1
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Bohdan DR, Voronina VV, Bujnicki JM, Baulin EF. A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures. Nucleic Acids Res 2023; 51:8367-8382. [PMID: 37471030 PMCID: PMC10484739 DOI: 10.1093/nar/gkad605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
Understanding the 3D structure of RNA is key to understanding RNA function. RNA 3D structure is modular and can be seen as a composition of building blocks of various sizes called tertiary motifs. Currently, long-range motifs formed between distant loops and helical regions are largely less studied than the local motifs determined by the RNA secondary structure. We surveyed long-range tertiary interactions and motifs in a non-redundant set of non-coding RNA 3D structures. A new dataset of annotated LOng-RAnge RNA 3D modules (LORA) was built using an approach that does not rely on the automatic annotations of non-canonical interactions. An original algorithm, ARTEM, was developed for annotation-, sequence- and topology-independent superposition of two arbitrary RNA 3D modules. The proposed methods allowed us to identify and describe the most common long-range RNA tertiary motifs. Along with the prevalent canonical A-minor interactions, a large number of previously undescribed staple interactions were observed. The most frequent long-range motifs were found to belong to three main motif families: planar staples, tilted staples, and helical packing motifs.
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Affiliation(s)
- Davyd R Bohdan
- Department of Innovation and High Technology, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valeria V Voronina
- Department of Information Systems, Ulyanovsk State Technical University, Ulyanovsk 432027, Russia
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Eugene F Baulin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
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2
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Rivas M, Fox GE. Ancestry of RNA/RNA interaction regions within segmented ribosomes. RNA (NEW YORK, N.Y.) 2023; 29:1388-1399. [PMID: 37263782 PMCID: PMC10573304 DOI: 10.1261/rna.079654.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/14/2023] [Indexed: 06/03/2023]
Abstract
The ribosome is the universally conserved ribozyme that translates DNA coded instructions into proteins with the assistance of other RNA molecules, including transfer and messenger RNAs. Of particular interest is the segmentation phenomena, which is found in trypanosomatids and other protists. In these organisms, the large subunit ribosomal RNA is assembled from multiple smaller RNAs. This phenomenon posits several challenges to the folding and stabilization of such ribosomes to retain functionality and efficiency. In earlier studies, RNA/protein interactions were suggested to fully compensate for the fragmentation. Recently, several conserved RNA/RNA interaction regions were described in the cryo-EM structures of segmented ribosomes from trypanosomatids. These regions also seemed to aid in the folding and stabilization of such ribosomes, even before the ribosomal proteins start their association. In the present study, the existence of conserved RNA/RNA interaction regions shared between trypanosomatid and Euglena gracilis segmented ribosomes was confirmed, despite differences in segmentation patterns. Analysis of the crystallographic structures of unsegmented ribosomes from other Eukaryotes, Bacteria, and Archaea allowed us to estimate the relative age of highly conserved RNA/RNA interaction regions. These results strongly suggest that common interaction regions likely date far back into the ribosomes of the last common ancestor. Results also revealed that single hydrogen bonds are overwhelmingly facilitated by the 2'OH, a distinctive RNA feature. This supports the notion that RNA predates DNA and places some constraints on alternative nucleic acids proposals.
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Affiliation(s)
- Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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3
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Harp JM, Lybrand TP, Pallan PS, Coates L, Sullivan B, Egli M. Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure. Nucleic Acids Res 2022; 50:7721-7738. [PMID: 35819202 PMCID: PMC9303348 DOI: 10.1093/nar/gkac577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/14/2022] Open
Abstract
The ribose 2′-hydroxyl is the key chemical difference between RNA and DNA and primary source of their divergent structural and functional characteristics. Macromolecular X-ray diffraction experiments typically do not reveal the positions of hydrogen atoms. Thus, standard crystallography cannot determine 2′-OH orientation (H2′-C2′-O2′-HO2′ torsion angle) and its potential roles in sculpting the RNA backbone and the expansive fold space. Here, we report the first neutron crystal structure of an RNA, the Escherichia coli rRNA Sarcin-Ricin Loop (SRL). 2′-OD orientations were established for all 27 residues and revealed O-D bonds pointing toward backbone (O3′, 13 observations), nucleobase (11) or sugar (3). Most riboses in the SRL stem region show a 2′-OD backbone-orientation. GAGA-tetraloop riboses display a 2′-OD base-orientation. An atypical C2′-endo sugar pucker is strictly correlated with a 2′-OD sugar-orientation. Neutrons reveal the strong preference of the 2′-OH to donate in H-bonds and that 2′-OH orientation affects both backbone geometry and ribose pucker. We discuss 2′-OH and water molecule orientations in the SRL neutron structure and compare with results from a solution phase 10 μs MD simulation. We demonstrate that joint cryo-neutron/X-ray crystallography offers an all-in-one approach to determine the complete structural properties of RNA, i.e. geometry, conformation, protonation state and hydration structure.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Terry P Lybrand
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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4
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Fröhlking T, Mlýnský V, Janeček M, Kührová P, Krepl M, Banáš P, Šponer J, Bussi G. Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. J Chem Theory Comput 2022; 18:4490-4502. [PMID: 35699952 PMCID: PMC9281393 DOI: 10.1021/acs.jctc.2c00200] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
The
capability of
current force fields to reproduce RNA structural
dynamics is limited. Several methods have been developed to take advantage
of experimental data in order to enforce agreement with experiments.
Here, we extend an existing framework which allows arbitrarily chosen
force-field correction terms to be fitted by quantification of the
discrepancy between observables back-calculated from simulation and
corresponding experiments. We apply a robust regularization protocol
to avoid overfitting and additionally introduce and compare a number
of different regularization strategies, namely, L1, L2, Kish size,
relative Kish size, and relative entropy penalties. The training set
includes a GACC tetramer as well as more challenging systems, namely,
gcGAGAgc and gcUUCGgc RNA tetraloops. Specific intramolecular hydrogen
bonds in the AMBER RNA force field are corrected with automatically
determined parameters that we call gHBfixopt. A validation
involving a separate simulation of a system present in the training
set (gcUUCGgc) and new systems not seen during training (CAAU and
UUUU tetramers) displays improvements regarding the native population
of the tetraloop as well as good agreement with NMR experiments for
tetramers when using the new parameters. Then, we simulate folded
RNAs (a kink–turn and L1 stalk rRNA) including hydrogen bond
types not sufficiently present in the training set. This allows a
final modification of the parameter set which is named gHBfix21 and
is suggested to be applicable to a wider range of RNA systems.
