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[PMID]:28471098
[Au] Autor:Costanzo G; Giorgi A; Scipioni A; Timperio AM; Mancone C; Tripodi M; Kapralov M; Krasavin E; Kruse H; Sponer J; Sponer JE; Ranc V; Otyepka M; Pino S; Di Mauro E
[Ad] Endereço:Istituto di Biologia e Patologia Molecolari, CNR, Piazzale Aldo Moro 5, 00185, Rome, Italy.
[Ti] Título:Nonenzymatic Oligomerization of 3',5'-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA.
[So] Source:Chembiochem;18(15):1535-1543, 2017 08 04.
[Is] ISSN:1439-7633
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:We report that 3',5'-cyclic CMP undergoes nonenzymatic di- and trimerization at 20 °C under dry conditions upon proton or UV irradiation. The reaction involves stacking of the cyclic monomers and subsequent polymerization through serial transphosphorylations between the stacked monomers. Proton- and UV-induced oligomerization of 3',5'-cyclic CMP demonstrates that pyrimidines-similar to purines-might also have taken part in the spontaneous generation of RNA under plausible prebiotic conditions as well as in an extraterrestrial context. The observed polymerization of naturally occurring 3',5'-cyclic nucleotides supports the possibility that the extant genetic nucleic acids might have originated by way of a straight Occamian path, starting from simple reactions between plausibly preactivated monomers.
[Mh] Termos MeSH primário: CMP Cíclico/química
CMP Cíclico/efeitos da radiação
Oligorribonucleotídeos/síntese química
RNA/síntese química
[Mh] Termos MeSH secundário: Dicroísmo Circular
Evolução Química
Modelos Químicos
Polimerização
Prótons
Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
Raios Ultravioleta
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Oligoribonucleotides); 0 (Protons); 3616-08-8 (Cyclic CMP); 63231-63-0 (RNA)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180122
[Lr] Data última revisão:
180122
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1002/cbic.201700122


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[PMID]:28911094
[Au] Autor:Sheng G; Gogakos T; Wang J; Zhao H; Serganov A; Juranek S; Tuschl T; Patel DJ; Wang Y
[Ad] Endereço:Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
[Ti] Título:Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes.
[So] Source:Nucleic Acids Res;45(15):9149-9163, 2017 Sep 06.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6'U7' and 6'A7' on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6'N7' bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson-Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction.
[Mh] Termos MeSH primário: Proteínas Argonauta/química
Proteínas de Bactérias/química
DNA Bacteriano/química
Oligodesoxirribonucleotídeos/química
Oligorribonucleotídeos/química
Thermus thermophilus/enzimologia
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Proteínas Argonauta/genética
Proteínas Argonauta/metabolismo
Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Pareamento de Bases
Sequência de Bases
Sítios de Ligação
Cristalografia por Raios X
Clivagem do DNA
DNA Bacteriano/genética
DNA Bacteriano/metabolismo
Expressão Gênica
Cinética
Modelos Moleculares
Mutação
Conformação de Ácido Nucleico
Oligodesoxirribonucleotídeos/metabolismo
Oligorribonucleotídeos/metabolismo
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
Especificidade por Substrato
Termodinâmica
Thermus thermophilus/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Argonaute Proteins); 0 (Bacterial Proteins); 0 (DNA, Bacterial); 0 (Oligodeoxyribonucleotides); 0 (Oligoribonucleotides); 0 (Recombinant Proteins)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171012
[Lr] Data última revisão:
171012
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170916
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx547


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[PMID]:28893424
[Au] Autor:Appling FD; Lucius AL; Schneider DA
[Ad] Endereço:Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
[Ti] Título:Quantifying the influence of 5'-RNA modifications on RNA polymerase I activity.
[So] Source:Biophys Chem;230:84-88, 2017 Nov.
