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1.
BMC Bioinformatics ; 20(1): 421, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409274

RESUMO

BACKGROUND: Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantification. This coupling precludes the direct usage of pseudo-alignment to other expression analyses, including alternative splicing or differential gene expression analysis, without including a non-essential transcript quantification step. RESULTS: In this paper, we introduce a transcriptome segmentation approach to decouple these two tasks. We propose an efficient algorithm to generate maximal disjoint segments given a transcriptome reference library on which ultra-fast pseudo-alignment can be used to produce per-sample segment counts. We show how to apply these maximally unambiguous count statistics in two specific expression analyses - alternative splicing and gene differential expression - without the need of a transcript quantification step. Our experiments based on simulated and experimental data showed that the use of segment counts, like other methods that rely on local coverage statistics, provides an advantage over approaches that rely on transcript quantification in detecting and correctly estimating local splicing in the case of incomplete transcript annotations. CONCLUSIONS: The transcriptome segmentation approach implemented in Yanagi exploits the computational and space efficiency of pseudo-alignment approaches. It significantly expands their applicability and interpretability in a variety of RNA-seq analyses by providing the means to model and capture local coverage variation in these analyses.


Assuntos
Algoritmos , Transcriptoma , Processamento Alternativo , Animais , Área Sob a Curva , Drosophila/genética , Humanos , RNA/química , RNA/metabolismo , Curva ROC , Análise de Sequência de RNA
2.
BMC Bioinformatics ; 20(1): 418, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409293

RESUMO

BACKGROUND: Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequencing. In cases of single-cell and low-input RNAseq methods, the library is further amplified by PCR after the pooling. Preparation of hundreds or more samples for a large study often requires multiple library pools. However, sometimes correlation between expression profiles among the libraries is low and batch effect biases make integration of data between library pools difficult. RESULTS: We investigated 166 technical replicates in 14 RNAseq libraries made using the STRT method. The patterns of the library biases differed by genes, and uneven library yields were associated with library biases. The former bias was corrected using the NBGLM-LBC algorithm, which we present in the current study. The latter bias could not be corrected directly, but could be solved by omitting libraries with particularly low yields. A simulation experiment suggested that the library bias correction using NBGLM-LBC requires a consistent sample layout. The NBGLM-LBC correction method was applied to an expression profile for a cohort study of childhood acute respiratory illness, and the library biases were resolved. CONCLUSIONS: The R source code for the library bias correction named NBGLM-LBC is available at https://shka.github.io/NBGLM-LBC and https://shka.bitbucket.io/NBGLM-LBC . This method is applicable to correct the library biases in various studies that use highly multiplexed sequencing-based profiling methods with a consistent sample layout with samples to be compared (e.g., "cases" and "controls") equally distributed in each library.


Assuntos
Biblioteca Gênica , Análise de Sequência de RNA/métodos , Transcriptoma , Linhagem Celular , Análise por Conglomerados , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Análise de Componente Principal , RNA/química , RNA/metabolismo , Interface Usuário-Computador
4.
Phys Rev Lett ; 123(3): 038101, 2019 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-31386470

RESUMO

Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. The performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal fluctuations in these single-molecule processes, both error and speed are inherently stochastic quantities. In this Letter, we study fluctuations of error and speed in biopolymer synthesis and show that they are in general correlated. This means that, under equal conditions, polymers that are synthesized faster due to a fluctuation tend to have either better or worse errors than the average. The error-correction mechanism implemented by the enzyme determines which of the two cases holds. For example, discrimination in the forward reaction rates tends to grant smaller errors to polymers with faster synthesis. The opposite occurs for discrimination in monomer rejection rates. Our results provide an experimentally feasible way to identify error-correction mechanisms by measuring the error-speed correlations.