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Affiliation(s)
- Thorben Fröhlking
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 65, Czech Republic
| | - Michal Janeček
- Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, Olomouc 771 46, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 779 00 Olomouc, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 65, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 779 00 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 779 00 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 65, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 779 00 Olomouc, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
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5
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Rivas M, Fox GE. Nonstandard RNA/RNA interactions likely enhance folding and stability of segmented ribosomes. RNA (NEW YORK, N.Y.) 2022; 28:340-352. [PMID: 34876487 PMCID: PMC8848935 DOI: 10.1261/rna.079006.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/26/2021] [Indexed: 05/21/2023]
Abstract
The ribosome is the molecular factory that catalyzes all coded protein synthesis in extant organisms. Eukaryotic ribosomes are typically assembled out of four rRNAs; namely, 5S, 5.8S, 18S, and 28S. However, the 28S rRNA of some trypanosomatid organisms has been found to be segmented into six independent rRNAs of different sizes. The two largest segments have multiple sites where they jointly form stems comprised of standard base pairs that can hold them together. However, such regions of interaction are not observed among the four smaller RNAs. Early reports suggested that trypanosomatid segmented ribosome assembly was essentially achieved thanks to their association with rProteins. However, examination of cryo-EM ribosomal structures from Trypanosoma brucei, Leishmania donovani, and Trypanosoma cruzi reveals several long-range nonstandard RNA/RNA interactions. Most of these interactions are clusters of individual hydrogen bonds and so are not readily predictable. However, taken as a whole, they represent significant stabilizing energy that likely facilitates rRNA assembly and the overall stability of the segmented ribosomes. In the context of origin of life studies, the current results provide a better understanding of the true nature of RNA sequence space and what might be possible without an RNA replicase.
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Affiliation(s)
- Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
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6
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Skeparnias I, Zhang J. Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions. Noncoding RNA 2021; 7:ncrna7040081. [PMID: 34940761 PMCID: PMC8704770 DOI: 10.3390/ncrna7040081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. Herein, we discuss different modalities of RNA–RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure. We dissect recently structurally elucidated RNA–RNA complexes including RNA triplexes, riboswitches, ribozymes, and reverse transcription complexes. These analyses highlight a reciprocal relationship that intimately links RNA structure formation with RNA–RNA interactions. The interactions not only shape and sculpt RNA structures but also are enabled and modulated by the structures they create. Understanding this two-way relationship between RNA structure and interactions provides mechanistic insights into the expanding repertoire of noncoding RNA functions, and may inform the design of novel therapeutics that target RNA structures or interactions.
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7
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Kiliszek A, Błaszczyk L, Bejger M, Rypniewski W. Broken symmetry between RNA enantiomers in a crystal lattice. Nucleic Acids Res 2021; 49:12535-12539. [PMID: 34107036 PMCID: PMC8643679 DOI: 10.1093/nar/gkab480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 11/19/2022] Open
Abstract
Explaining the origin of the homochirality of biological molecules requires a mechanism of disrupting the natural equilibrium between enantiomers and amplifying the initial imbalance to significant levels. Authors of existing models have sought an explanation in the parity-breaking weak nuclear force, in some selectively acting external factor, or in random fluctuations that subsequently became amplified by an autocatalytic process. We have obtained crystals in which l- and d-enantiomers of short RNA duplexes assemble in an asymmetric manner. These enantiomers make different lattice contacts and have different exposures to water and metal ions present in the crystal. Apparently, asymmetry between enantiomers can arise upon their mutual interactions and then propagate via crystallization. Asymmetric racemic compounds are worth considering as possible factors in symmetry breaking and enantioenrichment that took place in the early biosphere.
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Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
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8
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Baulin EF. Features and Functions of the A-Minor Motif, the Most Common Motif in RNA Structure. BIOCHEMISTRY (MOSCOW) 2021; 86:952-961. [PMID: 34488572 DOI: 10.1134/s000629792108006x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A-minor motifs are RNA tertiary structure motifs that generally involve a canonical base pair and an adenine base forming hydrogen bonds with the minor groove of the base pair. Such motifs are among the most common tertiary interactions in known RNA structures, comparable in number with the non-canonical base pairs. They are often found in functionally important regions of non-coding RNAs and, in particular, play a central role in protein synthesis. Here, we review local variations of the A-minor geometry and discuss difficulties associated with their annotation, as well as various structural contexts and common A-minor co-motifs, and diverse functions of A-minors in various processes in a living cell.
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Affiliation(s)
- Eugene F Baulin
- Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
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9
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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10
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Shalybkova AA, Mikhailova DS, Kulakovskiy IV, Fakhranurova LI, Baulin EF. Annotation of the local context of the RNA secondary structure improves the classification and prediction of A-minors. RNA (NEW YORK, N.Y.) 2021; 27:rna.078535.120. [PMID: 34016706 PMCID: PMC8284323 DOI: 10.1261/rna.078535.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/17/2021] [Indexed: 05/15/2023]
Abstract
Non-coding RNAs play a crucial role in various cellular processes in living organisms, and RNA functions heavily depend on molecule structures composed of stems, loops, and various tertiary motifs. Among those, the most frequent are A-minor interactions, which are often involved in the formation of more complex motifs such as kink-turns and pseudoknots. We present a novel classification of A-minors in terms of RNA secondary structure where each nucleotide of an A-minor is attributed to the stem or loop, and each pair of nucleotides is attributed to their relative position within the secondary structure. By analyzing classes of A-minors in known RNA structures, we found that the largest classes are mostly homogeneous and preferably localize with known A-minor co-motifs, e.g. tetraloop-tetraloop receptor and coaxial stacking. Detailed analysis of local A-minors within internal loops revealed a novel recurrent RNA tertiary motif, the across-bulged motif. Interestingly, the motif resembles the previously known GAAA/11nt motif but with the local adenines performing the role of the GAAA-tetraloop. By using machine learning, we show that particular classes of local A-minors can be predicted from sequence and secondary structure. The proposed classification is the first step toward automatic annotation of not only A-minors and their co-motifs but various types of RNA tertiary motifs as well.
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Affiliation(s)
| | | | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences; Vavilov Institute of General Genetics, Russian Academy of Sciences; Institute of Protein Research, Russian Academy of Sciences
| | - Liliia I Fakhranurova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences; Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences
| | - Eugene F Baulin
- Institute of Mathematical Problems of Biology RAS; Moscow Institute of Physics and Technology
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11
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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12
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Pallan PS, Lybrand TP, Schlegel MK, Harp JM, Jahns H, Manoharan M, Egli M. Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost. Biochemistry 2020; 59:4627-4637. [PMID: 33275419 DOI: 10.1021/acs.biochem.0c00685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
GNRA (N = A, C, G, or U; R = A or G) tetraloops are common RNA secondary structural motifs and feature a phosphate stacked atop a nucleobase. The rRNA sarcin/ricin loop (SRL) is capped by GApGA, and the phosphate p stacks on G. We recently found that regiospecific incorporation of a single dithiophosphate (PS2) but not a monothiophosphate (PSO) instead of phosphate in the backbone of RNA aptamers dramatically increases the binding affinity for their targets. In the RNA:thrombin complex, the key contribution to the 1000-fold tighter binding stems from an edge-on contact between PS2 and a phenylalanine ring. Here we investigated the consequences of replacing the SRL phosphate engaged in a face-on interaction with guanine with either PS2 or PSO for stability. We found that PS2···G and Rp-PSO···G contacts stabilize modified SRLs compared to the parent loop to unexpected levels: up to 6.3 °C in melting temperature Tm and -4.7 kcal/mol in ΔΔG°. Crystal structures demonstrate that the vertical distance to guanine for the closest sulfur is just 0.05 Å longer on average compared to that of oxygen despite the larger van der Waals radius of the former (1.80 Å for S vs 1.52 Å for O). The higher stability is enthalpy-based, and the negative charge as assessed by a neutral methylphosphonate modification plays only a minor role. Quantum mechanical/molecular mechanical calculations are supportive of favorable dispersion attraction interactions by sulfur making the dominant contribution. A stacking interaction between phosphate and guanine (SRL) or uracil (U-turn) is also found in newly classified RNA tetraloop families besides GNRA.