[Is] ISSN:1873-4200
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:For ensemble and single-molecule analyses of transcription, the use of synthetic transcription elongation complexes has been a versatile and powerful tool. However, structural analyses demonstrate that short RNA substrates, often employed in these assays, would occupy space within the RNA polymerase. Most commercial RNA oligonucleotides do not carry a 5'-triphosphate as would be present on a natural, de novo synthesized RNA. To examine the effects of 5'-moities on transcription kinetics, we measured nucleotide addition and 3'-dinucleotide cleavage by eukaryotic RNA polymerase I using 5'-hydroxyl and 5'-triphosphate RNA substrates. We found that 5' modifications had no discernable effect on the kinetics of nucleotide addition; however, we observed clear, but modest, effects on the rate of backtracking and/or dinucleotide cleavage. These data suggest that the 5'-end may influence RNA polymerase translocation, consistent with previous prokaryotic studies, and these findings may have implications on kinetic barriers that confront RNA polymerases during the transition from initiation to elongation.
[Mh] Termos MeSH primário: RNA Polimerase I/metabolismo
RNA/metabolismo
[Mh] Termos MeSH secundário: Monofosfato de Adenosina/metabolismo
Cinética
Oligorribonucleotídeos/química
Oligorribonucleotídeos/metabolismo
RNA/química
Saccharomyces cerevisiae/enzimologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Oligoribonucleotides); 415SHH325A (Adenosine Monophosphate); 63231-63-0 (RNA); EC 2.7.7.6 (RNA Polymerase I)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171030
[Lr] Data última revisão:
171030
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170913
[St] Status:MEDLINE


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[PMID]:28823833
[Au] Autor:Tang F; Yang TL; Zhang Z; Li XG; Zhong QQ; Zhao TT; Gong L
[Ad] Endereço:Department of Cardiology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, PR China; Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou, PR China.
[Ti] Título:MicroRNA-21 suppresses ox-LDL-induced human aortic endothelial cells injuries in atherosclerosis through enhancement of autophagic flux: Involvement in promotion of lysosomal function.
[So] Source:Exp Cell Res;359(2):374-383, 2017 Oct 15.
[Is] ISSN:1090-2422
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Atherosclerosis is a common pathological basis of cardiovascular disease and remains the leading cause of mortality. Endothelial cell (EC) injury and autophagy dysfunction have been proved to contribute to the development of atherosclerosis. Recently, accumulating evidence confirms that microRNAs (miRNAs) have emerged as vital regulators and fine-tuners of various pathophysiological cellular impacts and molecular signaling pathways involved in atherosclerosis. Herein, the objective of the present study was to explore the biological function of miR-21 in oxidized low-density lipoprotein (ox-LDL)-induced human aortic endothelial cells (HAECs) injury and the underlying molecular mechanism. The results showed that ox-LDL treatment significantly decreased HAECs viability, increased caspase-3 activity, apoptosis ratio and Bax protein expression, and reduced Bcl-2 protein expression resulting in EC injuries. Simultaneously, ox-LDL treatment obviously reduced miR-21 level in a time-and dose-dependent manner. Notably, ox-LDL-induced EC injuries were abolished by miR-21 mimics transfection. In addition, miR-21 mimics alleviated ox-LDL-induced impaired autophagic flux as illustrated by the increases in LC3-II/LC3-I ratio and Beclin-1 protein expression, and the decrease in p62 protein expression in HAECs. Moreover, ox-LDL suppressed the expressions of lysosomal membrane protein (LAMP1) and cathepsin D proteins, and attenuated cathepsin D activity in HAECs, leading to lysosomal dysfunction, while these effects were also blocked by miR-21 mimics. These findings indicated that miR-21 restored impaired autophagic flux and lysosomal dysfunction, thereby attenuating ox-LDL-induced HAECs injuries.
