T-loops as interaction modules is also discussed.
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Affiliation(s)
- Clarence W Chan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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87
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Grabow WW, Zhuang Z, Shea JE, Jaeger L. The GA-minor submotif as a case study of RNA modularity, prediction, and design. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:181-203. [PMID: 23378290 DOI: 10.1002/wrna.1153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Complex natural RNAs such as the ribosome, group I and group II introns, and RNase P exemplify the fact that three-dimensional (3D) RNA structures are highly modular and hierarchical in nature. Tertiary RNA folding typically takes advantage of a rather limited set of recurrent structural motifs that are responsible for controlling bends or stacks between adjacent helices. Herein, the GA minor and related structural motifs are presented as a case study to highlight several structural and folding principles, to gain further insight into the structural evolution of naturally occurring RNAs, as well as to assist the rational design of artificial RNAs.
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Affiliation(s)
- Wade W Grabow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
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88
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Wu S, Kikovska E, Lindell M, Kirsebom LA. Cleavage mediated by the catalytic domain of bacterial RNase P RNA. J Mol Biol 2012; 422:204-14. [PMID: 22626870 DOI: 10.1016/j.jmb.2012.05.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 05/11/2012] [Accepted: 05/15/2012] [Indexed: 12/21/2022]
Abstract
Like other RNA molecules, RNase P RNA (RPR) is composed of domains, and these have different functions. Here, we provide data demonstrating that the catalytic (C) domain of Escherichia coli (Eco) RPR when separated from the specificity (S) domain mediates cleavage using various model RNA hairpin loop substrates. Compared to full-length Eco RPR, the rate constant, k(obs), of cleavage for the truncated RPR (CP RPR) was reduced 30- to 13,000-fold depending on substrate. Specifically, the structural architecture of the -1/+73 played a significant role where a C(-1)/G(+73) pair had the most dramatic effect on k(obs). Substitution of A(248) (E. coli numbering), positioned near the cleavage site in the RNase P-substrate complex, with G in the CP RPR resulted in 30-fold improvement in rate. In contrast, strengthening the interaction between the RPR and the 3' end of the substrate only had a modest effect. Interestingly, although deleting the S-domain gave a reduction in the rate, it resulted in a less erroneous RPR with respect to cleavage site selection. These data support and extend our understanding of the coupling between the distal interaction between the S-domain and events at the active site. Our findings will also be discussed with respect to the structure of RPR derived from different organisms.
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Affiliation(s)
- Shiying Wu
- Department of Cell and Molecular Biology, Biomedical Centre, SE-751 24 Uppsala, Sweden
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89
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Hoksza D, Svozil D. Efficient RNA pairwise structure comparison by SETTER method. Bioinformatics 2012; 28:1858-64. [DOI: 10.1093/bioinformatics/bts301] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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90
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Gude L, Berkovitch SS, Santos WL, Kutchukian PS, Pawloski AR, Kuimelis R, McGall G, Verdine GL. Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays. J Biol Chem 2012; 287:18843-53. [PMID: 22451672 DOI: 10.1074/jbc.m111.316596] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Most cellular RNAs engage in intrastrand base-pairing that gives rise to complex three-dimensional folds. This self-pairing presents an impediment toward binding of the RNA by nucleic acid-based ligands. An important step in the discovery of RNA-targeting ligands is therefore to identify those regions in a folded RNA that are accessible toward the nucleic acid-based ligand. Because the folding of RNA targets can involve interactions between nonadjacent regions and employ both Watson-Crick and non-Watson-Crick base-pairing, screening of candidate binder ensembles is typically necessary. Microarray-based screening approaches have shown great promise in this regard and have suggested that achieving complete sequence coverage would be a valuable attribute of a next generation system. Here, we report a custom microarray displaying a library of RNA-interacting polynucleotides comprising all possible 2'-OMe RNA sequences from 4- to 8-nucleotides in length. We demonstrate the utility of this array in identifying RNA-interacting polynucleotides that bind tightly and specifically to the highly conserved, functionally essential template/pseudoknot domain of human telomerase RNA and that inhibit telomerase function in vitro.
