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1.
J Chem Phys ; 151(19): 195102, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31757139

RESUMO

Here, we investigate the unfolding behavior of a streptomycin-binding ribonucleic acid (RNA) aptamer under application of force in shear geometry. Using Langevin out-of-equilibrium simulations to emulate the single-molecule force spectroscopy (SMFS) experiment, we were able to understand the hierarchical unfolding process that occurs in the RNA molecule under application of stretching force and the influence of streptomycin modifying this unfolding. Subsequently, the application of the Jarzynski equality to the force profiles obtained in the pulling simulations shows that the free energies for individual systems and the difference of unfolding free energy upon streptomycin binding to the RNA free aptamer are in fair agreement with the experimental values, obtained through SMFS by Nick et al. [J. Phys. Chem. B 120, 6479 (2016)].


Assuntos
Aptâmeros de Nucleotídeos/química , Aptâmeros de Nucleotídeos/metabolismo , Microscopia de Força Atômica , Simulação de Dinâmica Molecular , Estreptomicina/metabolismo , Conformação de Ácido Nucleico , Ligação Proteica , Termodinâmica
2.
J Chem Phys ; 151(16): 164902, 2019 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-31675856

RESUMO

Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here, we probe, via all-atom molecular dynamics (MD) simulations, the change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, the stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs, i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.


Assuntos
Antineoplásicos/química , DNA/química , Substâncias Intercalantes/química , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico
3.
J Chem Phys ; 151(16): 165101, 2019 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-31675878

RESUMO

As an extremely common structural motif, RNA hairpins with bulge loops [e.g., the human immunodeficiency virus type 1 (HIV-1) transactivation response (TAR) RNA] can play essential roles in normal cellular processes by binding to proteins and small ligands, which could be very dependent on their three-dimensional (3D) structures and stability. Although the structures and conformational dynamics of the HIV-1 TAR RNA have been extensively studied, there are few investigations on the thermodynamic stability of the TAR RNA, especially in ion solutions, and the existing studies also have some divergence on the unfolding process of the RNA. Here, we employed our previously developed coarse-grained model with implicit salt to predict the 3D structure, stability, and unfolding pathway for the HIV-1 TAR RNA over a wide range of ion concentrations. As compared with the extensive experimental/theoretical results, the present model can give reliable predictions on the 3D structure stability of the TAR RNA from the sequence. Based on the predictions, our further comprehensive analyses on the stability of the TAR RNA as well as its variants revealed that the unfolding pathway of an RNA hairpin with a bulge loop is mainly determined by the relative stability between different states (folded state, intermediate state, and unfolded state) and the strength of the coaxial stacking between two stems in folded structures, both of which can be apparently modulated by the ion concentrations as well as the sequences.


Assuntos
HIV-1/química , Conformação de Ácido Nucleico , RNA Viral/química , Íons/química , Modelos Moleculares , Soluções
4.
Biochemistry (Mosc) ; 84(11): 1221-1232, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31760913

RESUMO

The review covers three independent blocks of research. The first one is discovery, isolation, and investigation of snake venom RNases and their use in studying RNA macrostructure. It has been established that snake venom RNases are not specific to the primary RNA structure but rather to the RNA helical conformation (double, single, or hybrid helix). Snake venom RNases hydrolyze RNA to short oligomers with the 5'-terminal phosphate. Analysis of the kinetics and products of tRNA hydrolysis exemplifies the use of snake venom RNases for deciphering RNA macrostructure. The second block is devoted to the principle formulated by the author for analyzing the primary structure of nucleic acids and describes the method of direct RNA sequencing that has been developed with author's participation. The third block describes the results of genotyping and etiologic control of epidemic influenza A viruses circulating in the Soviet Union in 1968 to 1992. The method for comparative analysis of genome sequences of viral isolates has made it possible to detect and characterize epidemic influenza virus strains that had emerged in the circulation as a result of reactivation of inactivated vaccines.


