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Lis JA, Domagała PJ. Inconsistencies in the Classification of the Family Cydnidae (Hemiptera: Heteroptera: Pentatomoidea) Revealed by Molecular Apomorphies in the Secondary and Tertiary Structures of 18S rRNA Length-Variable Region L (LVR L). Int J Mol Sci 2024; 25:939. [PMID: 38256014 PMCID: PMC10815949 DOI: 10.3390/ijms25020939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The SSU nuclear rDNA (encoding 18S ribosomal RNA) is one of the most frequently sequenced genes in the molecular analysis of insects. Molecular apomorphies in the secondary and tertiary structures of several 18S rRNA length-variable regions (LVRs) located within the V2, V4, and V7 hypervariable regions can be good indicators for recovering monophyletic groups within some heteropteran families. Among the LVRs that have been analysed, the LVR L in the V4 hypervariable region is the longest and most crucial for such assessments. We analysed the 18S rRNA V4 hypervariable region sequences of 45 species from the family Cydnidae, including all 6 subfamilies (Amaurocorinae, Amnestinae, Cephalocteinae, Cydninae, Garsauriinae, and Sehirinae) and three pentatomoid families (Parastrachiidae, Thaumastellidae, and Thyreocoridae), which have often been included in the broadly defined Cydnidae family. This is the first time that representatives of all Cydnidae subfamilies have been included in a molecular analysis. Only taxa from two subfamilies, Sehirinae and Cydninae, have been used in previous molecular studies. The secondary and tertiary structures of the LVR L were predicted for each species using the two-step procedure already accepted for such analyses to recover any molecular apomorphy essential for determining monophyly. The results of our comparative studies contradict the current understanding of the relationships among burrowing bugs and the current family classification.
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Affiliation(s)
- Jerzy A. Lis
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
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2
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Hansen LN, Kletzien OA, Urquijo M, Schwanz LT, Batey RT. Context-dependence of T-loop Mediated Long-range RNA Tertiary Interactions. J Mol Biol 2023; 435:168070. [PMID: 37003469 PMCID: PMC10152882 DOI: 10.1016/j.jmb.2023.168070] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 04/03/2023]
Abstract
The architecture and folding of complex RNAs is governed by a limited set of highly recurrent structural motifs that form long-range tertiary interactions. One of these motifs is the T-loop, which was first identified in tRNA but is broadly distributed across biological RNAs. While the T-loop has been examined in detail in different biological contexts, the various receptors that it interacts with are not as well defined. In this study, we use a cell-based genetic screen in concert with bioinformatic analysis to examine three different, but related, T-loop receptor motifs found in the flavin mononucleotide (FMN) and cobalamin (Cbl) riboswitches. As a host for different T-loop receptors, we employed the env8 class-II Cbl riboswitch, an RNA that uses two T-loop motifs for both folding and supporting the ligand binding pocket. A set of libraries was created in which select nucleotides that participate in the T-loop/T-loop receptor (TL/TLR) interaction were fully randomized. Library members were screened for their ability to support Cbl-dependent expression of a reporter gene. While T-loops appear to be variable in sequence, we find that the functional sequence space is more restricted in the Cbl riboswitch, suggesting that TL/TLR interactions are context dependent. Our data reveal clear sequence signatures for the different types of receptor motifs that align with phylogenic analysis of these motifs in the FMN and Cbl riboswitches. Finally, our data suggest the functional contribution of various nucleobase-mediated long-range interactions within the riboswitch subclass of TL/TLR interactions that are distinct from those found in other RNAs.
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Affiliation(s)
- Lisa N Hansen
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Otto A Kletzien
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Marcus Urquijo
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Logan T Schwanz
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA. https://twitter.com/Lschwanzbio
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA.