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Affiliation(s)
| | | | - Mark K Schlegel
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Hartmut Jahns
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
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13
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Ruszkowska A, Ruszkowski M, Hulewicz JP, Dauter Z, Brown JA. Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples. Nucleic Acids Res 2020; 48:3304-3314. [PMID: 31930330 PMCID: PMC7102945 DOI: 10.1093/nar/gkz1222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple helix with 11 continuous base triples. Due to helical unwinding, the RNA triple helix spans an average of 12 base triples per turn. The double helix portion of the RNA triple helix is more similar to both the helical and base step structural parameters of A′-RNA rather than A-RNA. Its most striking features are its wide and deep major groove, a smaller inclination angle and all three strands favoring a C3′-endo sugar pucker. Despite the presence of a third strand, the diameter of an RNA triple helix remains nearly identical to those of DNA and RNA double helices. Contrary to our previous modeling predictions, this structure demonstrates that an RNA triple helix is not limited in length to six consecutive base triples and that longer RNA triple helices may exist in nature. Our structure provides a starting point to establish structural parameters of the so-called ‘ideal’ RNA triple helix, analogous to A-RNA and B-DNA double helices.
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Affiliation(s)
- Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL 60439 USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL 60439 USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
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14
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Zhao J, Kennedy SD, Berger KD, Turner DH. Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:1968-1984. [PMID: 31904966 DOI: 10.1021/acs.jctc.9b00912] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA and DNA are rapidly emerging as targets for therapeutics and as potential frameworks for nanotechnology. Accurate methods for predicting and designing structures and dynamics of nucleic acids would accelerate progress in these and other applications. Suitable approximations for modeling nucleic acids are being developed but require validation against disparate experimental observations. Here, nuclear magnetic resonance spectra for RNA and DNA single strands, CAAU and UCAAUC, are used as benchmarks to test molecular dynamics simulations with AMBER force fields OL3 and ROC-RNA for RNA and BSC1 for DNA. A detailed scheme for making comparisons is also presented. The results reflect recent progress in approximations and reveal remaining challenges.
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Affiliation(s)
- Jianbo Zhao
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| | - Scott D Kennedy
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.,Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Kyle D Berger
- Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States.,Department of Biochemistry and Biophysics, School of Medicine & Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
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15
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Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A. SAM-VI riboswitch structure and signature for ligand discrimination. Nat Commun 2019; 10:5728. [PMID: 31844059 PMCID: PMC6914780 DOI: 10.1038/s41467-019-13600-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022] Open
Abstract
Riboswitches are metabolite-sensing, conserved domains located in non-coding regions of mRNA that are central to regulation of gene expression. Here we report the first three-dimensional structure of the recently discovered S-adenosyl-L-methionine responsive SAM-VI riboswitch. SAM-VI adopts a unique fold and ligand pocket that are distinct from all other known SAM riboswitch classes. The ligand binds to the junctional region with its adenine tightly intercalated and Hoogsteen base-paired. Furthermore, we reveal the ligand discrimination mode of SAM-VI by additional X-ray structures of this riboswitch bound to S-adenosyl-L-homocysteine and a synthetic ligand mimic, in combination with isothermal titration calorimetry and fluorescence spectroscopy to explore binding thermodynamics and kinetics. The structure is further evaluated by analysis of ligand binding to SAM-VI mutants. It thus provides a thorough basis for developing synthetic SAM cofactors for applications in chemical and synthetic RNA biology.
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Affiliation(s)
- Aiai Sun
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Catherina Gasser
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria
| | - Fudong Li
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics and School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Stefan Mair
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria
| | - Olga Krasheninina
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
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16
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Montemayor EJ, Virta JM, Hagler LD, Zimmerman SC, Butcher SE. Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking. Acta Crystallogr F Struct Biol Commun 2019; 75:652-656. [PMID: 31584014 PMCID: PMC6777134 DOI: 10.1107/s2053230x19012172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/02/2019] [Indexed: 01/29/2023] Open
Abstract
The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U-U mismatch sandwiched between Watson-Crick pairs. Additionally, the center of the helix contains a dimerized UUCG motif with tandem pyrimidine (U-C/C-U) mismatches flanked by U-G wobble pairs. This region of the structure is significantly different from previously observed structures that share the same sequence and neighboring base pairs. The tandem pyrimidine mismatches are unusual and display sheared, cross-strand stacking geometries that locally constrict the helical width, a type of stacking previously associated with purines in internal loops. Thus, pyrimidine-rich regions of RNA have a high degree of structural diversity.
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Affiliation(s)
- Eric J. Montemayor
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Johanna M. Virta
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Lauren D. Hagler
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Steven C. Zimmerman
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
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17
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Gupta A, Bansal M. The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study. Phys Chem Chem Phys 2016; 18:28767-28780. [DOI: 10.1039/c6cp04617g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This work highlights a sequence dependent unfolding pathway of an RNA pseudoknot under force-induced pulling conditions.
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Affiliation(s)
- Asmita Gupta
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore-560012
- India
| | - Manju Bansal
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore-560012
- India
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18
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Appasamy SD, Hamdani HY, Ramlan EI, Firdaus-Raih M. InterRNA: a database of base interactions in RNA structures. Nucleic Acids Res 2015; 44:D266-71. [PMID: 26553798 PMCID: PMC4702846 DOI: 10.1093/nar/gkv1186] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/24/2015] [Indexed: 11/17/2022] Open
Abstract
A major component of RNA structure stabilization are the hydrogen bonded interactions between the base residues. The importance and biological relevance for large clusters of base interactions can be much more easily investigated when their occurrences have been systematically detected, catalogued and compared. In this paper, we describe the database InterRNA (INTERactions in RNA structures database—http://mfrlab.org/interrna/) that contains records of known RNA 3D motifs as well as records for clusters of bases that are interconnected by hydrogen bonds. The contents of the database were compiled from RNA structural annotations carried out by the NASSAM (http://mfrlab.org/grafss/nassam) and COGNAC (http://mfrlab.org/grafss/cognac) computer programs. An analysis of the database content and comparisons with the existing corpus of knowledge regarding RNA 3D motifs clearly show that InterRNA is able to provide an extension of the annotations for known motifs as well as able to provide novel interactions for further investigations.