Assuntos
Biopolímeros/biossíntese , Enzimas/química , Enzimas/metabolismo , Biopolímeros/química , DNA/biossíntese , DNA/química , Humanos , Modelos Biológicos , Modelos Químicos , RNA/biossíntese , RNA/química
5.
BMC Bioinformatics ; 20(1): 394, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311497

RESUMO

BACKGROUND: High-dimensional data of discrete and skewed nature is commonly encountered in high-throughput sequencing studies. Analyzing the network itself or the interplay between genes in this type of data continues to present many challenges. As data visualization techniques become cumbersome for higher dimensions and unconvincing when there is no clear separation between homogeneous subgroups within the data, cluster analysis provides an intuitive alternative. The aim of applying mixture model-based clustering in this context is to discover groups of co-expressed genes, which can shed light on biological functions and pathways of gene products. RESULTS: A mixture of multivariate Poisson-log normal (MPLN) model is developed for clustering of high-throughput transcriptome sequencing data. Parameter estimation is carried out using a Markov chain Monte Carlo expectation-maximization (MCMC-EM) algorithm, and information criteria are used for model selection. CONCLUSIONS: The mixture of MPLN model is able to fit a wide range of correlation and overdispersion situations, and is suited for modeling multivariate count data from RNA sequencing studies. All scripts used for implementing the method can be found at https://github.com/anjalisilva/MPLNClust .


Assuntos
Algoritmos , RNA/química , Análise por Conglomerados , Sequenciamento de Nucleotídeos em Larga Escala , Cadeias de Markov , Modelos Teóricos , Método de Monte Carlo , RNA/genética , RNA/metabolismo , Análise de Sequência de RNA , Interface Usuário-Computador
6.
Nat Commun ; 10(1): 2909, 2019 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-31266957

RESUMO

Cells form and use biomolecular condensates to execute biochemical reactions. The molecular properties of non-membrane-bound condensates are directly connected to the amino acid content of disordered protein regions. Lysine plays an important role in cellular function, but little is known about its role in biomolecular condensation. Here we show that protein disorder is abundant in protein/RNA granules and lysine is enriched in disordered regions of proteins in P-bodies compared to the entire human disordered proteome. Lysine-rich polypeptides phase separate into lysine/RNA-coacervates that are more dynamic and differ at the molecular level from arginine/RNA-coacervates. Consistent with the ability of lysine to drive phase separation, lysine-rich variants of the Alzheimer's disease-linked protein tau undergo coacervation with RNA in vitro and bind to stress granules in cells. Acetylation of lysine reverses liquid-liquid phase separation and reduces colocalization of tau with stress granules. Our study establishes lysine as an important regulator of cellular condensation.


Assuntos
Lisina/metabolismo , RNA/química , RNA/metabolismo , Proteínas tau/química , Proteínas tau/metabolismo , Acetilação , Doença de Alzheimer/genética , Doença de Alzheimer/metabolismo , Linhagem Celular , Grânulos Citoplasmáticos/genética , Grânulos Citoplasmáticos/metabolismo , Humanos , Lisina/química , Lisina/genética , RNA/genética , Proteínas tau/genética
7.
Adv Clin Chem ; 91: 31-98, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31331490

RESUMO

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.


Assuntos
DNA/química , RNA/química , Técnicas Biossensoriais/métodos , Humanos , Nanotecnologia , Técnicas de Amplificação de Ácido Nucleico/métodos
8.
Chem Commun (Camb) ; 55(65): 9709-9712, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31353371

RESUMO

We functionalize nucleic acid nanostructures with click chemistry (for attachment of cargos) and a photocleavable linker (for release). We demonstrate cargo attachment using a fluorescein dye and release using UV trigger from an RNA three-way junction, a DNA star motif and a DNA tetrahedron. Such multifunctional nucleic acid nanostructures have potential in targeted drug delivery.