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3
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Sweeney BA, Hoksza D, Nawrocki EP, Ribas CE, Madeira F, Cannone JJ, Gutell R, Maddala A, Meade CD, Williams LD, Petrov AS, Chan PP, Lowe TM, Finn RD, Petrov AI. R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nat Commun 2021; 12:3494. [PMID: 34108470 PMCID: PMC8190129 DOI: 10.1038/s41467-021-23555-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world's largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt .
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Affiliation(s)
- Blake A Sweeney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Carlos Eduardo Ribas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Fábio Madeira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Jamie J Cannone
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Robin Gutell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Aparna Maddala
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Caeden D Meade
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patricia P Chan
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Anton I Petrov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
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4
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Osmer PS, Singh G, Boris-Lawrie K. A New Approach to 3D Modeling of Inhomogeneous Populations of Viral Regulatory RNA. Viruses 2020; 12:v12101108. [PMID: 33003639 PMCID: PMC7650772 DOI: 10.3390/v12101108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Tertiary structure (3D) is the physical context of RNA regulatory activity. Retroviruses are RNA viruses that replicate through the proviral DNA intermediate transcribed by hosts. Proviral transcripts form inhomogeneous populations due to variable structural ensembles of overlapping regulatory RNA motifs in the 5′-untranslated region (UTR), which drive RNAs to be spliced or translated, and/or dimerized and packaged into virions. Genetic studies and structural techniques have provided fundamental input constraints to begin predicting HIV 3D conformations in silico. Using SimRNA and sets of experimentally-determined input constraints of HIVNL4-3 trans-activation responsive sequence (TAR) and pairings of unique-5′ (U5) with dimerization (DIS) or AUG motifs, we calculated a series of 3D models that differ in proximity of 5′-Cap and the junction of TAR and PolyA helices; configuration of primer binding site (PBS)-segment; and two host cofactors binding sites. Input constraints on U5-AUG pairings were most compatible with intramolecular folding of 5′-UTR motifs in energetic minima. Introducing theoretical constraints predicted metastable PolyA region drives orientation of 5′-Cap with TAR, U5 and PBS-segment helices. SimRNA and the workflow developed herein provides viable options to predict 3D conformations of inhomogeneous populations of large RNAs that have been intractable to conventional ensemble methods.
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Affiliation(s)
- Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
- Correspondence: ; Tel.: +1-612-625-2100
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5
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Meyer M, Walbott H, Oliéric V, Kondo J, Costa M, Masquida B. Conformational adaptation of UNCG loops upon crowding. RNA (NEW YORK, N.Y.) 2019; 25:1522-1531. [PMID: 31427457 PMCID: PMC6795143 DOI: 10.1261/rna.072694.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
If the A-form helix is the major structural motif found in RNA, the loops that cap them constitute the second most important family of motifs. Among those, two are overrepresented, GNRA and UNCG tetraloops. Recent surveys of RNA structures deposited in the PDB show that GNRA and UNCG tetraloops can adopt tertiary folds that are very different from their canonical conformations, characterized by the presence of a U-turn of a Z-turn, respectively. Crystallographic data from both a lariat-capping (LC) ribozyme and a group II intron ribozyme reveal that a given UUCG tetraloop can adopt a distinct fold depending on its structural environment. Specifically, when the crystal packing applies relaxed constraints on the loop, the canonical Z-turn conformation is observed. In contrast, a highly packed environment induces "squashing" of the tetraloop by distorting its sugar-phosphate backbone in a specific way that expels the first and fourth nucleobases out of the loop, and falls in van der Waals distance of the last base pair of the helix, taking the place of the pair formed between the first and fourth residues in Z-turn loops. The biological relevance of our observations is supported by the presence of similarly deformed loops in the highly packed environment of the ribosome and in a complex between a dsRNA and a RNase III. The finding that Z-turn loops change conformation under higher molecular packing suggests that, in addition to their demonstrated role in stabilizing RNA folding, they may contribute to the three-dimensional structure of RNA by mediating tertiary interactions with distal residues.