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Affiliation(s)
- Sri Devan Appasamy
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Hazrina Yusof Hamdani
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Effirul Ikhwan Ramlan
- Department of Artificial Intelligence, Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Firdaus-Raih
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
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19
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Bernhardt HS. The Juxtaposition of Ribose Hydroxyl Groups: The Root of Biological Catalysis and the RNA World? ORIGINS LIFE EVOL B 2015; 45:15-9. [DOI: 10.1007/s11084-015-9403-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 10/10/2014] [Indexed: 10/24/2022]
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20
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Bonneau E, Legault P. Nuclear magnetic resonance structure of the III-IV-V three-way junction from the Varkud satellite ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement. Biochemistry 2014; 53:6264-75. [PMID: 25238589 DOI: 10.1021/bi500826n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The VS ribozyme is a catalytic RNA found within some natural isolates of Neurospora that is being used as a model system to improve our understanding of RNA structure, catalysis, and engineering. The catalytic domain contains five helical domains (SLII-SLVI) that are organized by two three-way junctions. The III-IV-V junction is required for high-affinity binding of the substrate domain (SLI) through formation of a kissing loop interaction with SLV. Here, we determine the high-resolution nuclear magnetic resonance (NMR) structure of a 47-nucleotide RNA containing the III-IV-V junction (J345). The J345 RNA adopts a Y-shaped fold typical of the family C three-way junctions, with coaxial stacking between stems III and IV and an acute angle between stems III and V. The NMR structure reveals that the core of the III-IV-V junction contains four stacked base triples, a U-turn motif, a cross-strand stacking interaction, an A-minor interaction, and a ribose zipper. In addition, the NMR structure shows that the cCUUGg tetraloop used to stabilize stem IV adopts a novel RNA tetraloop fold, different from the known gCUUGc tetraloop structure. Using Mn(2+)-induced paramagnetic relaxation enhancement, we identify six Mg(2+)-binding sites within J345, including one associated with the cCUUGg tetraloop and two with the junction core. The NMR structure of J345 likely represents the conformation of the III-IV-V junction in the context of the active VS ribozyme and suggests that this junction functions as a dynamic hinge that contributes to substrate recognition and catalysis. Moreover, this study highlights a new role for family C three-way junctions in long-range tertiary interactions.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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21
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A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing. Nature 2014; 515:591-5. [PMID: 25209668 DOI: 10.1038/nature13709] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023]
Abstract
To prime reverse transcription, retroviruses require annealing of a transfer RNA molecule to the U5 primer binding site (U5-PBS) region of the viral genome. The residues essential for primer annealing are initially locked in intramolecular interactions; hence, annealing requires the chaperone activity of the retroviral nucleocapsid (NC) protein to facilitate structural rearrangements. Here we show that, unlike classical chaperones, the Moloney murine leukaemia virus NC uses a unique mechanism for remodelling: it specifically targets multiple structured regions in both the U5-PBS and tRNA(Pro) primer that otherwise sequester residues necessary for annealing. This high-specificity and high-affinity binding by NC consequently liberates these sequestered residues--which are exactly complementary--for intermolecular interactions. Furthermore, NC utilizes a step-wise, entropy-driven mechanism to trigger both residue-specific destabilization and residue-specific release. Our structures of NC bound to U5-PBS and tRNA(Pro) reveal the structure-based mechanism for retroviral primer annealing and provide insights as to how ATP-independent chaperones can target specific RNAs amidst the cellular milieu of non-target RNAs.
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22
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Bernhardt HS, Sandwick RK. Purine biosynthetic intermediate-containing ribose-phosphate polymers as evolutionary precursors to RNA. J Mol Evol 2014; 79:91-104. [PMID: 25179142 DOI: 10.1007/s00239-014-9640-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/13/2014] [Indexed: 12/27/2022]
Abstract
The RNA world hypothesis proposes that RNA once functioned as the principal genetic material and biological catalyst. However, RNA is a complex molecule made up of phosphate, ribose, and nucleobase moieties, and its evolution is unclear. Yakhnin has proposed a period of prebiotic chemical evolution prior to the advent of replication and Darwinian evolution, in which macromolecules containing polyols joined by phosphodiester linkages underwent spontaneous transesterification reactions with selection for stability. Although he proposes that the nucleobases were obtained during this stage from less stable macromolecules, the ultimate source of the nucleobases is not addressed. We propose that the purine nucleobases arose in situ from simpler precursors attached to a ribose-phosphate backbone, and that the weaker and less specific intra- and interstrand interactions between these precursors were the forerunners to the base pairing and base stacking interactions of the modern RNA nucleobases. Further, in line with Granick's hypothesis of biosynthetic pathways recapitulating evolution, we propose that these simpler precursors were the same or similar to intermediates of the modern de novo purine biosynthetic pathway. We propose that successive nucleobase precursors formed progressively stronger interactions that stabilized the ribose-phosphate polymer, and that the increased stability of the parent polymer drove the selection and further chemical evolution of the purine nucleobases. Such interactions may have included hydrogen bonding between ribose hydroxyls, hydrogen bonding between carbonyl oxygens and protonated amine side groups, the intra- and interstrand coordination of metal cations, and the stacking of imidazole rings. Five of the eleven steps of the modern de novo purine biosynthetic pathway have previously been shown to have alternative nonenzymatic syntheses, while a sixth step has also been proposed to occur nonenzymatically, supporting a prebiotic origin for the pathway.
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Affiliation(s)
- Harold S Bernhardt
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand,
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23
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Devi G, Zhou Y, Zhong Z, Toh DFK, Chen G. RNA triplexes: from structural principles to biological and biotech applications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:111-28. [DOI: 10.1002/wrna.1261] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 06/30/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Yuan Zhou
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
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24
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Ribonucleotides as nucleotide excision repair substrates. DNA Repair (Amst) 2013; 13:55-60. [PMID: 24290807 DOI: 10.1016/j.dnarep.2013.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 11/22/2022]
Abstract
The incorporation of ribonucleotides in DNA has attracted considerable notice in recent years, since the pool of ribonucleotides can exceed that of the deoxyribonucleotides by at least 10-20-fold, and single ribonucleotide incorporation by DNA polymerases appears to be a common event. Moreover ribonucleotides are potentially mutagenic and lead to genome instability. As a consequence, errantly incorporated ribonucleotides are rapidly repaired in a process dependent upon RNase H enzymes. On the other hand, global genomic nucleotide excision repair (NER) in prokaryotes and eukaryotes removes damage caused by covalent modifications that typically distort and destabilize DNA through the production of lesions derived from bulky chemical carcinogens, such as polycyclic aromatic hydrocarbon metabolites, or via crosslinking. However, a recent study challenges this lesion-recognition paradigm. The work of Vaisman et al. (2013) [34] reveals that even a single ribonucleotide embedded in a deoxyribonucleotide duplex is recognized by the bacterial NER machinery in vitro. In their report, the authors show that spontaneous mutagenesis promoted by a steric-gate pol V mutant increases in uvrA, uvrB, or uvrC strains lacking rnhB (encoding RNase HII) and to a greater extent in an NER-deficient strain lacking both RNase HI and RNase HII. Using purified UvrA, UvrB, and UvrC proteins in in vitro assays they show that despite causing little distortion, a single ribonucleotide embedded in a DNA duplex is recognized and doubly-incised by the NER complex. We present the hypothesis to explain the recognition and/or verification of this small lesion, that the critical 2'-OH of the ribonucleotide - with its unique electrostatic and hydrogen bonding properties - may act as a signal through interactions with amino acid residues of the prokaryotic NER complex that are not possible with DNA. Such a mechanism might also be relevant if it were demonstrated that the eukaryotic NER machinery likewise incises an embedded ribonucleotide in DNA.
