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1.
Nucleic Acids Res ; 49(17): 9625-9632, 2021 09 27.
Artigo em Inglês | MEDLINE | ID: mdl-34432024

RESUMO

Computational methods to predict RNA 3D structure have more and more practical applications in molecular biology and medicine. Therefore, it is crucial to intensify efforts to improve the accuracy and quality of predicted three-dimensional structures. A significant role in this is played by the RNA-Puzzles initiative that collects, evaluates, and shares RNAs built computationally within currently nearly 30 challenges. RNA-Puzzles datasets, subjected to multi-criteria analysis, allow revealing the strengths and weaknesses of computer prediction methods. Here, we study the issue of entangled RNA fragments in the predicted RNA 3D structure models. By entanglement, we mean an arrangement of two structural elements such that one of them passes through the other. We propose the classification of entanglements driven by their topology and components. It distinguishes two general classes, interlaces and lassos, and subclasses characterized by element types-loops, dinucleotide steps, open single-stranded fragments-and puncture multiplicity. Our computational pipeline for entanglement detection, applied for 1,017 non-redundant models from RNA-Puzzles, has shown the frequency of different entanglements and allowed identifying 138 structures with intersected assemblies.


Assuntos
Modelos Moleculares , RNA/química , Biologia Computacional , Conformação de Ácido Nucleico
2.
RNA ; 26(8): 982-995, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32371455

RESUMO

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of 3D structures for six RNA sequences: four nucleolytic ribozymes and two riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss (i) the comparison between the automated web servers and human experts; (ii) the prediction of coaxial stacking; (iii) the prediction of structural details and ligand binding; (iv) the development of novel prediction methods; and (v) the potential improvements to be made. We show that correct prediction of coaxial stacking and tertiary contacts is essential for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution and simultaneous prediction of RNA structure with accurate ligand binding still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.


Assuntos
Aptâmeros de Nucleotídeos/química , RNA Catalítico/química , RNA/química , Sequência de Bases , Ligantes , Conformação de Ácido Nucleico , Riboswitch/genética
3.
Int J Mol Sci ; 23(17)2022 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-36077037

RESUMO

RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5'- and 3'-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.


Assuntos
COVID-19 , RNA , Regiões 3' não Traduzidas , Humanos , Conformação de Ácido Nucleico , RNA/química , SARS-CoV-2
4.
Nucleic Acids Res ; 46(W1): W30-W35, 2018 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-29718468

RESUMO

In the field of RNA structural biology and bioinformatics, an access to correctly annotated RNA structure is of crucial importance, especially in the secondary and 3D structure predictions. RNApdbee webserver, introduced in 2014, primarily aimed to address the problem of RNA secondary structure extraction from the PDB files. Its new version, RNApdbee 2.0, is a highly advanced multifunctional tool for RNA structure annotation, revealing the relationship between RNA secondary and 3D structure given in the PDB or PDBx/mmCIF format. The upgraded version incorporates new algorithms for recognition and classification of high-ordered pseudoknots in large RNA structures. It allows analysis of isolated base pairs impact on RNA structure. It can visualize RNA secondary structures-including that of quadruplexes-with depiction of non-canonical interactions. It also annotates motifs to ease identification of stems, loops and single-stranded fragments in the input RNA structure. RNApdbee 2.0 is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.


Assuntos
Biologia Computacional , Internet , RNA/genética , Software , Algoritmos , Pareamento de Bases/genética , Bases de Dados de Ácidos Nucleicos , Conformação de Ácido Nucleico , Estrutura Secundária de Proteína/genética , RNA/química
5.
RNA ; 23(5): 655-672, 2017 05.
Artigo em Inglês | MEDLINE | ID: mdl-28138060

RESUMO

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.