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Affiliation(s)
| | - Hélène Walbott
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Vincent Oliéric
- Paul Scherrer Institute, Swiss Light Source, 5232 Villigen PSI, Switzerland
| | - Jiro Kondo
- Department of Materials and Life Sciences, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan
| | - Maria Costa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Benoît Masquida
- UMR7156 GMGM Université de Strasbourg - CNRS, 67084 Strasbourg, France
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6
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Abstract
The three-dimensional structures of RNA molecules provide rich and often critical information for understanding their functions, including how they recognize small molecule and protein partners. Computational modeling of RNA 3D structure is becoming increasingly accurate, particularly with the availability of growing numbers of template structures already solved experimentally and the development of sequence alignment and 3D modeling tools to take advantage of this database. For several recent "RNA puzzle" blind modeling challenges, we have successfully identified useful template structures and achieved accurate structure predictions through homology modeling tools developed in the Rosetta software suite. We describe our semi-automated methodology here and walk through two illustrative examples: an adenine riboswitch aptamer, modeled from a template guanine riboswitch structure, and a SAM I/IV riboswitch aptamer, modeled from a template SAM I riboswitch structure.
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Affiliation(s)
- Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, United States
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States; Biophysics Program, Stanford University, Stanford, CA, United States.
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7
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Tanzer A, Hofacker IL, Lorenz R. RNA modifications in structure prediction - Status quo and future challenges. Methods 2018; 156:32-39. [PMID: 30385321 DOI: 10.1016/j.ymeth.2018.10.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/12/2018] [Accepted: 10/26/2018] [Indexed: 01/01/2023] Open
Abstract
Chemical modifications of RNA nucleotides change their identity and characteristics and thus alter genetic and structural information encoded in the genomic DNA. tRNA and rRNA are probably the most heavily modified genes, and often depend on derivatization or isomerization of their nucleobases in order to correctly fold into their functional structures. Recent RNomics studies, however, report transcriptome wide RNA modification and suggest a more general regulation of structuredness of RNAs by this so called epitranscriptome. Modification seems to require specific substrate structures, which in turn are stabilized or destabilized and thus promote or inhibit refolding events of regulatory RNA structures. In this review, we revisit RNA modifications and the related structures from a computational point of view. We discuss known substrate structures, their properties such as sub-motifs as well as consequences of modifications on base pairing patterns and possible refolding events. Given that efficient RNA structure prediction methods for canonical base pairs have been established several decades ago, we review to what extend these methods allow the inclusion of modified nucleotides to model and study epitranscriptomic effects on RNA structures.
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Affiliation(s)
- Andrea Tanzer
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria; Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Waehringerstrasse 29, 1090 Vienna, Austria
| | - Ronny Lorenz
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria
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8
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Hill AC, Schroeder SJ. Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA. RNA (NEW YORK, N.Y.) 2017; 23:521-529. [PMID: 28069889 PMCID: PMC5340915 DOI: 10.1261/rna.059220.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/24/2016] [Indexed: 06/06/2023]
Abstract
The thermodynamic stabilities of four natural prohead or packaging RNA (pRNA) three-way junction (3WJ) nanomotifs and seven phi29 pRNA 3WJ deletion mutant nanomotifs were investigated using UV optical melting on a three-component RNA system. Our data reveal that some pRNA 3WJs are more stable than the phi29 pRNA 3WJ. The stability of the 3WJ contributes to the unique self-assembly properties of pRNA. Thus, ultrastable pRNA 3WJ motifs suggest new scaffolds for pRNA-based nanotechnology. We present data demonstrating that pRNA 3WJs differentially respond to the presence of metal ions. A comparison of our data with free energies predicted by currently available RNA secondary structure prediction programs shows that these programs do not accurately predict multibranch loop stabilities. These results will expand the existing parameters used for RNA secondary structure prediction from sequence in order to better inform RNA structure-function hypotheses and guide the rational design of functional RNA supramolecular assemblies.