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Affiliation(s)
- Lourdes Gude
- Departmens of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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91
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Kikovska E, Wu S, Mao G, Kirsebom LA. Cleavage mediated by the P15 domain of bacterial RNase P RNA. Nucleic Acids Res 2011; 40:2224-33. [PMID: 22102593 PMCID: PMC3299987 DOI: 10.1093/nar/gkr1001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Independently folded domains in RNAs frequently adopt identical tertiary structures regardless of whether they are in isolation or are part of larger RNA molecules. This is exemplified by the P15 domain in the RNA subunit (RPR) of the universally conserved endoribonuclease P, which is involved in the processing of tRNA precursors. One of its domains, encompassing the P15 loop, binds to the 3'-end of tRNA precursors resulting in the formation of the RCCA-RNase P RNA interaction (interacting residues underlined) in the bacterial RPR-substrate complex. The function of this interaction was hypothesized to anchor the substrate, expose the cleavage site and result in re-coordination of Mg(2+) at the cleavage site. Here we show that small model-RNA molecules (~30 nt) carrying the P15-loop mediated cleavage at the canonical RNase P cleavage site with significantly reduced rates compared to cleavage with full-size RPR. These data provide further experimental evidence for our model that the P15 domain contributes to both substrate binding and catalysis. Our data raises intriguing evolutionary possibilities for 'RNA-mediated' cleavage of RNA.
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Affiliation(s)
- Ema Kikovska
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24 Uppsala, Sweden
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92
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Kirillova S, Carugo O. Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures. BMC STRUCTURAL BIOLOGY 2011; 11:41. [PMID: 22011380 PMCID: PMC3206426 DOI: 10.1186/1472-6807-11-41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/19/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. RESULTS A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. CONCLUSIONS The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.
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Affiliation(s)
- Svetlana Kirillova
- Department of Structural and Computational Biology, Max F, Perutz Laboratories, Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
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93
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Wu S, Chen Y, Lindell M, Mao G, Kirsebom LA. Functional Coupling between a Distal Interaction and the Cleavage Site in Bacterial RNase-P-RNA-Mediated Cleavage. J Mol Biol 2011; 411:384-96. [DOI: 10.1016/j.jmb.2011.05.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/31/2011] [Accepted: 05/31/2011] [Indexed: 01/26/2023]
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94
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Ouldridge TE, Louis AA, Doye JPK. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Chem Phys 2011; 134:085101. [PMID: 21361556 DOI: 10.1063/1.3552946] [Citation(s) in RCA: 312] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson-Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an "average base" description of DNA. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.
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95
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Garst AD, Edwards AL, Batey RT. Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a003533. [PMID: 20943759 DOI: 10.1101/cshperspect.a003533] [Citation(s) in RCA: 250] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A critical feature of the hypothesized RNA world would have been the ability to control chemical processes in response to environmental cues. Riboswitches present themselves as viable candidates for a sophisticated mechanism of regulatory control in RNA-based life. These regulatory elements in the modern world are most commonly found in the 5'-untranslated regions of bacterial mRNAs, directly interacting with metabolites as a means of regulating expression of the coding region via a secondary structural switch. In this review, we focus on recent insights into how these RNAs fold into complex architectures capable of both recognizing a specific small molecule compound and exerting regulatory control over downstream sequences, with an emphasis on transcriptional regulation.
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Affiliation(s)
- Andrew D Garst
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 80309-0215, USA
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96
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Ishikawa J, Fujita Y, Maeda Y, Furuta H, Ikawa Y. GNRA/receptor interacting modules: Versatile modular units for natural and artificial RNA architectures. Methods 2011; 54:226-38. [DOI: 10.1016/j.ymeth.2010.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 12/25/2022] Open
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97
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Izzo JA, Kim N, Elmetwaly S, Schlick T. RAG: an update to the RNA-As-Graphs resource. BMC Bioinformatics 2011; 12:219. [PMID: 21627789 PMCID: PMC3123240 DOI: 10.1186/1471-2105-12-219] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 05/31/2011] [Indexed: 02/08/2023] Open
Abstract
Background In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structure motifs using clustering and build-up approaches. With the increased availability of secondary structures in recent years, we update the RAG resource and provide various improvements for analyzing RNA structures. Description Our RAG update includes a new supervised clustering algorithm that can suggest RNA motifs that may be "RNA-like". We use this utility to describe RNA motifs as three classes: existing, RNA-like, and non-RNA-like. This produces 126 tree and 16,658 dual graphs as candidate RNA-like topologies using the supervised clustering algorithm with existing RNAs serving as the training data. A comparison of this clustering approach to an earlier method shows considerable improvements. Additional RAG features include greatly expanded search capabilities, an interface to better utilize the benefits of relational database, and improvements to several of the utilities such as directed/labeled graphs and a subgraph search program. Conclusions The RAG updates presented here augment the database's intended function - stimulating the search for novel RNA functionality - by classifying available motifs, suggesting new motifs for design, and allowing for more specific searches for specific topologies. The updated RAG web resource offers users a graph-based tool for exploring available RNA motifs and suggesting new RNAs for design.