Assuntos
RNA/química , Humanos , Hidrólise , Vírus da Influenza A/genética , Cinética , Conformação de Ácido Nucleico , RNA/metabolismo , RNA/ultraestrutura , RNA Viral/química , RNA Viral/metabolismo , Ribonucleases/metabolismo , Venenos de Serpentes/metabolismo
5.
BMC Bioinformatics ; 20(1): 497, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31615418

RESUMO

BACKGROUND: It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequence from its homologous sequence alignment across different species. DCA and similar approaches that use sequence information alone typically yield a low accuracy, especially when the available homologous sequences are limited. Therefore, new methods for RNA structural contact inference are desirable because even a single correctly predicted tertiary contact can potentially make the difference between a correct and incorrectly predicted structure. Here we present a new method DIRECT (Direct Information REweighted by Contact Templates) that incorporates a Restricted Boltzmann Machine (RBM) to augment the information on sequence co-variations with structural features in contact inference. RESULTS: Benchmark tests demonstrate that DIRECT achieves better overall performance than DCA approaches. Compared to mfDCA and plmDCA, DIRECT produces a substantial increase of 41 and 18%, respectively, in accuracy on average for contact prediction. DIRECT improves predictions for long-range contacts and captures more tertiary structural features. CONCLUSIONS: We developed a hybrid approach that incorporates a Restricted Boltzmann Machine (RBM) to augment the information on sequence co-variations with structural templates in contact inference. Our results demonstrate that DIRECT is able to improve the RNA contact prediction.


Assuntos
Algoritmos , Modelos Moleculares , Conformação de Ácido Nucleico , Análise de Sequência de RNA/métodos , Software
6.
Nucleic Acids Res ; 47(16): 8874-8887, 2019 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-31616952

RESUMO

Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein-protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage λ from the chromosome, the bacterial DNA architectural protein Fis recruits multiple λ-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis ß-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.


Assuntos
Bacteriófago lambda/genética , Cromossomos Bacterianos/química , DNA Nucleotidiltransferases/química , DNA Bacteriano/química , Proteínas de Escherichia coli/química , Escherichia coli/genética , Fator Proteico para Inversão de Estimulação/química , Proteínas Virais/química , Sítio Alostérico , Bacteriófago lambda/metabolismo , Sequência de Bases , Sítios de Ligação , Cromossomos Bacterianos/metabolismo , Clonagem Molecular , Cristalografia por Raios X , DNA Nucleotidiltransferases/genética , DNA Nucleotidiltransferases/metabolismo , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Fator Proteico para Inversão de Estimulação/genética , Fator Proteico para Inversão de Estimulação/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Cinética , Modelos Moleculares , Conformação de Ácido Nucleico , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Reparo de DNA por Recombinação , Alinhamento de Sequência , Termodinâmica , Proteínas Virais/genética , Proteínas Virais/metabolismo
7.
Arch Virol ; 164(12): 3137-3140, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31598842

RESUMO

Viroid-like symptoms were observed in 2016 on apple fruits of the cultivar "Ilzer Rose" in southern Burgenland, Austria. Preliminary molecular biological investigations indicated that the symptoms were caused by a new unknown viroid. Therefore, new primers were designed, and the whole genome sequence of the viroid (354 nt) was determined by next-generation amplicon sequencing using the Illumina MiSeq® platform (San Diego, California, USA). The viroid secondary structure has a rod-like conformation and contains conserved regions (the TCR, CCR upper strand, and CCR lower strand) that are characteristic of members of the genus Apscaviroid. Based on our results and the demarcation criteria for viroids, the tentatively named "apple chlorotic fruit spot viroid" should be considered a putative new member of the genus Apscaviroid.


Assuntos
Malus/virologia , Doenças das Plantas/virologia , Viroides/isolamento & purificação , Sequência de Bases , Frutas/virologia , Conformação de Ácido Nucleico , RNA Viral/química , RNA Viral/genética , Viroides/química , Viroides/classificação , Viroides/genética
8.
Chem Commun (Camb) ; 55(83): 12571-12574, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31577282

RESUMO

We herein demonstrate the UV resistance of glycol nucleic acid (GNA) dinucleotides. This resistance sustains the hypothesis of GNA as a nucleic acid prebiotic ancestor on early Earth, a time of intense solar UV light. Such photorobustness, due to the absence of intrastrand base stacking, could offer an opportunity for nanodevice development requiring challenging UV conditions.