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25
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Abstract
RNA molecules are highly modular components that can be used in a variety of contexts for building new metabolic, regulatory and genetic circuits in cells. The majority of synthetic RNA systems to date predominately rely on two-dimensional modularity. However, a better understanding and integration of three-dimensional RNA modularity at structural and functional levels is critical to the development of more complex, functional bio-systems and molecular machines for synthetic biology applications.
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Affiliation(s)
- Wade Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University3307 Third Avenue West, Seattle, WA 98119USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Bio-Molecular Science and Engineering Program, University of CaliforniaSanta Barbara, CA 93106-9510USA
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26
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Appasamy SD, Ramlan EI, Firdaus-Raih M. Comparative sequence and structure analysis reveals the conservation and diversity of nucleotide positions and their associated tertiary interactions in the riboswitches. PLoS One 2013; 8:e73984. [PMID: 24040136 PMCID: PMC3764141 DOI: 10.1371/journal.pone.0073984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 07/25/2013] [Indexed: 12/17/2022] Open
Abstract
The tertiary motifs in complex RNA molecules play vital roles to either stabilize the formation of RNA 3D structure or to provide important biological functionality to the molecule. In order to better understand the roles of these tertiary motifs in riboswitches, we examined 11 representative riboswitch PDB structures for potential agreement of both motif occurrences and conservations. A total of 61 unique tertiary interactions were found in the reference structures. In addition to the expected common A-minor motifs and base-triples mainly involved in linking distant regions the riboswitch structures three highly conserved variants of A-minor interactions called G-minors were found in the SAM-I and FMN riboswitches where they appear to be involved in the recognition of the respective ligand’s functional groups. From our structural survey as well as corresponding structure and sequence alignments, the agreement between motif occurrences and conservations are very prominent across the representative riboswitches. Our analysis provide evidence that some of these tertiary interactions are essential components to form the structure where their sequence positions are conserved despite a high degree of diversity in other parts of the respective riboswitches sequences. This is indicative of a vital role for these tertiary interactions in determining the specific biological function of riboswitch.
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Affiliation(s)
- Sri D Appasamy
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
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27
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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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28
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Propensities for loop structures of RNA & DNA backbones. Biophys Chem 2013; 180-181:110-8. [PMID: 23933331 DOI: 10.1016/j.bpc.2013.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 11/21/2022]
Abstract
RNA oligonucleotides exhibit a large tendency to bend and form a loop conformation which is a major motif contributing to their complex three-dimensional structure. This is in contrast to DNA molecules that predominantly form the double-helix structure. In this paper we investigate by molecular dynamics simulation, as well as, by its combination with the replica-exchange method, the propensity of RNA chains containing the GCUAA pentaloop to form spontaneously a hairpin conformation. The results were then compared with those of analogous hybrid oligonucleotides in which the ribose groups in the loop-region were substituted by deoxyriboses. We find that the RNA oligomers exhibit a marginal excess stability to form loop structures. The equilibrium constant for opening the loop to an extended conformation is twice as large in the hybrid than it is in the RNA chain. Analyses of the hydrogen bonds indicate that the excess stability for forming a hairpin is a result of hydrogen bonds the 2'-hydroxyls in the loop region form with other groups in the loop. Of these hydrogen bonds, the most important is the hydrogen bond donated from the 2'-OH at the first position of the loop to N7 of adenine at the forth position. RNA and DNA backbones are characterized by different backbone dihedral angles and sugar puckering that can potentially facilitate or hamper the hydrogen bonds involving the 2'-OH. Nevertheless, the sugar puckerings of all the pentaloop nucleotides were not significantly different between the two chains displaying the C3'-endo conformation characteristic to the A-form double helix. All of the other backbone dihedrals also did not show any considerable difference in the loop-region except of the δ-dihedral. In this case, the RNA loop exhibited bimodal distributions corresponding to, both, the RNA and DNA backbones, whereas the loop of the hybrid chain behaved mostly as that of a DNA backbone. Thus, it is possible that the behavior of the δ-dihedrals in the loop-region of the RNA adopts conformations that facilitate the intra-nucleotide hydrogen bondings of the 2'-hydroxyls, and consequently renders loop structures in RNA more stable.
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29
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Kondo J, Dock-Bregeon AC, Willkomm DK, Hartmann RK, Westhof E. Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:634-9. [PMID: 23722840 PMCID: PMC3668581 DOI: 10.1107/s1744309113013018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/13/2013] [Indexed: 12/29/2022]
Abstract
In the course of a crystallographic study of a 132 nt variant of Aquifex aeolicus 6S RNA, a crystal structure of an A-form RNA duplex containing 12 base pairs was solved at a resolution of 2.6 Å. In fact, the RNA duplex is part of the 6S RNA and was obtained by accidental but precise degradation of the 6S RNA in a crystallization droplet. 6S RNA degradation was confirmed by microscopic observation of crystals and gel electrophoresis of crystallization droplets. The RNA oligomers obtained form regular A-form duplexes containing three GoU wobble-type base pairs, one of which engages in intermolecular contacts through a ribose-zipper motif at the crystal-packing interface.
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Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan.
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30
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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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31
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Paladino A, Zangi R. Ribose 2'-Hydroxyl Groups Stabilize RNA Hairpin Structures Containing GCUAA Pentaloop. J Chem Theory Comput 2013; 9:1214-21. [PMID: 26588764 DOI: 10.1021/ct3006216] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The chemical structure of RNA and DNA is very similar; however, the three-dimensional conformation of these two nucleic acids is very different. Whereas the DNA adopts a repetitive structure of a double-stranded helix, RNA is primarily single stranded with a complex three-dimensional structure in which the hairpin is the most common secondary structure. Apart from the difference between uracil and thymine, the difference in the chemical structure between RNA and DNA is the presence of a hydroxyl group at position 2' of the sugar (ribose) instead of a hydrogen (deoxyribose). In this paper, we present molecular dynamics simulations addressing the contribution of 2'-hydroxyls to the stability of a GCUAA pentaloop motif. The results indicate that the 2'-hydroxyls stabilize the hairpin conformation of the GCUAA pentaloop relative to an analogous oligonucleotide in which the ribose sugars in the loop region were substituted with deoxyriboses. The magnitude of the stabilization was found to be 23.8 ± 4.1 kJ/mol using an alchemical mutations free energy method and 4.2 ± 6.5 kJ/mol using potential of mean force calculations. The latter indicates that in addition to its larger thermodynamic stability the RNA hairpin is also kinetically more stable. We find that the excess stability is a result of intrahairpin hydrogen bonds in the loop region between the 2'-hydroxyls and sugars, bases, and phosphates. The hydrogen bonds with the sugars and phosphates involve predominantly interactions with adjacent nucleotides. However, the hydrogen bonds with the bases involve also interactions between groups on opposite sides of the loop or with the middle base of the loop and are therefore likely to contribute significantly to the stability of the loop. Of these hydrogen bonds, the most frequent is observed between the 2'-hydroxyl at the first position of the pentaloop with N6/N7 of adenine at the forth position, as well as between the 2'-hydroxyl at position -1 with N6 of adenine at the fifth position. Our results contribute to the notion that one of the important roles of the ribose sugars in RNA is to facilitate hairpin formation.