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Affiliation(s)
| | - Susan J Schroeder
- Department of Microbiology and Plant Biology
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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9
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Abstract
High mortality from breast cancer is associated with the high heterogeneity of tumor and the frequent recurrences of the pathological process, which are due to the presence of tumor stem cells. The review considers the biological properties of tumor stem cells, the molecular mechanisms of their regulation, interaction with the microenvironment, and their role in the heterogeneity of the morphological and clinical forms of breast cancer.
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Affiliation(s)
- A A Ivanov
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation
| | - O P Popova
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation
| | - A V Kuznetsova
- N.K. Koltsov Institute for Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - T I Danilova
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation
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10
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Grzybkowska A, Jędrzejczyk D, Rostkowski M, Chworos A, Dybala-Defratyka A. RNA model evaluation based on MD simulation of four tRNA analogs. RSC Adv 2016. [DOI: 10.1039/c6ra14933b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Characteristic of 3D structures of tRNA analogs generated from primary sequence, subjected to all-atom MD simulation and assessed using selected RNA model evaluation methods.
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Affiliation(s)
- Anna Grzybkowska
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Dominika Jędrzejczyk
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
| | - Michał Rostkowski
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Arkadiusz Chworos
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
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11
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Sweeney BA, Roy P, Leontis NB. An introduction to recurrent nucleotide interactions in RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:17-45. [PMID: 25664365 DOI: 10.1002/wrna.1258] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA secondary structure diagrams familiar to molecular biologists summarize at a glance the folding of RNA chains to form Watson–Crick paired double helices. However, they can be misleading: First of all, they imply that the nucleotides in loops and linker segments, which can amount to 35% to 50% of a structured RNA, do not significantly interact with other nucleotides. Secondly, they give the impression that RNA molecules are loosely organized in three-dimensional (3D) space. In fact, structured RNAs are compactly folded as a result of numerous long-range, sequence-specific interactions, many of which involve loop or linker nucleotides. Here, we provide an introduction for students and researchers of RNA on the types, prevalence, and sequence variations of inter-nucleotide interactions that structure and stabilize RNA 3D motifs and architectures, using Escherichia coli (E. coli) 16S ribosomal RNA as a concrete example. The picture that emerges is that almost all nucleotides in structured RNA molecules, including those in nominally single-stranded loop or linker regions, form specific interactions that stabilize functional structures or mediate interactions with other molecules. The small number of noninteracting, ‘looped-out’ nucleotides make it possible for the RNA chain to form sharp turns. Base-pairing is the most specific interaction in RNA as it involves edge-to-edge hydrogen bonding (H-bonding) of the bases. Non-Watson–Crick base pairs are a significant fraction (30% or more) of base pairs in structured RNAs.
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12
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Dufour D, Marti-Renom MA. Software for predicting the 3D structure of RNA molecules. WILEY INTERDISCIPLINARY REVIEWS: COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- David Dufour
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG) and Gene Regulacion, Stem Cells and Cancer Program; Centre de Regulació Genòmica (CRG); Barcelona Spain
| | - Marc A. Marti-Renom
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG) and Gene Regulacion, Stem Cells and Cancer Program, Centre de Regulació Genòmica (CRG); Barcelona Spain
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13