Assuntos
Nucleotídeos/química , Nucleotídeos/efeitos da radiação , Timina/análogos & derivados , Raios Ultravioleta , Conformação de Ácido Nucleico/efeitos da radiação , Timina/química
9.
Phys Chem Chem Phys ; 21(44): 24527-24534, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31663550

RESUMO

Folding is generally assumed to be a Markov process, without memory. When the molecular motion is coupled to that of a probe as in single-molecule force spectroscopy (SMFS) experiments, however, theory predicts that the coupling to a second Markov process should induce memory when monitoring a projection of the full multi-dimensional motion onto a reduced coordinate. We developed a method to evaluate the time constant of the induced memory from its effects on the autocorrelation function, which can be readily determined from experimental data. Applying this method to both simulated SMFS measurements and experimental trajectories of DNA hairpin folding measured by optical tweezers as a model system, we validated the prediction that the linker induces memory. For these measurements, the timescale of the induced memory was found to be similar to the time required for the force probe to respond to changes in the molecule, and in the regime where the experimentally observed dynamics were not significantly perturbed by probe-molecule coupling artifacts. Memory effects are thus a general feature of SMFS measurements induced by the mechanical connection between the molecule and force probe that should be considered when interpreting experimental data.


Assuntos
DNA/química , Imagem Individual de Molécula , DNA/metabolismo , Sequências Repetidas Invertidas , Cinética , Cadeias de Markov , Conformação de Ácido Nucleico , Pinças Ópticas
10.
Nature ; 574(7779): 571-574, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31645724

RESUMO

To safeguard genome integrity in response to DNA double-strand breaks (DSBs), mammalian cells mobilize the neighbouring chromatin to shield DNA ends against excessive resection that could undermine repair fidelity and cause damage to healthy chromosomes1. This form of genome surveillance is orchestrated by 53BP1, whose accumulation at DSBs triggers sequential recruitment of RIF1 and the shieldin-CST-POLα complex2. How this pathway reflects and influences the three-dimensional nuclear architecture is not known. Here we use super-resolution microscopy to show that 53BP1 and RIF1 form an autonomous functional module that stabilizes three-dimensional chromatin topology at sites of DNA breakage. This process is initiated by accumulation of 53BP1 at regions of compact chromatin that colocalize with topologically associating domain (TAD) sequences, followed by recruitment of RIF1 to the boundaries between such domains. The alternating distribution of 53BP1 and RIF1 stabilizes several neighbouring TAD-sized structures at a single DBS site into an ordered, circular arrangement. Depletion of 53BP1 or RIF1 (but not shieldin) disrupts this arrangement and leads to decompaction of DSB-flanking chromatin, reduction in interchromatin space, aberrant spreading of DNA repair proteins, and hyper-resection of DNA ends. Similar topological distortions are triggered by depletion of cohesin, which suggests that the maintenance of chromatin structure after DNA breakage involves basic mechanisms that shape three-dimensional nuclear organization. As topological stabilization of DSB-flanking chromatin is independent of DNA repair, we propose that, besides providing a structural scaffold to protect DNA ends against aberrant processing, 53BP1 and RIF1 safeguard epigenetic integrity at loci that are disrupted by DNA breakage.


Assuntos
Cromatina/genética , Cromatina/metabolismo , Instabilidade Genômica , Conformação de Ácido Nucleico , Proteínas de Ciclo Celular/deficiência , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular Tumoral , Cromatina/química , Quebras de DNA de Cadeia Dupla , Reparo do DNA , Proteínas de Ligação a DNA/deficiência , Proteínas de Ligação a DNA/metabolismo , Humanos , Proteínas de Ligação a Telômeros/deficiência , Proteínas de Ligação a Telômeros/metabolismo , Proteína 1 de Ligação à Proteína Supressora de Tumor p53/deficiência , Proteína 1 de Ligação à Proteína Supressora de Tumor p53/metabolismo
11.
J Phys Chem Lett ; 10(21): 6750-6754, 2019 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-31609626