Assuntos
DNA/química , Portadores de Fármacos/química , Fluoresceínas/química , Corantes Fluorescentes/química , Nanoestruturas/química , RNA/química , Animais , Fagos Bacilares/genética , Sequência de Bases , Bovinos , Química Click , DNA/sangue , DNA/síntese química , DNA/efeitos da radiação , Portadores de Fármacos/síntese química , Portadores de Fármacos/efeitos da radiação , Fluorescência , Nanoestruturas/efeitos da radiação , Conformação de Ácido Nucleico , RNA/sangue , RNA/síntese química , RNA/efeitos da radiação , Raios Ultravioleta
9.
Naturwissenschaften ; 106(7-8): 44, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31267209

RESUMO

Deaminations (A->G, C->T) increase with DNA singlestrandedness during replication, presumably creating spontaneous genomic mutational and nucleotide frequency gradients. Alternatively, genes are positioned to avoid deaminations. Deamination gradients affect directly mitogene third codon positions; conserved vertebrate mitochondrial tRNA and protein coding gene arrangements minimize deaminations in anticodons, and first and second codon positions in mitogenes. Here we describe deamination gradients across theoretical minimal RNA rings, 22 nucleotide-long RNAs designed to simulate prebiotic RNAs. These RNA rings code for a start/stop codon and a single codon for each amino acid, and form stem-loop hairpins slowing degradation. They resemble consensus tRNAs, defining potential anticodons and cognate amino acids. Theoretical minimal RNA rings are not designed to include deamination gradients, yet deamination gradients occur in RNA rings. tRNA homology produces stronger evidence for deamination gradients than RNA ring homology defined by coding properties. Deamination gradients start at predicted RNA ring anticodons, corresponding to known homologies between mitochondrial tRNAs and replication origins, and between bacterial tRNA synthetases and mitochondrial DNA polymerase gamma. Deamination gradients are strongest for RNA rings with predicted anticodons matching cognate amino acids that integrated early the genetic code. Presumably protections against deaminations evolved while amino acids integrated the genetic code. Results confirm tRNA-RNA ring homologies. Coding constraints defining RNA rings presumably produce deamination gradients starting at predicted anticodons. Hence, the universal genetic code determines nucleotide deamination gradients in theoretical minimal RNA rings, suggesting adaptation to prevent consequences of deamination mutations. Results also indicate that the genetic code's structure determined evolution of tRNAs, their cognates, tRNA synthetases, and polymerases.


Assuntos
Evolução Molecular , Modelos Químicos , RNA/química , Códon/química , Simulação por Computador , Desaminação , RNA de Transferência/química
10.
BMC Bioinformatics ; 20(1): 373, 2019 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-31269893

RESUMO

BACKGROUND: RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particular, RNA secondary structures, is critical for elucidating biological functions. Existing literature has focused on RNA design as either an RNA structure prediction problem or an RNA inverse folding problem where free energy has played a key role. RESULTS: In this research, we propose a Positive-Unlabeled data- driven framework termed ENTRNA. Other than free energy and commonly studied sequence and structural features, we propose a new feature, Sequence Segment Entropy (SSE), to measure the diversity of RNA sequences. ENTRNA is trained and cross-validated using 1024 pseudoknot-free RNAs and 1060 pseudoknotted RNAs from the RNASTRAND database respectively. To test the robustness of the ENTRNA, the models are further blind tested on 206 pseudoknot-free and 93 pseudoknotted RNAs from the PDB database. For pseudoknot-free RNAs, ENTRNA has 86.5% sensitivity on the training dataset and 80.6% sensitivity on the testing dataset. For pseudoknotted RNAs, ENTRNA shows 81.5% sensitivity on the training dataset and 71.0% on the testing dataset. To test the applicability of ENTRNA to long structural-complex RNA, we collect 5 laboratory synthetic RNAs ranging from 1618 to 1790 nucleotides. ENTRNA is able to predict the foldability of 4 RNAs. CONCLUSION: In this article, we reformulate the RNA design problem as a foldability prediction problem which is to predict the likelihood of the co-existence of a sequence-structure pair. This new construct has the potential for both RNA structure prediction and the inverse folding problem. In addition, this new construct enables us to explore data-driven approaches in RNA research.