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Devi G, Yuan Z, Lu Y, Zhao Y, Chen G. Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes. Nucleic Acids Res 2014; 42:4008-18. [PMID: 24423869 PMCID: PMC3973316 DOI: 10.1093/nar/gkt1367] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Peptide nucleic acids (PNAs) have been developed for applications in biotechnology and therapeutics. There is great potential in the development of chemically modified PNAs or other triplex-forming ligands that selectively bind to RNA duplexes, but not single-stranded regions, at near-physiological conditions. Here, we report on a convenient synthesis route to a modified PNA monomer, thio-pseudoisocytosine (L), and binding studies of PNAs incorporating the monomer L. Thermal melting and gel electrophoresis studies reveal that L-incorporated 8-mer PNAs have superior affinity and specificity in recognizing the duplex region of a model RNA hairpin to form a pyrimidine motif major-groove RNA2–PNA triplex, without appreciable binding to single-stranded regions to form an RNA–PNA duplex or, via strand invasion, forming an RNA–PNA2 triplex at near-physiological buffer condition. In addition, an L-incorporated 8-mer PNA shows essentially no binding to single-stranded or double-stranded DNA. Furthermore, an L-modified 6-mer PNA, but not pseudoisocytosine (J) modified or unmodified PNA, binds to the HIV-1 programmed −1 ribosomal frameshift stimulatory RNA hairpin at near-physiological buffer conditions. The stabilization of an RNA2–PNA triplex by L modification is facilitated by enhanced van der Waals contacts, base stacking, hydrogen bonding and reduced dehydration energy. The destabilization of RNA–PNA and DNA–PNA duplexes by L modification is due to the steric clash and loss of two hydrogen bonds in a Watson–Crick-like G–L pair. An RNA2–PNA triplex is significantly more stable than a DNA2–PNA triplex, probably because the RNA duplex major groove provides geometry compatibility and favorable backbone–backbone interactions with PNA. Thus, L-modified triplex-forming PNAs may be utilized for sequence-specifically targeting duplex regions in RNAs for biological and therapeutic applications.
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Affiliation(s)
- Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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14
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Anokhina M, Bessonov S, Miao Z, Westhof E, Hartmuth K, Lührmann R. RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core. EMBO J 2013; 32:2804-18. [PMID: 24002212 DOI: 10.1038/emboj.2013.198] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 07/24/2013] [Indexed: 11/09/2022] Open
Abstract
Although U snRNAs play essential roles in splicing, little is known about the 3D arrangement of U2, U6, and U5 snRNAs and the pre-mRNA in active spliceosomes. To elucidate their relative spatial organization and dynamic rearrangement, we examined the RNA structure of affinity-purified, human spliceosomes before and after catalytic step 1 by chemical RNA structure probing. We found a stable 3-way junction of the U2/U6 snRNA duplex in active spliceosomes that persists minimally through step 1. Moreover, the formation of alternating, mutually exclusive, U2 snRNA conformations, as observed in yeast, was not detected in different assembly stages of human spliceosomal complexes (that is, B, B(act), or C complexes). Psoralen crosslinking revealed an interaction during/after step 1 between internal loop 1 of the U5 snRNA, and intron nucleotides immediately downstream of the branchpoint. Using the experimentally derived structural constraints, we generated a model of the RNA network of the step 1 spliceosome, based on the crystal structure of a group II intron through homology modelling. The model is topologically consistent with current genetic, biochemical, and structural data.
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Affiliation(s)
- Maria Anokhina
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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15
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Smith MA, Gesell T, Stadler PF, Mattick JS. Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res 2013; 41:8220-36. [PMID: 23847102 PMCID: PMC3783177 DOI: 10.1093/nar/gkt596] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/29/2013] [Accepted: 06/16/2013] [Indexed: 12/14/2022] Open
Abstract
Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies >4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5-22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1. This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes.