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Affiliation(s)
- Antonella Paladino
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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Wu L, Chai D, Fraser ME, Zimmerly S. Structural variation and uniformity among tetraloop-receptor interactions and other loop-helix interactions in RNA crystal structures. PLoS One 2012; 7:e49225. [PMID: 23152878 PMCID: PMC3494683 DOI: 10.1371/journal.pone.0049225] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 10/08/2012] [Indexed: 11/19/2022] Open
Abstract
Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48) were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the "standard" GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature.
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Affiliation(s)
- Li Wu
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Dinggeng Chai
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Steven Zimmerly
- Department of Biological Sciences, University of Calgary, Calgary, Canada
- * E-mail:
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Grabow WW, Zhuang Z, Swank ZN, Shea JE, Jaeger L. The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns. J Mol Biol 2012; 424:54-67. [PMID: 22999957 DOI: 10.1016/j.jmb.2012.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/11/2012] [Accepted: 09/12/2012] [Indexed: 12/16/2022]
Abstract
The right angle (RA) motif, previously identified in the ribosome and used as a structural module for nano-construction, is a recurrent structural motif of 13 nucleotides that establishes a 90° bend between two adjacent helices. Comparative sequence analysis was used to explore the sequence space of the RA motif within ribosomal RNAs in order to define its canonical sequence space signature. We investigated the sequence constraints associated with the RA signature using several artificial self-assembly systems. Thermodynamic and topological investigations of sequence variants associated with the RA motif in both minimal and expanded structural contexts reveal that the presence of a helix at the 3' end of the RA motif increases the thermodynamic stability and rigidity of the resulting three-helix junction domain. A search for the RA in naturally occurring RNAs as well as its experimental characterization led to the identification of the RA in groups IC1 and ID intron ribozymes, where it is suggested to play an integral role in stabilizing peripheral structural domains. The present study exemplifies the need of empirical analysis of RNA structural motifs for facilitating the rational design and structure prediction of RNAs.
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Affiliation(s)
- Wade W Grabow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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Hamdani HY, Appasamy SD, Willett P, Artymiuk PJ, Firdaus-Raih M. NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. Nucleic Acids Res 2012; 40:W35-41. [PMID: 22661578 PMCID: PMC3394293 DOI: 10.1093/nar/gks513] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph’s nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/.
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Affiliation(s)
- Hazrina Y Hamdani
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
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Butcher SE, Pyle AM. The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc Chem Res 2011; 44:1302-11. [PMID: 21899297 DOI: 10.1021/ar200098t] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA molecules adopt specific three-dimensional structures critical to their function. Many essential metabolic processes, including protein synthesis and RNA splicing, are carried out by RNA molecules with elaborate tertiary structures (e.g. 3QIQ, right). Indeed, the ribosome and self-splicing introns are complex RNA machines. But even the coding regions in messenger RNAs and viral RNAs are flanked by highly structured untranslated regions, which provide regulatory information necessary for gene expression. RNA tertiary structure is defined as the three-dimensional arrangement of RNA building blocks, which include helical duplexes, triple-stranded structures, and other components that are held together through connections collectively termed RNA tertiary interactions. The structural diversity of these interactions is now a subject of intense investigation, involving the techniques of NMR, X-ray crystallography, chemical genetics, and phylogenetic analysis. At the same time, many investigators are using biophysical techniques to elucidate the driving forces for tertiary structure formation and the mechanisms for its stabilization. RNA tertiary folding is promoted by maximization of base stacking, much like the hydrophobic effect that drives protein folding. RNA folding also requires electrostatic stabilization, both through charge screening and site binding of metals, and it is enhanced by desolvation of the phosphate backbone. In this Account, we provide an overview of the features that specify and stabilize RNA tertiary structure. A major determinant for overall tertiary RNA architecture is local conformation in secondary-structure junctions, which are regions from which two or more duplexes project. At junctions and other structures, such as pseudoknots and kissing loops, adjacent helices stack on one another, and these coaxial stacks play a major role in dictating the overall architectural form of an RNA molecule. In addition to RNA junction topology, a second determinant for RNA tertiary structure is the formation of sequence-specific interactions. Networks of triple helices, tetraloop-receptor interactions, and other sequence-specific contacts establish the framework for the overall tertiary fold. The third determinant of tertiary structure is the formation of stabilizing stacking and backbone interactions, and many are not sequence specific. For example, ribose zippers allow 2'-hydroxyl groups on different RNA strands to form networks of interdigitated hydrogen bonds, serving to seal strands together and thereby stabilize adjacent substructures. These motifs often require monovalent and divalent cations, which can interact diffusely or through chelation to specific RNA functional groups. As we learn more about the components of RNA tertiary structure, we will be able to predict the structures of RNA molecules from their sequences, thereby obtaining key information about biological function. Understanding and predicting RNA structure is particularly important given the recent discovery that although most of our genome is transcribed into RNA molecules, few of them have a known function. The prevalence of RNA viruses and pathogens with RNA genomes makes RNA drug discovery an active area of research. Finally, knowledge of RNA structure will facilitate the engineering of supramolecular RNA structures, which can be used as nanomechanical components for new materials. But all of this promise depends on a better understanding of the RNA parts list, and how the pieces fit together.
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Affiliation(s)
- Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin—Madison, 433 Babcock
Drive, Madison, Wisconsin 53706-1544, United States
| | - Anna Marie Pyle
- Department of Molecular, Cellular
and Developmental Biology and Department of Chemistry, Yale University, New Haven, Connecticut, United States
- Howard Hughes Medical Institute
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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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Abstract
Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (η and θ, analogous to φ and ψ in proteins). When these torsion angles are calculated for nucleotides in a crystallographic database and plotted against one another, one obtains a plot analogous to a Ramachandran plot (the η/θ plot), with highly populated and unpopulated regions. Nucleotides that occupy proximal positions on the plot have identical structures and are found in the same units of tertiary structure. In this review, we describe the statistical validation of the η/θ formalism and the exploration of features within the η/θ plot. We also describe the application of the η/θ formalism in RNA motif discovery, structural comparison, RNA structure building and tertiary structure prediction. More than a tool, however, the η/θ formalism has provided new insights into RNA structure itself, revealing its fundamental components and the factors underlying RNA architectural form.
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Šponer J, Šponer JE, Petrov AI, Leontis NB. Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J Phys Chem B 2010; 114:15723-41. [PMID: 21049899 PMCID: PMC4868365 DOI: 10.1021/jp104361m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics. Our main aim is to demonstrate that these research areas, while largely separated in contemporary literature, have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids. We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches. The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Anton I. Petrov
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
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Pyle AM. The tertiary structure of group II introns: implications for biological function and evolution. Crit Rev Biochem Mol Biol 2010; 45:215-32. [PMID: 20446804 DOI: 10.3109/10409231003796523] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Group II introns are some of the largest ribozymes in nature, and they are a major source of information about RNA assembly and tertiary structural organization. These introns are of biological significance because they are self-splicing mobile elements that have migrated into diverse genomes and played a major role in the genomic organization and metabolism of most life forms. The tertiary structure of group II introns has been the subject of many phylogenetic, genetic, biochemical and biophysical investigations, all of which are consistent with the recent crystal structure of an intact group IIC intron from the alkaliphilic eubacterium Oceanobacillus iheyensis. The crystal structure reveals that catalytic intron domain V is enfolded within the other intronic domains through an elaborate network of diverse tertiary interactions. Within the folded core, DV adopts an activated conformation that readily binds catalytic metal ions and positions them in a manner appropriate for reaction with nucleic acid targets. The tertiary structure of the group II intron reveals new information on motifs for RNA architectural organization, mechanisms of group II intron catalysis, and the evolutionary relationships among RNA processing systems. Guided by the structure and the wealth of previous genetic and biochemical work, it is now possible to deduce the probable location of DVI and the site of additional domains that contribute to the function of the highly derived group IIB and IIA introns.