Assuntos
RNA Catalítico/química , Riboswitch , Aminoimidazol Carboxamida/química , Aminoimidazol Carboxamida/metabolismo , Aptâmeros de Nucleotídeos/química , Aptâmeros de Nucleotídeos/metabolismo , Fosfatos de Dinucleosídeos/metabolismo , Endorribonucleases/química , Endorribonucleases/metabolismo , Glutamina/química , Glutamina/metabolismo , Ligantes , Modelos Moleculares , Conformação de Ácido Nucleico , RNA Catalítico/metabolismo , Ribonucleotídeos/química , Ribonucleotídeos/metabolismo , S-Adenosilmetionina/química , S-Adenosilmetionina/metabolismo
6.
Bioinformatics ; 34(8): 1304-1312, 2018 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-29236971

RESUMO

Motivation: Understanding the formation, architecture and roles of pseudoknots in RNA structures are one of the most difficult challenges in RNA computational biology and structural bioinformatics. Methods predicting pseudoknots typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ in terms of pseudoknots' recognition and revealing their nature. A few ways of pseudoknot classification exist, most common ones refer to a genus or order. Following the latter one, we propose new algorithms that identify pseudoknots in RNA structure provided in BPSEQ format, determine their order and encode in dot-bracket-letter notation. The proposed encoding aims to illustrate the hierarchy of RNA folding. Results: New algorithms are based on dynamic programming and hybrid (combining exhaustive search and random walk) approaches. They evolved from elementary algorithm implemented within the workflow of RNA FRABASE 1.0, our database of RNA structure fragments. They use different scoring functions to rank dissimilar dot-bracket representations of RNA structure. Computational experiments show an advantage of new methods over the others, especially for large RNA structures. Availability and implementation: Presented algorithms have been implemented as new functionality of RNApdbee webserver and are ready to use at http://rnapdbee.cs.put.poznan.pl. Contact: mszachniuk@cs.put.poznan.pl. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Algoritmos , Conformação de Ácido Nucleico , Dobramento de RNA , RNA/metabolismo , Análise de Sequência de RNA/métodos , Biologia Computacional/métodos , Bases de Dados Factuais , Humanos , Modelos Moleculares , RNA/química
7.
BMC Bioinformatics ; 19(1): 304, 2018 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-30134831

RESUMO

BACKGROUND: Computational RNA 3D structure prediction and modeling are rising as complementary approaches to high-resolution experimental techniques for structure determination. They often apply to substitute or complement them. Recently, researchers' interests have directed towards in silico methods to fit, remodel and refine RNA tertiary structure models. Their power lies in a problem-specific exploration of RNA conformational space and efficient optimization procedures. The aim is to improve the accuracy of models obtained either computationally or experimentally. RESULTS: Here, we present RNAfitme, a versatile webserver tool for remodeling of nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structures. Our approach makes use of dedicated libraries that define RNA conformational space. They have been built upon torsional angle characteristics of PDB-deposited RNA structures. RNAfitme can be applied to reconstruct full-atom model of RNA from its backbone; remodel user-selected nucleobase/nucleoside residues in a given RNA structure; predict RNA 3D structure based on the sequence and the template of a homologous molecule of the same size; refine RNA 3D model by reducing steric clashes indicated during structure quality assessment. RNAfitme is a publicly available tool with an intuitive interface. It is freely accessible at http://rnafitme.cs.put.poznan.pl/ CONCLUSIONS: RNAfitme has been applied in various RNA 3D remodeling scenarios for several types of input data. Computational experiments proved its efficiency, accuracy, and usefulness in the processing of RNAs of any size. Fidelity of RNAfitme predictions has been thoroughly tested for RNA 3D structures determined experimentally and modeled in silico.


Assuntos
Internet , Conformação de Ácido Nucleico , Nucleosídeos/genética , RNA/química , RNA/genética , Software , Algoritmos , Sequência de Bases , Glutamina/química , Modelos Moleculares , Motivos de Nucleotídeos , RNA de Transferência/química , RNA de Transferência/genética , Análise de Sequência de RNA
8.
RNA ; 21(6): 1066-84, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25883046

RESUMO

This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5-3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson-Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/.


Assuntos
Biologia Computacional/métodos , RNA/química , Cristalografia por Raios X , Modelos Moleculares , Conformação de Ácido Nucleico , RNA Mensageiro/química , RNA de Transferência/química , Software
9.
Methods ; 103: 120-7, 2016 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-27016145

RESUMO

RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary structure is fundamental to understand RNA functions beginning with transcription and ending with turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy when experimental data are integrated into the prediction, tertiary structure prediction of large RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is rapidly developing and new computational methods based on different strategies are emerging. RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500 nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary structure specified by the user. Importantly, this method allows incorporation of distance restraints derived from the experimental data to strengthen the 3D predictions. The potential and limitations of RNAComposer are discussed and an application to RNA design for nanotechnology is presented.