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Affiliation(s)
- Martin A. Smith
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology; and Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany, Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent’s Clinical School, University of New South Wales, Level 5, de Lacy, Victoria St, St Vincent's Hospital, Sydney, NSW 2010 Australia
| | - Tanja Gesell
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology; and Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany, Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent’s Clinical School, University of New South Wales, Level 5, de Lacy, Victoria St, St Vincent's Hospital, Sydney, NSW 2010 Australia
| | - Peter F. Stadler
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology; and Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany, Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent’s Clinical School, University of New South Wales, Level 5, de Lacy, Victoria St, St Vincent's Hospital, Sydney, NSW 2010 Australia
| | - John S. Mattick
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia, Genomics and Computational Biology Division, Institute for Molecular Bioscience, 306 Carmody Rd, University of Queensland, Brisbane, 4067 Australia, Department of Structural and Computational Biology; and Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria, Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany, Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark, Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA and St Vincent’s Clinical School, University of New South Wales, Level 5, de Lacy, Victoria St, St Vincent's Hospital, Sydney, NSW 2010 Australia
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16
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Stephenson W, Asare-Okai PN, Chen AA, Keller S, Santiago R, Tenenbaum SA, Garcia AE, Fabris D, Li PTX. The essential role of stacking adenines in a two-base-pair RNA kissing complex. J Am Chem Soc 2013; 135:5602-11. [PMID: 23517345 DOI: 10.1021/ja310820h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In minimal RNA kissing complexes formed between hairpins with cognate GACG tetraloops, the two tertiary GC pairs are likely stabilized by the stacking of 5'-unpaired adenines at each end of the short helix. To test this hypothesis, we mutated the flanking adenines to various nucleosides and examined their effects on the kissing interaction. Electrospray ionization mass spectrometry was used to detect kissing dimers in a multiequilibria mixture, whereas optical tweezers were applied to monitor the (un)folding trajectories of single RNA molecules. The experimental findings were rationalized by molecular dynamics simulations. Together, the results showed that the stacked adenines are indispensable for the tertiary interaction. By shielding the tertiary base pairs from solvent and reducing their fraying, the stacked adenines made terminal pairs act more like interior base pairs. The purine double-ring of adenine was essential for effective stacking, whereas additional functional groups modulated the stabilizing effects through varying hydrophobic and electrostatic forces. Furthermore, formation of the kissing complex was dominated by base pairing, whereas its dissociation was significantly influenced by the flanking bases. Together, these findings indicate that unpaired flanking nucleotides play essential roles in the formation of otherwise unstable two-base-pair RNA tertiary interactions.
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Affiliation(s)
- William Stephenson
- Nanoscale Engineering Graduate Program, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA
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17
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Ray SS, Pal SK. RNA secondary structure prediction using soft computing. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:2-17. [PMID: 23702539 DOI: 10.1109/tcbb.2012.159] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.
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18
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Manzourolajdad A, Wang Y, Shaw TI, Malmberg RL. Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA. J Theor Biol 2012; 318:140-63. [PMID: 23160142 DOI: 10.1016/j.jtbi.2012.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 10/11/2012] [Accepted: 10/18/2012] [Indexed: 10/27/2022]
Abstract
UNLABELLED RNA secondary structure ensembles define probability distributions for alternative equilibrium secondary structures of an RNA sequence. Shannon's entropy is a measure for the amount of diversity present in any ensemble. In this work, Shannon's entropy of the SCFG ensemble on an RNA sequence is derived and implemented in polynomial time for both structurally ambiguous and unambiguous grammars. Micro RNA sequences generally have low folding entropy, as previously discovered. Surprisingly, signs of significantly high folding entropy were observed in certain ncRNA families. More effective models coupled with targeted randomization tests can lead to a better insight into folding features of these families. AVAILABILITY URL http://www.plantbio.uga.edu/~russell/index.php?s=1&n=5&r=0.
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Affiliation(s)
- Amirhossein Manzourolajdad
- Institute of Bioinformatics, University of Georgia, Davison Life Sciences Bldg, Room B118B, 120 Green St, Athens, GA 30602, USA.