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Affiliation(s)
- Joseph A Izzo
- Department of Chemistry, New York University, New York, NY 10003, USA
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98
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Pietropaolo A, Parrinello M. A quantitative measure of chirality inside nucleic acid databank. Chirality 2011; 23:534-42. [PMID: 21618614 DOI: 10.1002/chir.20961] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Accepted: 02/24/2011] [Indexed: 11/11/2022]
Abstract
We show the capability of a chirality index (Pietropaolo et al., Proteins 2008;70:667-677) to investigate nucleic acid structures because of its high sensitivity to helical conformations. By analyzing selected structures of DNA and RNA, we have found that sequences rich in cytosine and guanine have a tendency to left-handed chirality, in contrast to regions rich in adenine or thymine which show strong negative, right-handed, chirality values. We also analyze RNA structures, where specific loops and hairpin motifs are characterized by a well-defined chirality value. We find that in nucleosome the chirality is exalted, whereas in ribosome it is reduced. Our results illustrate the sensitivity of this descriptor for nucleic acid conformations.
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Affiliation(s)
- Adriana Pietropaolo
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Lugano, Switzerland.
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99
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McCown PJ, Roth A, Breaker RR. An expanded collection and refined consensus model of glmS ribozymes. RNA (NEW YORK, N.Y.) 2011; 17:728-36. [PMID: 21367971 PMCID: PMC3062183 DOI: 10.1261/rna.2590811] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 01/17/2011] [Indexed: 05/21/2023]
Abstract
Self-cleaving glmS ribozymes selectively bind glucosamine-6-phosphate (GlcN6P) and use this metabolite as a cofactor to promote self-cleavage by internal phosphoester transfer. Representatives of the glmS ribozyme class are found in Gram-positive bacteria where they reside in the 5' untranslated regions (UTRs) of glmS messenger RNAs that code for the essential enzyme L-glutamine:D-fructose-6-phosphate aminotransferase. By using comparative sequence analyses, we have expanded the number of glmS ribozyme representatives from 160 to 463. All but two glmS ribozymes are present in glmS mRNAs and most exhibit striking uniformity in sequence and structure, which are features that make representatives attractive targets for antibacterial drug development. However, our discovery of rare variants broadens the consensus sequence and structure model. For example, in the Deinococcus-Thermus phylum, several structural variants exist that carry additional stems within the catalytic core and changes to the architecture of core-supporting substructures. These findings reveal that glmS ribozymes have a broader phylogenetic distribution than previously known and suggest that additional rare structural variants may remain to be discovered.
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Affiliation(s)
- Phillip J McCown
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
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100
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Novikova IV, Hassan BH, Mirzoyan MG, Leontis NB. Engineering cooperative tecto-RNA complexes having programmable stoichiometries. Nucleic Acids Res 2010; 39:2903-17. [PMID: 21138969 PMCID: PMC3074147 DOI: 10.1093/nar/gkq1231] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High affinity and specificity RNA-RNA binding interfaces can be constructed by combining pairs of GNRA loop/loop-receptor interaction motifs. These interactions can be fused using flexible four-way junction motifs to create divalent, self-assembling scaffolding units ('tecto-RNA') that have favorable properties for nanomedicine and other applications. We describe the design and directed assembly of tecto-RNA units ranging from closed, cooperatively assembling ring-shaped complexes of programmable stoichiometries (dimers, trimers and tetramers) to open multimeric structures. The novelty of this work is that tuning of the stoichiometries of self-assembled complexes is achieved by precise positioning of the interaction motifs in the monomer units rather than changing their binding specificities. Structure-probing and transmission electron microscopy studies as well as thermodynamic analysis support formation of closed cooperative complexes that are highly resistant to nuclease digestion. The present designs provide two helical arms per RNA monomer for further functionalization aims.
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Affiliation(s)
- Irina V Novikova
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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