RESUMO

Photodynamic therapy is a promising approach to treat a variety of superficial tumors and other diseases. One of its major limitations arises from its dependence on molecular oxygen, which decreases the efficiency of the therapy in hypoxia conditions commonly developed by solid tumors. The present contribution reveals the molecular mechanism of a modified thymine bearing a nitroimidazole substituent, a photosensitizer able to produce highly harmful interstrand cross-links in the DNA double strand after irradiation selectively in absence of oxygen. The mechanism is resolved at a fully atomistic and electronic level relying on quantum mechanics (CASPT2, coupled-cluster, DFT, and TD-DFT methods), classical molecular dynamics, and advanced biased QM/MM simulations, revealing an energy penalty of ∼8 kcal/mol for the anionic nitromidazole release. Our findings indicate that the global interstrand cross-link production is driven by a combination of multiple factors, namely, the reverse energy penalty, the diffusion of the nitroimidazole anion, and the further reactivity of the formed thymine radical. On the basis of these results, we also suggest some possible strategies to improve the efficiency of interstrand cross-link production.


Assuntos
DNA/química , Nitroimidazóis/química , DNA/metabolismo , Ligações de Hidrogênio , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Fármacos Fotossensibilizantes/química , Teoria Quântica
12.
J Phys Chem Lett ; 10(21): 6771-6779, 2019 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-31609632

RESUMO

Strand hybridization is not only a fundamental molecular mechanism underlying the biological functions of nucleic acids but is also a key step in the design of efficient nanodevices. Despite recent efforts, the microscopic rules governing the hybridization mechanisms remain largely unknown. In this study, we exploit the energy landscape framework to assess how sequence-specificity modulates the hybridization mechanisms in DNA. We find that GG-tracts hybridize much more rapidly compared to GC-tracts, via either zippering or slithering pathways. For the hybridization of GG-tracts, both zippering and slithering mechanisms appear to be kinetically relevant. In contrast, for the GC-tracts, the zippering mechanism is dominant. Our work reveals that even for the relatively small systems considered, the energy landscapes feature multiple metastable states and kinetic traps, which is at odds with the conventional "all-or-nothing" model of DNA hybridization formulated on the basis of thermodynamic arguments alone. Interestingly, entropic effects are found to play an important role in determining the thermal stability of competing conformational ensembles and in determining the preferred hybridization pathways.


Assuntos
Oligonucleotídeos/química , Guanina/química , Conformação de Ácido Nucleico , Hibridização de Ácido Nucleico , Oligonucleotídeos/metabolismo , Termodinâmica
13.
Chem Commun (Camb) ; 55(77): 11615-11618, 2019 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-31501837

RESUMO

To date, implementation of renewable DNA circuits remains challenging due to issues including reactant depletion and waste accumulation. Herein we simultaneously addressed both issues through nicking enzyme-assisted waste-to-reactant transformation. As a proof-of-concept, a renewable entropy-driven catalytic DNA circuit was implemented, exhibiting a good renewability when replenishing fuel.


Assuntos
DNA Catalítico/química , Endonucleases/química , Redes Reguladoras de Genes , Pareamento Incorreto de Bases , Catálise , Entropia , Corantes Fluorescentes/química , Cinética , Conformação de Ácido Nucleico , Estudo de Prova de Conceito , Espectrometria de Fluorescência
14.
Nucleic Acids Res ; 47(18): 9950-9966, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31504744

RESUMO

HMGB1 is a ubiquitous non-histone protein, which biological effects depend on its expression and subcellular location. Inside the nucleus, HMGB1 is engaged in many DNA events such as DNA repair, transcription and telomere maintenance. HMGB1 has been reported to bind preferentially to bent DNA as well as to noncanonical DNA structures like 4-way junctions and, more recently, to G-quadruplexes. These are four-stranded conformations of nucleic acids involved in important cellular processes, including telomere maintenance. In this frame, G-quadruplex recognition by specific proteins represents a key event to modulate physiological or pathological pathways. Herein, to get insights into the telomeric G-quadruplex DNA recognition by HMGB1, we performed detailed biophysical studies complemented with biological analyses. The obtained results provided information about the molecular determinants for the interaction and showed that the structural variability of human telomeric G-quadruplex DNA may have significant implications in HMGB1 recognition. The biological data identified HMGB1 as a telomere-associated protein in both telomerase-positive and -negative tumor cells and showed that HMGB1 gene silencing in such cells induces telomere DNA damage foci. Altogether, these findings provide a deeper understanding of telomeric G-quadruplex recognition by HMGB1 and suggest that this protein could actually represent a new target for cancer therapy.