Assuntos
Algoritmos , RNA/metabolismo , Bases de Dados Genéticas , RNA/química , Dobramento de RNA , Termodinâmica
11.
Chem Pharm Bull (Tokyo) ; 67(6): 505-518, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31155555

RESUMO

Nucleic acid therapeutics such as antisense and small interfering RNA (siRNA) have attracted increasing attention as innovative medicines that interfere with and/or modify gene expression systems. We have developed new functional oligonucleotides that can target DNA and RNA with high efficiency and selectivity. This review summarizes our achievements, including (1) the formation of non-natural triplex DNA for sequence-specific inhibition of transcription; (2) artificial receptor molecules for 8-oxidized-guanosine nucleosides; and (3) reactive oligonucleotides with a cross-linking agent or a functionality-transfer nucleoside for RNA pinpoint modification.


Assuntos
DNA/química , RNA/química , Reagentes para Ligações Cruzadas/química , DNA/metabolismo , DNA/farmacologia , Humanos , Nucleosídeos/análogos & derivados , Nucleosídeos/farmacologia , Oligonucleotídeos/química , Oligonucleotídeos/metabolismo , Polietilenoglicóis/química , RNA/metabolismo , Telomerase/genética , Telomerase/metabolismo , Transcrição Genética/efeitos dos fármacos
12.
Nat Commun ; 10(1): 2682, 2019 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-31213602

RESUMO

RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence.


Assuntos
Evolução Molecular , Proteômica/métodos , Motivos de Ligação ao RNA/genética , Proteínas de Ligação a RNA/genética , RNA/metabolismo , Sequência de Aminoácidos/genética , Animais , Linhagem Celular , Sequência Conservada/genética , Reagentes para Ligações Cruzadas/química , Drosophila , Humanos , Peptídeos/química , Peptídeos/genética , Ligação Proteica/genética , Proteoma/genética , RNA/química , Proteínas de Ligação a RNA/química
13.
Chem Commun (Camb) ; 55(53): 7595-7598, 2019 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-31180413

RESUMO

A label-free ultrasensitive determination of eight RNA modified nucleotides simultaneously was first established based on a sheathless capillary electrophoresis-tandem mass spectrometry system. This system performed well using only 500 pg-5 ng practical RNA samples, and a downward trend of most target nucleotides in HCT 116 cells was observed with the increase of nickel concentration.


Assuntos
Nucleotídeos/análise , RNA/química , Eletroforese Capilar , Células HCT116 , Humanos , Espectrometria de Massas em Tandem
14.
Chem Commun (Camb) ; 55(51): 7378-7381, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31173001

RESUMO

We propose synthetic DNA/RNA transcription circuits based on specific aptamer recognition. By mimicking transcription factor regulation, combined with specific enzyme/DNA aptamer binding, multiple biomolecules including DNA, RNA, polymerase, restriction enzymes and methylase were used as regulators. In addition, multi-level cascading networks and methylation-switch circuits were also established. This regulation strategy has the potential to expand the toolkit of in vitro synthetic biology.


Assuntos
Aptâmeros de Nucleotídeos/química , Fatores de Transcrição/química , DNA/química , Enzimas de Restrição do DNA/química , DNA Polimerase Dirigida por DNA/química , RNA Polimerases Dirigidas por DNA/química , Metilação , RNA/química , Transcrição Genética
15.
Chem Biol Interact ; 309: 108675, 2019 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-31150632

RESUMO

Liver fibrosis is a progression of chronic liver disease with lacks effective therapies at present. Schisandrin B (Sch B), a bioactive compound extracted from the traditional Chinese medicine Schisandra chinensis, was reported to benefit liver diseases. This study aimed to investigate the therapeutic effects and molecular mechanisms of Sch B against CCl4-induced liver fibrosis in rats. RNA sequencing and transcriptome analysis were performed collaboratively, including analysis of differential gene expression, gene ontology (GO) analysis, pathway analysis and pathway-act-network analysis. The results demonstrated that Sch B effectively alleviated CCl4-induced liver damage and fibrosis in rats, as evidenced by improved liver function and decreased extracellular matrix deposition. Furthermore, 4440 (1878 up-regulated, 2562 down-regulated) genes in the model group versus (vs) normal group, 4243 (2584 up-regulated, 1659 down-regulated) genes in Sch B-treated group vs model group were identified as differentially expressed genes (DEGs). Subsequently, GO analysis revealed that DEGs were mainly enriched in metabolism, oxidation-reduction, endoplasmic reticulum stress and apoptosis-related biological processes. Pathway analysis suggested that Sch B up-regulated cytochrome P450 drug metabolism, PPAR signaling pathways, and down-regulated glutathione metabolism pathways. In addition, the regulatory patterns of Sch B on key genes and pathways were also confirmed. In conclusion, our study demonstrated Sch B alleviated CCl4-induced liver fibrosis by multiple modulatory mechanisms, which provide new clues for further pharmacological study of Sch B.