Assuntos
RNA/química , Software , Algoritmos , Simulação por Computador , Modelos Moleculares , Nanotecnologia , Conformação de Ácido Nucleico
10.
Nucleic Acids Res ; 43(W1): W502-6, 2015 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-26068469

RESUMO

Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of 3D models has a fundamental impact on the progress of structural bioinformatics. Here, we present RNAssess server, a novel tool dedicated to visual evaluation of RNA 3D models in the context of the known reference structure for a wide range of accuracy levels (from atomic to the whole molecule perspective). The proposed server is based on the concept of local neighborhood, defined as a set of atoms observed within a sphere localized around a central atom of a particular residue. A distinctive feature of our server is the ability to perform simultaneous visual analysis of the model-reference structure coherence. RNAssess supports the quality assessment through delivering both static and interactive visualizations that allows an easy identification of native-like models and/or chosen structural regions of the analyzed molecule. A combination of results provided by RNAssess allows us to rank analyzed models. RNAssess offers new route to a fast and efficient 3D model evaluation suitable for the RNA-Puzzles challenge. The proposed automated tool is implemented as a free and open to all users web server with an user-friendly interface and can be accessed at: http://rnassess.cs.put.poznan.pl/.


Assuntos
Modelos Moleculares , RNA/química , Software , Internet , Conformação de Ácido Nucleico , Análise de Sequência de RNA
11.
Retrovirology ; 13: 18, 2016 Mar 17.
Artigo em Inglês | MEDLINE | ID: mdl-26987314

RESUMO

BACKGROUND: The Gag polyprotein is a multifunctional regulator of retroviral replication and major structural component of immature virions. The nucleic acid chaperone (NAC) activity is considered necessary to retroviral Gag functions, but so far, NAC activity has only been confirmed for HIV-1 and RSV Gag polyproteins. The nucleocapsid (NC) domain of Gag is proposed to be crucial for interactions with nucleic acids and NAC activity. The major function of matrix (MA) domain is targeting and binding of Gag to the plasma membrane but MA can also interact with RNA and influence NAC activity of Gag. Here, we characterize RNA binding properties and NAC activity of HIV-2 MA and Gag, lacking p6 domain (GagΔp6) and discuss potential contribution of NC and MA domains to HIV-2 GagΔp6 functions and interactions with RNA. RESULTS: We found that HIV-2 GagΔp6 is a robust nucleic acid chaperone. HIV-2 MA protein promotes nucleic acids aggregation and tRNA(Lys3) annealing in vitro. The NAC activity of HIV-2 NC is affected by salt which is in contrast to HIV-2 GagΔp6 and MA. At a physiological NaCl concentration the tRNA(Lys3) annealing activity of HIV-2 GagΔp6 or MA is higher than HIV-2 NC. The HIV-2 NC and GagΔp6 show strong binding to the packaging signal (Ψ) of HIV-2 RNA and preference for the purine-rich sequences, while MA protein binds mainly to G residues without favouring Ψ RNA. Moreover, HIV-2 GagΔp6 and NC promote HIV-2 RNA dimerization while our data do not support MA domain participation in this process in vitro. CONCLUSIONS: We present that contrary to HIV-1 MA, HIV-2 MA displays NAC activity and we propose that MA domain may enhance the activity of HIV-2 GagΔp6. The role of the MA domain in the NAC activity of Gag may differ significantly between HIV-1 and HIV-2. The HIV-2 NC and MA interactions with RNA are not equivalent. Even though both NC and MA can facilitate tRNA(Lys3) annealing, MA does not participate in RNA dimerization in vitro. Our data on HIV-2 indicate that the role of the MA domain in the NAC activity of Gag differs not only between, but also within, retroviral genera.


Assuntos
HIV-2/fisiologia , Chaperonas Moleculares/metabolismo , RNA Viral/metabolismo , Proteínas de Ligação a RNA/metabolismo , Produtos do Gene gag do Vírus da Imunodeficiência Humana/metabolismo , Humanos , Concentração Osmolar , RNA de Transferência de Lisina/metabolismo , Cloreto de Sódio/metabolismo
12.
Nucleic Acids Res ; 42(Web Server issue): W368-72, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24771339

RESUMO

In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee-a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.