Assuntos
Quadruplex G , Proteína HMGB1/genética , Conformação de Ácido Nucleico , Telômero/genética , DNA/química , DNA/genética , Escherichia coli/genética , Proteína HMGB1/química , Humanos , Telomerase/química , Telomerase/genética , Telômero/química
15.
Nucleic Acids Res ; 47(18): 9502-9510, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31504779

RESUMO

Distinct from intermolecular split G-quadruplex (Inter-SG), intramolecular split G-quadruplex (Intra-SG) which could be generated in a DNA spacer-inserted G-quadruplex strand has not been systematically explored. Not only is it essential for the purpose of simplicity of DNA-based bioanalytical applications, but also it will give us hints how to design split G-quadruplex-based system. Herein, comprehensive information is provided about influences of spacer length and split mode on the formation of Intra-SG, how to adjust its thermodynamic stability, and selection of optimal Intra-SG for bioanalysis. For instances, non-classical Intra-SG (e.g. 2:10, 4:8 and 5:7) displays lower stability than classical split strands (3:9, 6:6 and 9:3), which is closely related to integrity of consecutive guanine tract; as compared to regular Intra-SG structures, single-thymine capped ones have reduced melting temperature, providing an effective approach to adjustment of stability. It is believed that the disclosed rules in this study will contribute to the effective application of split G-quadruplex in the field of DNA technology in the future.


Assuntos
DNA Intergênico/genética , DNA/genética , Quadruplex G , Conformação de Ácido Nucleico , Dicroísmo Circular/métodos , DNA/química , DNA Intergênico/química , DNA Intergênico/ultraestrutura , Guanina/química , Termodinâmica , Timina/química
16.
Nucleic Acids Res ; 47(18): 9480-9494, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31504786

RESUMO

Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.


Assuntos
Biologia Computacional/métodos , Motivos de Nucleotídeos/genética , RNA Catalítico/genética , Análise de Sequência de RNA/métodos , Catálise , Modelos Moleculares , Conformação de Ácido Nucleico , RNA Catalítico/química , RNA Catalítico/isolamento & purificação
17.
Inorg Chem ; 58(19): 13346-13352, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31525964

RESUMO

We have synthesized and structurally characterized examples of the well-known silver-mediated DNA base pair in its simplest possible form, as [AgI-bis-(N3-cytosine)]+. The compounds show differences such as variable coordination geometry, conformation with cisoid and transoid arrangements, and, in one case, intramolecular base pairing. Collectively, these compounds represent three of five permutations of linear/bent coordination geometry and cisoid/transoid arrangement of the cytosine ligands and contain the global minimum conformation as determined by DFT calculations: bent-transoid. Furthermore, these compounds show no argentophilic intercomplex interactions in the solid state, in marked contrast to alkylated and nucleoside analogues, and so do not form the supramolecular 1D "metallo-DNA" duplex observed in those cases but instead form hydrogen-bonded sheets. This marked difference may be attributed, in part, to the additional hydrogen bond donor site at N1 of the nucleobase that ubiquitously participates in intermolecular interactions.


Assuntos
Citosina/análogos & derivados , DNA/química , Prata/química , Pareamento de Bases , Ligações de Hidrogênio , Modelos Moleculares , Conformação de Ácido Nucleico
18.
Nat Chem Biol ; 15(10): 966-974, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31477916

RESUMO

Pseudouridine (Ψ) is a post-transcriptional RNA modification that alters RNA-RNA and RNA-protein interactions that affect gene expression. Messenger RNA pseudouridylation was recently discovered as a widespread and conserved phenomenon, but the mechanisms responsible for selective, regulated pseudouridylation of specific sequences within mRNAs were unknown. Here, we have revealed mRNA targets for five pseudouridine synthases and probed the determinants of mRNA target recognition by the predominant mRNA pseudouridylating enzyme, Pus1, by developing high-throughput kinetic analysis of pseudouridylation in vitro. Combining computational prediction and rational mutational analysis revealed an RNA structural motif that is both necessary and sufficient for mRNA pseudouridylation. Applying this structural context information predicted hundreds of additional mRNA targets that were pseudouridylated in vivo. These results demonstrate a structure-dependent mode of mRNA target recognition by a conserved pseudouridine synthase and implicate modulation of RNA structure as the probable mechanism to regulate mRNA pseudouridylation.