Assuntos
Lignanas/farmacologia , Cirrose Hepática/patologia , Fígado/metabolismo , Compostos Policíclicos/farmacologia , Transcriptoma , Animais , Apoptose/efeitos dos fármacos , Tetracloreto de Carbono/toxicidade , Ciclo-Octanos/química , Ciclo-Octanos/farmacologia , Ciclo-Octanos/uso terapêutico , Regulação para Baixo/efeitos dos fármacos , Estresse do Retículo Endoplasmático/efeitos dos fármacos , Perfilação da Expressão Gênica , Lignanas/química , Lignanas/uso terapêutico , Fígado/efeitos dos fármacos , Fígado/patologia , Cirrose Hepática/induzido quimicamente , Cirrose Hepática/tratamento farmacológico , Cirrose Hepática/metabolismo , Masculino , Medicina Tradicional Chinesa , Compostos Policíclicos/química , Compostos Policíclicos/uso terapêutico , RNA/química , RNA/isolamento & purificação , RNA/metabolismo , Ratos , Ratos Wistar , Schisandra/química , Schisandra/metabolismo , Análise de Sequência de RNA , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/genética , Regulação para Cima/efeitos dos fármacos
16.
J Chem Theory Comput ; 15(8): 4687-4698, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31251056

RESUMO

Small-angle X-ray and small-angle neutron scattering (SAXS/SANS) provide unique structural information on biomolecules and their complexes in solution. SANS may provide multiple independent data sets by means of contrast variation experiments, that is, by measuring at different D2O concentrations and different perdeuteration conditions of the biomolecular complex. However, even the combined data from multiple SAXS/SANS sets is by far insufficient to define all degrees of freedom of a complex, leading to a significant risk of overfitting when refining biomolecular structures against SAXS/SANS data. Hence, to control against overfitting, the low-information SAXS/SANS data must be complemented by accurate physical models, and, if possible, refined models should be cross-validated against independent data not used during the refinement. We present a method for refining atomic biomolecular structures against multiple sets of SAXS and SANS data using all-atom molecular dynamics simulations. Using the protein citrate synthase and the protein/RNA complex Sxl-Unr-msl2 mRNA as test cases, we demonstrate how multiple SAXS and SANS sets may be used for refinement and cross-validation, thereby excluding overfitting during refinement. For the Sxl-Unr-msl2 complex, we find that perdeuteration of the Unr domain leads to a unique, slightly compacted conformation, whereas other perdeuteration conditions lead to similar solution conformations compared to the nondeuterated state. In line with our previous method for predicting SAXS curves, SANS curves were predicted with explicit-solvent calculations, taking atomic models for both the hydration layer and the excluded solvent into account, thereby avoiding the use of solvent-related fitting parameters and solvent-reduced neutron scattering lengths. We expect the method to be useful for deriving and validating solution structures of biomolecules and soft-matter complexes, and for critically assessing whether multiple SAXS and SANS sets are mutually compatible.