Assuntos
RNA/química , Software , Pareamento de Bases , Internet , Conformação de Ácido Nucleico
13.
Nucleic Acids Res ; 41(12): 5978-90, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23620294

RESUMO

The continuously increasing amount of RNA sequence and experimentally determined 3D structure data drives the development of computational methods supporting exploration of these data. Contemporary functional analysis of RNA molecules, such as ribozymes or riboswitches, covers various issues, among which tertiary structure modeling becomes more and more important. A growing number of tools to model and predict RNA structure calls for an evaluation of these tools and the quality of outcomes their produce. Thus, the development of reliable methods designed to meet this need is relevant in the context of RNA tertiary structure analysis and can highly influence the quality and usefulness of RNA tertiary structure prediction in the nearest future. Here, we present RNAlyzer-a computational method for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models. Our approach is based on the idea of local neighborhood, defined as a set of atoms included in the sphere centered around a user-defined atom. A unique feature of the RNAlyzer is the simultaneous visualization of the model-reference structure distance at different levels of detail, from the individual residues to the entire molecules.


Assuntos
Modelos Moleculares , RNA/química , Software , Biologia Computacional/métodos , Conformação de Ácido Nucleico
14.
Nucleic Acids Res ; 40(14): e112, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22539264

RESUMO

Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.


Assuntos
Algoritmos , Modelos Moleculares , RNA/química , Bases de Dados de Ácidos Nucleicos , Internet , Conformação de Ácido Nucleico , RNA Ribossômico 5S/química , Retroelementos , Software
15.
Nucleic Acids Res ; 39(16): 7234-48, 2011 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-21622659

RESUMO

RNA dimerization is an essential step in the retroviral life cycle. Dimerization and encapsidation signals, closely linked in HIV-2, are located in the leader RNA region. The SL1 motif and nucleocapsid protein are considered important for both processes. In this study, we show the structure of the HIV-2 leader RNA (+1-560) captured as a loose dimer. Potential structural rearrangements within the leader RNA were studied. In the loose dimer form, the HIV-2 leader RNA strand exists in vitro as a single global fold. Two kissing loop interfaces within the loose dimer were identified: SL1/SL1 and TAR/TAR. Evidence for these findings is provided by RNA probing using SHAPE, chemical reagents, enzymes, non-denaturing PAGE mobility assays, antisense oligonucleotides hybridization and analysis of an RNA mutant. Both TAR and SL1 as isolated domains are bound by recombinant NCp8 protein with high affinity, contrary to the hairpins downstream of SL1. Foot-printing of the SL1/NCp8 complex indicates that the major binding site maps to the SL1 upper stem. Taken together, these data suggest a model in which TAR hairpin III, the segment of SL1 proximal to the loop and the PAL palindromic sequence play specific roles in the initiation of dimerization.


Assuntos
Regiões 5' não Traduzidas , HIV-2/genética , RNA Viral/química , Sítios de Ligação , Proteínas do Capsídeo/metabolismo , Dimerização , Conformação de Ácido Nucleico , RNA Viral/metabolismo , Proteínas de Ligação a RNA/metabolismo
16.
BMC Bioinformatics ; 11: 231, 2010 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-20459631

RESUMO

BACKGROUND: Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. DESCRIPTION: RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. CONCLUSIONS: RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.


Assuntos
Bases de Dados de Ácidos Nucleicos , Genômica/métodos , RNA/química , Software , Internet , Conformação de Ácido Nucleico , Análise de Sequência de RNA , Interface Usuário-Computador
17.
RNA ; 14(9): 1845-51, 2008 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-18658118

RESUMO

The structures of two crystal forms of the RNA 16-mer with the sequence GUGGUCUGAUGAGGCC, grown in the presence of a high concentration of sulphate ions, have been determined using synchrotron radiation at 1.4- and 2.0-A resolution. RNA with this sequence is known as one of the two strands of the noncleavable form of the hammerhead ribozyme. In both crystal structures, two G(syn)-G(anti) noncanonical base pairs are observed in the middle of a 14 base-pair (bp) duplex having 5'-dangling GU residues. Both structures contain sulphate anions interacting with the G-G bp stabilizing G in its syn conformation and bridging the two RNA strands. In both cases the interactions take place in the major groove, although the anions are accommodated within different helix geometries, most pronounced in the changing width of the major groove. In one structure, where a single sulphate spans both G-G pairs, the major groove is closed around the anion, while in the other structure, where each of the two G-G pairs is associated with a separate sulphate, the groove is open. This work provides the first examples of a G-G pair in syn-anti conformation, which minimizes the purine-purine clash in the center of the duplex, while utilizing its residual hydrogen bonding potential in specific interactions with sulphate anions.