[Mh] Termos MeSH primário: Autofagia/genética
Células Endoteliais/efeitos dos fármacos
Lipoproteínas LDL/farmacologia
MicroRNAs/genética
[Mh] Termos MeSH secundário: Aorta/citologia
Aorta/efeitos dos fármacos
Aorta/metabolismo
Autofagia/efeitos dos fármacos
Beclina-1/genética
Beclina-1/metabolismo
Caspase 3/genética
Caspase 3/metabolismo
Catepsina D/genética
Catepsina D/metabolismo
Linhagem Celular
Sobrevivência Celular/efeitos dos fármacos
Células Endoteliais/citologia
Células Endoteliais/metabolismo
Regulação da Expressão Gênica
Seres Humanos
Glicoproteínas de Membrana Associadas ao Lisossomo/genética
Glicoproteínas de Membrana Associadas ao Lisossomo/metabolismo
Lisossomos/efeitos dos fármacos
Lisossomos/metabolismo
MicroRNAs/antagonistas & inibidores
MicroRNAs/metabolismo
Proteínas Associadas aos Microtúbulos/genética
Proteínas Associadas aos Microtúbulos/metabolismo
Mimetismo Molecular
Oligorribonucleotídeos/genética
Oligorribonucleotídeos/metabolismo
Proteínas Proto-Oncogênicas c-bcl-2/genética
Proteínas Proto-Oncogênicas c-bcl-2/metabolismo
Proteína Sequestossoma-1/genética
Proteína Sequestossoma-1/metabolismo
Transdução de Sinais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (BCL2 protein, human); 0 (BECN1 protein, human); 0 (Beclin-1); 0 (LAMP1 protein, human); 0 (Lipoproteins, LDL); 0 (Lysosome-Associated Membrane Glycoproteins); 0 (MAP1LC3A protein, human); 0 (MIRN21 microRNA, human); 0 (MicroRNAs); 0 (Microtubule-Associated Proteins); 0 (Oligoribonucleotides); 0 (Proto-Oncogene Proteins c-bcl-2); 0 (SQSTM1 protein, human); 0 (Sequestosome-1 Protein); 0 (light chain 3, human); 0 (oxidized low density lipoprotein); EC 3.4.22.- (CASP3 protein, human); EC 3.4.22.- (Caspase 3); EC 3.4.23.5 (CTSD protein, human); EC 3.4.23.5 (Cathepsin D)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171104
[Lr] Data última revisão:
171104
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170822
[St] Status:MEDLINE


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[PMID]:28808060
[Au] Autor:Yang L; Wang C; Li F; Zhang J; Nayab A; Wu J; Shi Y; Gong Q
[Ad] Endereço:From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and.
[Ti] Título:The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity.
[So] Source:J Biol Chem;292(39):16221-16234, 2017 Sep 29.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:MEX-3 is a K-homology (KH) domain-containing RNA-binding protein first identified as a translational repressor in , and its four orthologs (MEX-3A-D) in human and mouse were subsequently found to have E3 ubiquitin ligase activity mediated by a RING domain and critical for RNA degradation. Current evidence implicates human MEX-3C in many essential biological processes and suggests a strong connection with immune diseases and carcinogenesis. The highly conserved dual KH domains in MEX-3 proteins enable RNA binding and are essential for the recognition of the 3'-UTR and post-transcriptional regulation of MEX-3 target transcripts. However, the molecular mechanisms of translational repression and the consensus RNA sequence recognized by the MEX-3C KH domain are unknown. Here, using X-ray crystallography and isothermal titration calorimetry, we investigated the RNA-binding activity and selectivity of human MEX-3C dual KH domains. Our high-resolution crystal structures of individual KH domains complexed with a noncanonical U-rich and a GA-rich RNA sequence revealed that the KH1/2 domains of human MEX-3C bound MRE10, a 10-mer RNA (5'-CAGAGUUUAG-3') consisting of an eight-nucleotide MEX-3-recognition element (MRE) motif, with high affinity. Of note, we also identified a consensus RNA motif recognized by human MEX-3C. The potential RNA-binding sites in the 3'-UTR of the human leukocyte antigen serotype ( ) mRNA were mapped with this RNA-binding motif and further confirmed by fluorescence polarization. The binding motif identified here will provide valuable information for future investigations of the functional pathways controlled by human MEX-3C and for predicting potential mRNAs regulated by this enzyme.