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Affiliation(s)
- Anna Marie Pyle
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute and Yale University, New Haven, CT, USA.
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Banáš P, Walter NG, Šponer J, Otyepka M. Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. J Phys Chem B 2010; 114:8701-12. [PMID: 20536206 PMCID: PMC2900856 DOI: 10.1021/jp9109699] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The glmS catalytic riboswitch is part of the 5'-untranslated region of mRNAs encoding glucosamine-6-phosphate (GlcN6P) synthetase (glmS) in numerous gram-positive bacteria. Binding of the cofactor GlcN6P induces site-specific self-cleavage of the RNA. However, the detailed reaction mechanism as well as the protonation state of the glmS reactive form still remains elusive. To probe the dominant protonation states of key active site residues, we carried out explicit solvent molecular dynamic simulations involving various protonation states of three crucial active site moieties observed in the available crystal structures: (i) guanine G40 (following the Thermoanaerobacter tengcongensis numbering), (ii) the GlcN6P amino/ammonium group, and (iii) the GlcN6P phosphate moiety. We found that a deprotonated G40(-) seems incompatible with the observed glmS active site architecture. Our data suggest that the canonical form of G40 plays a structural role by stabilizing an in-line attack conformation of the cleavage site A-1(2'-OH) nucleophile, rather than a more direct chemical role. In addition, we observe weakened cofactor binding upon protonation of the GlcN6P phosphate moiety, which explains the experimentally observed increase in K(m) with decreasing pH. Finally, we discuss a possible role of cofactor binding and its interaction with the G65 and G1 purines in structural stabilization of the A-1(2'-OH) in-line attack conformation. On the basis of the identified dominant protonation state of the reaction precursor, we propose a hypothesis of the self-cleavage mechanism in which A-1(2'-OH) is activated as a nucleophile by the G1(pro-R(p)) nonbridging oxygen of the scissile phosphate, whereas the ammonium group of GlcN6P acts as the general acid protonating the G1(O5') leaving group.
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Affiliation(s)
- Pavel Banáš
- Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic; fax +420 585634761,
- Institute of Biophysics, Academy of Sciences of the Czech republic, Kralovopolska 135, 612 65 Brno, Czech Republic; phone: +420 541517133,
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA
| | - Jiří Šponer
- Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic; fax +420 585634761,
- Institute of Biophysics, Academy of Sciences of the Czech republic, Kralovopolska 135, 612 65 Brno, Czech Republic; phone: +420 541517133,
| | - Michal Otyepka
- Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic; fax +420 585634761,
- Institute of Biophysics, Academy of Sciences of the Czech republic, Kralovopolska 135, 612 65 Brno, Czech Republic; phone: +420 541517133,
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Capriotti E, Marti-Renom MA. Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. BMC Bioinformatics 2010; 11:322. [PMID: 20550657 PMCID: PMC2904352 DOI: 10.1186/1471-2105-11-322] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 06/15/2010] [Indexed: 11/17/2022] Open
Abstract
Background In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. Results Here we introduce an all-against-all sequence- and three-dimensional (3D) structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii) evolution tends to conserve more RNA structure than sequence, and (iii) there is a twilight zone for RNA homology detection. Discussion The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction.
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Affiliation(s)
- Emidio Capriotti
- Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
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Besseová I, Réblová K, Leontis NB, Sponer J. Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res 2010; 38:6247-64. [PMID: 20507916 PMCID: PMC2952862 DOI: 10.1093/nar/gkq414] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We present extensive explicit solvent molecular dynamics analysis of three RNA three-way junctions (3WJs) from the large ribosomal subunit: the 3WJ formed by Helices 90–92 (H90–H92) of 23S rRNA; the 3WJ formed by H42–H44 organizing the GTPase associated center (GAC) of 23S rRNA; and the 3WJ of 5S rRNA. H92 near the peptidyl transferase center binds the 3′-CCA end of amino-acylated tRNA. The GAC binds protein factors and stimulates GTP hydrolysis driving protein synthesis. The 5S rRNA binds the central protuberance and A-site finger (ASF) involved in bridges with the 30S subunit. The simulations reveal that all three 3WJs possess significant anisotropic hinge-like flexibility between their stacked stems and dynamics within the compact regions of their adjacent stems. The A-site 3WJ dynamics may facilitate accommodation of tRNA, while the 5S 3WJ flexibility appears to be essential for coordinated movements of ASF and 5S rRNA. The GAC 3WJ may support large-scale dynamics of the L7/L12-stalk region. The simulations reveal that H42–H44 rRNA segments are not fully relaxed and in the X-ray structures they are bent towards the large subunit. The bending may be related to L10 binding and is distributed between the 3WJ and the H42–H97 contact.
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Affiliation(s)
- Ivana Besseová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
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Lu XJ, Olson WK, Bussemaker HJ. The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. Nucleic Acids Res 2010; 38:4868-76. [PMID: 20223772 PMCID: PMC2919703 DOI: 10.1093/nar/gkq155] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The side-by-side interactions of nucleobases contribute to the organization of RNA, forming the planar building blocks of helices and mediating chain folding. Dinucleotide platforms, formed by side-by-side pairing of adjacent bases, frequently anchor helices against loops. Surprisingly, GpU steps account for over half of the dinucleotide platforms observed in RNA-containing structures. Why GpU should stand out from other dinucleotides in this respect is not clear from the single well-characterized H-bond found between the guanine N2 and the uracil O4 groups. Here, we describe how an RNA-specific H-bond between O2′(G) and O2P(U) adds to the stability of the GpU platform. Moreover, we show how this pair of oxygen atoms forms an out-of-plane backbone ‘edge’ that is specifically recognized by a non-adjacent guanine in over 90% of the cases, leading to the formation of an asymmetric miniduplex consisting of ‘complementary’ GpUpA and GpA subunits. Together, these five nucleotides constitute the conserved core of the well-known loop-E motif. The backbone-mediated intrinsic stabilities of the GpU dinucleotide platform and the GpUpA/GpA miniduplex plausibly underlie observed evolutionary constraints on base identity. We propose that they may also provide a reason for the extreme conservation of GpU observed at most 5′-splice sites.