Assuntos
Pareamento de Bases , Guanina/química , Oligorribonucleotídeos/química , RNA/química , Sulfatos/química , Ânions/química , Sequência de Bases , Cristalografia por Raios X , Conformação de Ácido Nucleico
18.
Nucleic Acids Res ; 36(Database issue): D386-91, 2008 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17921499

RESUMO

The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a 'dot-bracket' notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the 'dot-bracket' notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs. Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters. The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs. The RNA FRABASE is automatically, monthly updated and is freely accessible at http://rnafrabase.ibch.poznan.pl (mirror at http://cerber.cs.put.poznan.pl/rnadb).


Assuntos
Bases de Dados de Ácidos Nucleicos , RNA/química , Internet , Modelos Moleculares , Conformação de Ácido Nucleico , Análise de Sequência de RNA , Software , Interface Usuário-Computador
19.
Biochemistry ; 47(18): 5059-67, 2008 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-18399645

RESUMO

The RNA single bulge motif is an unpaired residue within a strand of several complementary base pairs. To gain insight into structural changes induced by the presence of the adenosine bulge on RNA duplex, the solution structures of RNA duplex containing a single adenine bulge (5'-GCAGAAGAGCG-3'/5'-CGCUCUCUGC-3') and a reference duplex with all Watson-Crick base pairs (5'-GCAGAGAGCG-3'/5'-CGCUCUCUGC-3') have been determined by NMR spectroscopy. The reference duplex structure is a regular right-handed helix with all of the attributes of an A-type helix. In the bulged duplex, single adenine bulge stacks into the helix, and the bulge region forms a well-defined structure. Both structures were analyzed by the use of calculated helical parameters. Distortions induced by the accommodation of unpaired residue into the helical structure propagate over the entire structure and are manifested as the reduced base pairs inclination and x-displacement. Intrahelical position of bulged adenine A5 is stabilized by efficient stacking with 5'-neighboring residues G4.


Assuntos
Adenosina/química , Conformação de Ácido Nucleico , RNA de Cadeia Dupla/química , Sequência de Bases , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Soluções
20.
Nucleic Acids Res ; 34(10): 2984-97, 2006.
Artigo em Inglês | MEDLINE | ID: mdl-16738137

RESUMO

The HIV-2 TAR RNA domain (TAR-2) plays a key role in the trans-activation of HIV-2 transcription as it is the target for the Tat-2 protein and several cell factors. Here, we show that the TAR-2 domain exists in vitro in two global, alternative forms: a new, extended hairpin form with two conformers and the already proposed branched hairpins form. This points strongly to the structural polymorphism of the 5' end of the HIV-2 leader RNA. The evidence comes from the non-denaturing PAGE mobility assay, 2D structure prediction, enzymatic and Pb2+- or Mg2+-induced RNA cleavages. Existence of the TAR-2 extended form was further proved by the examination of engineered TAR-2 mutants stabilized either in the branched or extended structure. The TAR-2 extended form predominates with an increasing magnesium concentration. Gel retardation assays reveal that both TAR-2 wt and its mutant, unable to form branched structure, bind Tat-2 protein with comparable, high affinity, while RNA hairpins I and II, derived from TAR-2 branched structure model, show much less protein binding. We propose that an internal loop region of the TAR-2 extended hairpin form is a potential Tat-2 binding site.


Assuntos
Regiões 5' não Traduzidas/química , Repetição Terminal Longa de HIV , HIV-2/genética , RNA Viral/química , Arginina/análogos & derivados , Arginina/química , Sequência de Bases , Sítios de Ligação , Dietil Pirocarbonato , Eletroforese em Gel de Poliacrilamida , Ensaio de Desvio de Mobilidade Eletroforética , Produtos do Gene tat/metabolismo , Chumbo/química , Magnésio/química , Dados de Sequência Molecular , Conformação de Ácido Nucleico , RNA Viral/metabolismo , Ribonucleases , Produtos do Gene tat do Vírus da Imunodeficiência Humana
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