Assuntos
Simulação de Dinâmica Molecular , Difração de Nêutrons , Espalhamento a Baixo Ângulo , Difração de Raios X , Animais , Citrato (si)-Sintase/química , Proteínas de Ligação a DNA/química , Drosophila , Proteínas de Drosophila/química , Difração de Nêutrons/métodos , RNA/química , Proteínas de Ligação a RNA/química , Suínos , Difração de Raios X/métodos
17.
Inorg Chem ; 58(10): 6804-6810, 2019 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-31046253

RESUMO

The substitution-inert polynuclear platinum complexes (SI-PPCs) are now recognized as a distinct subclass of platinum anticancer drugs with high DNA binding affinity. Here, we investigate the effects of SI-PPCs containing dangling amine groups in place of NH3 as ligands to increase the length of the molecule and therefore overall charge and its distribution. The results obtained with the aid of biophysical techniques, such as total intensity light scattering, gel electrophoresis, and atomic force microscopy, show that addition of dangling amine groups considerably augments the ability of SI-PPCs to condense/aggregate nucleic acids. Moreover, this enhanced capability of SI-PPCs correlates with their heightened efficiency to inhibit DNA-related enzymatic activities, such as those connected with DNA transcription, catalysis of DNA relaxation by DNA topoisomerase I, and DNA synthesis catalyzed by Taq DNA polymerase. Thus, the addition of the dangling amine groups resulting in structures of SI-PPCs, which differ so markedly from the derivatives of cisplatin used in the clinic, appears to contribute to the overall biological activity of these molecules.


Assuntos
Aminas/química , Complexos de Coordenação/química , DNA Topoisomerases Tipo I/efeitos dos fármacos , DNA/química , Compostos de Platina/química , RNA/química , Taq Polimerase/antagonistas & inibidores , Antineoplásicos/química , Microscopia de Força Atômica , Inibidores da Topoisomerase I
18.
J Chem Theory Comput ; 15(6): 3425-3431, 2019 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-31050905

RESUMO

Empirical force fields for biomolecular systems are usually derived from quantum chemistry calculations and validated against experimental data. We here show how it is possible to refine the full dihedral-angle potential of the Amber RNA force field by using solution NMR data as well as stability of known structural motifs. The procedure can be used to mix multiple systems and heterogeneous experimental information and crucially depends on a regularization term chosen with a cross-validation procedure. By fitting corrections to the dihedral angles on the order of less than 1 kJ/mol per angle, it is possible to increase the stability of difficult-to-fold RNA tetraloops by more than 1 order of magnitude.


Assuntos
Conformação de Ácido Nucleico , RNA/química , Algoritmos , Espectroscopia de Ressonância Magnética/métodos , Simulação de Dinâmica Molecular , Reprodutibilidade dos Testes
20.
BMC Bioinformatics ; 20(1): 293, 2019 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-31142266

RESUMO

BACKGROUND: Predicted RNA secondary structures are typically visualized using dot-plots for base pair binding probabilities and planar graphs for unique structures, such as the minimum free energy structure. These are however difficult to analyze simultaneously. RESULTS: This work introduces a compact unified view of the most stable conformation of an RNA secondary structure and its base pair probabilities, which is called the Circular Secondary Structure Base Pairs Probabilities Plot (CS2BP2-Plot). Along with our design we provide access to a web server implementation of our solution that facilitates pairwise comparison of short RNA (and DNA) sequences up to 200 base pairs. The web server first calculates the minimum free energy secondary structure and the base pair probabilities for up to 10 RNA or DNA sequences using RNAfold and then provides a two panel comparative view that includes CS2BP2-Plots along with the traditional graph, planar and circular diagrams obtained with VARNA. The CS2BP2-Plots include highlighting of the nucleotide differences between two selected sequences using ClustalW local alignments. We also provide descriptive statistics, dot-bracket secondary structure representations and ClustalW local alignments for compared sequences. CONCLUSIONS: Using circular diagrams and colour and weight-coded arcs, we demonstrate how a single image can replace the state-of-the-art dual representations (dot-plots and minimum free energy structures) for base-pair probabilities of RNA secondary structures while allowing efficient exploration and comparison of different RNA conformations via a web server front end. With that, we provide the community, especially the biologically oriented, with an intuitive tool for ncRNA visualization. Web-server: https://nrcmonsrv01.nrc.ca/cs2bp2plot.


Assuntos
Pareamento de Bases , Conformação de Ácido Nucleico , Probabilidade , RNA/química , Algoritmos , Sistemas CRISPR-Cas/genética , Evolução Molecular , Humanos , RNA Guia/genética , Virulência/genética , Yersinia/patogenicidade
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