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19
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Romilly C, Chevalier C, Marzi S, Masquida B, Geissmann T, Vandenesch F, Westhof E, Romby P. Loop-loop interactions involved in antisense regulation are processed by the endoribonuclease III in Staphylococcus aureus. RNA Biol 2012; 9:1461-72. [PMID: 23134978 DOI: 10.4161/rna.22710] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The endoribonuclease III (RNase III) belongs to the enzyme family known to process double-stranded RNAs. Staphylococcus aureus RNase III was shown to regulate, in concert with the quorum sensing induced RNAIII, the degradation of several mRNAs encoding virulence factors and the transcriptional repressor of toxins Rot. Two of the mRNA-RNAIII complexes involve fully base paired loop-loop interactions with similar sequences that are cleaved by RNase III at a unique position. We show here that the sequence of the base pairs within the loop-loop interaction is not critical for RNase III cleavage, but that the co-axial stacking of three consecutive helices provides an ideal topology for RNase III recognition. In contrast, RNase III induces several strong cleavages in a regular helix, which carries a sequence similar to the loop-loop interaction. The introduction of a bulged loop that interrupts the regular helix restrains the number of cleavages. This work shows that S. aureus RNase III is able to bind and cleave a variety of RNA-mRNA substrates, and that specific structure elements direct the action of RNase III.
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Affiliation(s)
- Cédric Romilly
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
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20
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Abstract
There are two RNA worlds. The first is the primordial RNA world, a hypothetical era when RNA served as both information and function, both genotype and phenotype. The second RNA world is that of today's biological systems, where RNA plays active roles in catalyzing biochemical reactions, in translating mRNA into proteins, in regulating gene expression, and in the constant battle between infectious agents trying to subvert host defense systems and host cells protecting themselves from infection. This second RNA world is not at all hypothetical, and although we do not have all the answers about how it works, we have the tools to continue our interrogation of this world and refine our understanding. The fun comes when we try to use our secure knowledge of the modern RNA world to infer what the primordial RNA world might have looked like.
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Affiliation(s)
- Thomas R Cech
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309-0215, USA.
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21
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Lease RA, Arluison V, Lavelle C. Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assembly in vivo.. FRONTIERS IN LIFE SCIENCE 2012; 6:19-32. [PMID: 23914307 PMCID: PMC3725660 DOI: 10.1080/21553769.2012.761163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/18/2012] [Indexed: 11/23/2022]
Abstract
The primacy and power of RNA in governing many processes of life has begun to be more fully appreciated in both the discovery and inventive sciences. A variety of RNA interactions regulate gene expression, and structural self-assembly underlies many of these processes. The understanding sparked by these discoveries has inspired and informed the engineering of novel RNA structures, control elements, and genetic circuits in cells. Many of these engineered systems are built up fundamentally from RNA–RNA interactions, often combining modular, rational design with functional selection and screening. It is therefore useful to review the particular class of RNA-based regulatory mechanisms that rely on RNA self-assembly either through homomeric (self–self) or heteromeric (self–nonself) RNA–RNA interactions. Structures and sequence elements within individual RNAs create a basis for the pairing interactions, and in some instances can even lead to the formation of RNA polymers. Example systems of dimers, multimers, and polymers are reviewed in this article in the context of natural systems, wherein the function and impact of self-assemblies are understood. Following this, a brief overview is presented of specific engineered RNA self-assembly systems implemented in vivo, with lessons learned from both discovery and engineering approaches to RNA–RNA self-assembly.
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Affiliation(s)
- Richard A Lease
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
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22
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Mathew A, Aravind A, Brahatheeswaran D, Fukuda T, Nagaoka Y, Hasumura T, Iwai S, Morimoto H, Yoshida Y, Maekawa T, Venugopal K, Kumar DS. Amyloid-Binding Aptamer Conjugated Curcumin–PLGA Nanoparticle for Potential Use in Alzheimer’s Disease. BIONANOSCIENCE 2012. [DOI: 10.1007/s12668-012-0040-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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23
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24
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Cao S, Chen SJ. A domain-based model for predicting large and complex pseudoknotted structures. RNA Biol 2012; 9:200-11. [PMID: 22418848 DOI: 10.4161/rna.18488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Pseudoknotted structures play important structural and functional roles in RNA cellular functions at the level of transcription, splicing and translation. However, the problem of computational prediction for large pseudoknotted folds remains. Here we develop a domain-based method for predicting complex and large pseudoknotted structures from RNA sequences. The model is based on the observation that large RNAs can be separated into different structural domains. The basic idea is to first identify the domains and then predict the structures for each domain. Assembly of the domain structures gives the full structure. The use of the domain-based approach leads to a reduction of computational time by a factor of about ~N ( 2) for an N-nt sequence. As applications of the model, we predict structures for a variety of RNA systems, such as regions in human telomerase RNA (hTR), internal ribosome entry site (IRES) and HIV genome. The lengths of these sequences range from 200-nt to 400-nt. The results show good agreements with the experiments.