Assuntos
Hidroliases/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Saccharomyces cerevisiae/metabolismo , Regulação Enzimológica da Expressão Gênica , Regulação Fúngica da Expressão Gênica , Humanos , Mutação , Conformação de Ácido Nucleico , Saccharomyces cerevisiae/genética
19.
Chem Asian J ; 14(19): 3380-3385, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31478313

RESUMO

An oligonucleotide of triazole-linked RNA (TL RNA) was synthesized by performing consecutive copper-catalyzed azide-alkyne cycloaddition reactions for elongation. The reaction conditions that had been optimized for the synthesis of 3-mer TL RNA were found to be inappropriate for longer oligonucleotides, and the conditions were reoptimized for the solid-phase synthesis of an 11-mer TL RNA oligonucleotide. Duplex formation of the 11-mer TL RNA oligonucleotide was examined with the complementary oligonucleotide of natural RNA to reveal the effects of the 2'-OH groups on the duplex stability.


Assuntos
Oligonucleotídeos/química , RNA/química , Triazóis/química , Alquinos/química , Azidas/química , Catálise , Cobre/química , Reação de Cicloadição , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Oligonucleotídeos/síntese química , Técnicas de Síntese em Fase Sólida
20.
Microbiol Res ; 229: 126319, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31479952

RESUMO

Methionine is critical for variety of metabolic processes in biological organisms, acting as a precursor or intermediate for many final products. The last step for the synthesis of methionine is the methylation of homocysteine, which is catalyzed by MetE. Here, we use Salmonella enterica serovar Typhimurium LT2 to study the regulation of the metE+ gene by an anaerobically induced small non-coding RNA-FnrS, the expression of which is strictly dependent on the anaerobic regulator-FNR. The MetE-HA protein was expressed at an increased level in the fnrS- and hfq- deficient strains under anaerobic conditions. The Hfq protein is predicted to stabilize the binding between small RNA(s) and their target mRNA(s). A transcriptional (op) and translational (pr) metE::lacZ fusion gene were separately constructed, with the metE+-promoter fused to a lacZ reporter gene. In an anaerobic environment, the metE::lacZ (pr) fusion gene and reverse transcription-PCR identified that FnrS and/or FNR negatively regulate metE+ mRNA levels in the rich media. Analysis of FnrS revealed a sequence complementary to the 5' mRNA translational initiation region (TIR) of the metE+ gene. Mutation(s) predicted to disrupt base pairing between FnrS and metE+ TIR were constructed in fnrS, and most of those resulted in the loss of repressive activity. When compensatory mutation(s) were made in metE+ 5' TIR to restore base pairing with FnrS, the repressive regulation was completely restored. Therefore, in this study, we identified that in anaerobic phase, there is a repression of metE+ gene expression by FnrS and that base-paring, between both expressive transcripts, plays an important role for this negative regulation.


Assuntos
Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Metiltransferases/genética , RNA Bacteriano/genética , RNA Mensageiro/genética , Pequeno RNA não Traduzido/genética , Salmonella typhimurium/enzimologia , Proteínas de Bactérias/metabolismo , Pareamento de Bases , Sequência de Bases , Regulação Enzimológica da Expressão Gênica , Metiltransferases/química , Metiltransferases/metabolismo , Conformação de Ácido Nucleico , RNA Bacteriano/química , RNA Bacteriano/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Pequeno RNA não Traduzido/química , Pequeno RNA não Traduzido/metabolismo , Salmonella typhimurium/genética , Salmonella typhimurium/metabolismo
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