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Affiliation(s)
- Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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Ulyanov NB, James TL. RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA. NEW J CHEM 2010; 34:910-917. [PMID: 20689681 DOI: 10.1039/b9nj00754g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The growing number of high-resolution crystal structures of large RNA molecules provides much information for understanding the principles of structural organization of these complex molecules. Several in-depth analyses of nucleobase-centered RNA structural motifs and backbone conformations have been published based on this information, including a systematic classification of base pairs by Leontis and Westhof. However, hydrogen bonds involving sugar-phosphate backbone atoms of RNA have not been analyzed systematically until recently, although such hydrogen bonds appear to be common both in local and tertiary interactions. Here we review some backbone structural motifs discussed in the literature and analyze a set of eight high-resolution multi-domain RNA structures. The analyzed RNAs are highly structured: among 5372 nucleotides in this set, 89% are involved in at least one "long-range" RNA-RNA hydrogen bond, i.e., hydrogen bonds between atoms in the same residue or sequential residues are ignored. These long-range hydrogen bonds frequently use backbone atoms as hydrogen bond acceptors, i.e., OP1, OP2, O2', O3', O4', or O5', or as a donor (2'OH). A surprisingly large number of such hydrogen bonds are found, considering that neither single-stranded nor double-stranded regions will contain such hydrogen bonds unless additional interactions with other residues exist. Among 8327 long-range hydrogen bonds found in this set of structures, 2811, or about one-third, are hydrogen bonds entailing RNA backbone atoms; they involve 39% of all nucleotides in the structures. The majority of them (2111) are hydrogen bonds entailing ribose hydroxyl groups, which can be used either as a donor or an acceptor; they constitute 25% of all hydrogen bonds and involve 31% of all nucleotides. The phosphate oxygens OP1 or OP2 are used as hydrogen bond acceptors in 12% of all nucleotides, and the ribose ring oxygen O4' and phosphodiester oxygens O3' and O5' are used in 4%, 4%, and 1% of all nucleotides, respectively. Distributions of geometric parameters and some examples of such hydrogen bonds are presented in this report. A novel motif involving backbone hydrogen bonds, the ribose-phosphate zipper, is also identified.
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Affiliation(s)
- Nikolai B Ulyanov
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517, USA
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Laing C, Jung S, Iqbal A, Schlick T. Tertiary motifs revealed in analyses of higher-order RNA junctions. J Mol Biol 2009; 393:67-82. [PMID: 19660472 DOI: 10.1016/j.jmb.2009.07.089] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/29/2009] [Accepted: 07/29/2009] [Indexed: 12/22/2022]
Abstract
RNA junctions are secondary-structure elements formed when three or more helices come together. They are present in diverse RNA molecules with various fundamental functions in the cell. To better understand the intricate architecture of three-dimensional (3D) RNAs, we analyze currently solved 3D RNA junctions in terms of base-pair interactions and 3D configurations. First, we study base-pair interaction diagrams for solved RNA junctions with 5 to 10 helices and discuss common features. Second, we compare these higher-order junctions to those containing 3 or 4 helices and identify global motif patterns such as coaxial stacking and parallel and perpendicular helical configurations. These analyses show that higher-order junctions organize their helical components in parallel and helical configurations similar to lower-order junctions. Their sub-junctions also resemble local helical configurations found in three- and four-way junctions and are stabilized by similar long-range interaction preferences such as A-minor interactions. Furthermore, loop regions within junctions are high in adenine but low in cytosine, and in agreement with previous studies, we suggest that coaxial stacking between helices likely forms when the common single-stranded loop is small in size; however, other factors such as stacking interactions involving noncanonical base pairs and proteins can greatly determine or disrupt coaxial stacking. Finally, we introduce the ribo-base interactions: when combined with the along-groove packing motif, these ribo-base interactions form novel motifs involved in perpendicular helix-helix interactions. Overall, these analyses suggest recurrent tertiary motifs that stabilize junction architecture, pack helices, and help form helical configurations that occur as sub-elements of larger junction networks. The frequent occurrence of similar helical motifs suggest nature's finite and perhaps limited repertoire of RNA helical conformation preferences. More generally, studies of RNA junctions and tertiary building blocks can ultimately help in the difficult task of RNA 3D structure prediction.
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Affiliation(s)
- Christian Laing
- Department of Chemistry, New York University, 251 Mercer Street, New York, NY 10012, USA
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Šponer J, Zgarbová M, Jurečka P, Riley KE, Šponer JE, Hobza P. Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose. J Chem Theory Comput 2009; 5:1166-79. [DOI: 10.1021/ct800547k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Marie Zgarbová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Petr Jurečka
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Kevin E. Riley
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
| | - Pavel Hobza
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto
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Kazantsev AV, Krivenko AA, Pace NR. Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA. RNA (NEW YORK, N.Y.) 2009; 15:266-76. [PMID: 19095619 PMCID: PMC2648716 DOI: 10.1261/rna.1331809] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein enzyme that contains a universally conserved, catalytically active RNA component. RNase P RNA requires divalent metal ions for folding, substrate binding, and catalysis. Despite recent advances in understanding the structure of RNase P RNA, no comprehensive analysis of metal-binding sites has been reported, in part due to the poor crystallization properties of this large RNA. We have developed an abbreviated yet still catalytic construct, Bst P7Delta RNA, which contains the catalytic domain of the bacterial RNase P RNA and has improved crystallization properties. We use this mutant RNA as well as the native RNA to map metal-binding sites in the catalytic core of the bacterial RNase P RNA, by anomalous scattering in diffraction analysis. The results provide insight into the interplay between RNA structure and focalization of metal ions, and a structural basis for some previous biochemical observations with RNase P. We use electrostatic calculations to extract the potential functional significance of these metal-binding sites with respect to binding Mg(2+). The results suggest that with at least one important exception of specific binding, these sites mainly map areas of diffuse association of magnesium ions.
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Affiliation(s)
- Alexei V Kazantsev
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, 80309, USA
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Barría MI, González A, Vera-Otarola J, León U, Vollrath V, Marsac D, Monasterio O, Pérez-Acle T, Soza A, López-Lastra M. Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation. Nucleic Acids Res 2008; 37:957-71. [PMID: 19106142 PMCID: PMC2647302 DOI: 10.1093/nar/gkn1022] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The HCV internal ribosome entry site (IRES) spans a region of ∼340 nt that encompasses most of the 5′ untranslated region (5′UTR) of the viral mRNA and the first 24–40 nt of the core-coding region. To investigate the implication of altering the primary sequence of the 5′UTR on IRES activity, naturally occurring variants of the 5′UTR were isolated from clinical samples and analyzed. The impact of the identified mutations on translation was evaluated in the context of RLuc/FLuc bicistronic RNAs. Results show that depending on their location within the RNA structure, these naturally occurring mutations cause a range of effects on IRES activity. However, mutations within subdomain IIId hinder HCV IRES-mediated translation. In an attempt to explain these data, the dynamic behavior of the subdomain IIId was analyzed by means of molecular dynamics (MD) simulations. Despite the loss of function, MD simulations predicted that mutant G266A/G268U possesses a structure similar to the wt-RNA. This prediction was validated by analyzing the secondary structure of the isolated IIId RNAs by circular dichroism spectroscopy in the presence or absence of Mg2+ ions. These data strongly suggest that the primary sequence of subdomain IIId plays a key role in HCV IRES-mediated translation.
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Affiliation(s)
- María Inés Barría
- Laboratorio de Virología Molecular, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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