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Affiliation(s)
- Song Cao
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, MO, USA
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25
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Abstract
We develop a unique algorithm implemented in the program MOSAICS (Methodologies for Optimization and Sampling in Computational Studies) that is capable of nanoscale modeling without compromising the resolution of interest. This is achieved by modeling with customizable hierarchical degrees of freedom, thereby circumventing major limitations of conventional molecular modeling. With the emergence of RNA-based nanotechnology, large RNAs in all-atom representation are used here to benchmark our algorithm. Our method locates all favorable structural states of a model RNA of significant complexity while improving sampling accuracy and increasing speed many fold over existing all-atom RNA modeling methods. We also modeled the effects of sequence mutations on the structural building blocks of tRNA-based nanotechnology. With its flexibility in choosing arbitrary degrees of freedom as well as in allowing different all-atom energy functions, MOSAICS is an ideal tool to model and design biomolecules of the nanoscale.
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26
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27
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Cao S, Chen SJ. Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA (NEW YORK, N.Y.) 2011; 17:2130-43. [PMID: 22028361 PMCID: PMC3222126 DOI: 10.1261/rna.026658.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 09/12/2011] [Indexed: 05/24/2023]
Abstract
We develop a statistical mechanical model to predict the structure and folding stability of the RNA/RNA kissing-loop complex. One of the key ingredients of the theory is the conformational entropy for the RNA/RNA kissing complex. We employ the recently developed virtual bond-based RNA folding model (Vfold model) to evaluate the entropy parameters for the different types of kissing loops. A benchmark test against experiments suggests that the entropy calculation is reliable. As an application of the model, we apply the model to investigate the structure and folding thermodynamics for the kissing complex of the HIV-1 dimerization initiation signal. With the physics-based energetic parameters, we compute the free energy landscape for the HIV-1 dimer. From the energy landscape, we identify two minimal free energy structures, which correspond to the kissing-loop dimer and the extended-duplex dimer, respectively. The results support the two-step dimerization process for the HIV-1 replication cycle. Furthermore, based on the Vfold model and energy minimization, the theory can predict the native structure as well as the local minima in the free energy landscape. The root-mean-square deviations (RMSDs) for the predicted kissing-loop dimer and extended-duplex dimer are ~3.0 Å. The method developed here provides a new method to study the RNA/RNA kissing complex.
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Affiliation(s)
- Song Cao
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
| | - Shi-Jie Chen
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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28
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Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH. NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions. RNA (NEW YORK, N.Y.) 2011; 17:1664-77. [PMID: 21778280 PMCID: PMC3162332 DOI: 10.1261/rna.2641911] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 05/08/2011] [Indexed: 05/31/2023]
Abstract
The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5'GAA/3'AGG, 5'GAG/3'AGG, 5'GAA/3'AAG, and 5'AAG/3'AGG. The structural information is compared with predictions made with the MC-Sym program.
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Affiliation(s)
- Yelena V. Lerman
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | - Scott D. Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Neelaabh Shankar
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Marc Parisien
- Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec H3C CJ7, Canada
| | - Francois Major
- Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec H3C CJ7, Canada
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
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29
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Mathews DH, Moss WN, Turner DH. Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol 2010; 2:a003665. [PMID: 20685845 DOI: 10.1101/cshperspect.a003665] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed.
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Affiliation(s)
- David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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