[Mh] Termos MeSH primário: Antígeno HLA-A2/metabolismo
Modelos Moleculares
RNA Mensageiro/metabolismo
Proteínas de Ligação a RNA/metabolismo
Elementos de Resposta
Ubiquitina-Proteína Ligases/metabolismo
[Mh] Termos MeSH secundário: Regiões 3' não Traduzidas
Sítios de Ligação
Cristalografia por Raios X
Antígeno HLA-A2/química
Antígeno HLA-A2/genética
Seres Humanos
Ligações de Hidrogênio
Cinética
Conformação de Ácido Nucleico
Motivos de Nucleotídeos
Oligorribonucleotídeos/química
Oligorribonucleotídeos/metabolismo
Fragmentos de Peptídeos/química
Fragmentos de Peptídeos/genética
Fragmentos de Peptídeos/metabolismo
Conformação Proteica
Domínios e Motivos de Interação entre Proteínas
Domínios RING Finger
RNA/química
RNA/metabolismo
RNA Mensageiro/química
Proteínas de Ligação a RNA/química
Proteínas de Ligação a RNA/genética
Proteínas Recombinantes/química
Proteínas Recombinantes/metabolismo
Ubiquitina-Proteína Ligases/química
Ubiquitina-Proteína Ligases/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (3' Untranslated Regions); 0 (HLA-A2 Antigen); 0 (MEX3C protein, human); 0 (Oligoribonucleotides); 0 (Peptide Fragments); 0 (RNA, Messenger); 0 (RNA-Binding Proteins); 0 (Recombinant Proteins); 63231-63-0 (RNA); EC 2.3.2.27 (Ubiquitin-Protein Ligases)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171016
[Lr] Data última revisão:
171016
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170816
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M117.797746


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[PMID]:28520497
[Au] Autor:Li Y; Li S; Luo Y; Liu Y; Yu N
[Ad] Endereço:1 Department of Surgery, Medical College, Hunan Normal University , Changsha, China .
[Ti] Título:LncRNA PVT1 Regulates Chondrocyte Apoptosis in Osteoarthritis by Acting as a Sponge for miR-488-3p.
[So] Source:DNA Cell Biol;36(7):571-580, 2017 Jul.
[Is] ISSN:1557-7430
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Long noncoding RNAs (lncRNAs) have been known to be involved in multiple diverse diseases, including osteoarthritis (OA). The present study aims at exploring the biological role of lncRNA plasmacytoma variant translocation 1 (PVT1) in OA and the underlying mechanism. Results showed that the expression of PVT1 was upregulated in OA chondrocytes compared with normal chondrocytes, silencing PVT1 inhibited the apoptosis of OA chondrocytes, and overexpression of PVT1 promoted the apoptosis of normal chondrocytes. To further investigate the underlying mechanism, miR-488-3p was predicted to be a targeted microRNA of PVT1. Different methods, including MS2 RNA immunoprecipitation (RIP), luciferase activity, and anti-AGO2 RIP, were performed to detect the interaction between PVT1 and miR-488-3p, which suggested that PVT1 negatively regulated miR-488-3p in OA chondrocytes. Moreover, PVT1 promoted the apoptosis of OA and normal chondrocytes through miR-488-3p. Collectively, this study revealed that lncRNA PVT1 regulated the apoptosis of chondrocytes by acting as a sponge for miR-488-3p in OA. PVT1 may be considered a new therapeutic target for the treatment of OA.
[Mh] Termos MeSH primário: Proteínas Argonauta/genética
Cartilagem Articular/metabolismo
Condrócitos/metabolismo
MicroRNAs/genética
Osteoartrite/genética
RNA Longo não Codificante/genética
[Mh] Termos MeSH secundário: Apoptose
Proteínas Argonauta/metabolismo
Sítios de Ligação
Cartilagem Articular/patologia
Condrócitos/patologia
Regulação da Expressão Gênica
Genes Reporter
Seres Humanos
Luciferases/genética
Luciferases/metabolismo
MicroRNAs/metabolismo
Oligorribonucleotídeos/genética
Oligorribonucleotídeos/metabolismo
Osteoartrite/metabolismo
Osteoartrite/patologia
Cultura Primária de Células
RNA Longo não Codificante/antagonistas & inibidores
RNA Longo não Codificante/metabolismo
Transdução de Sinais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Argonaute Proteins); 0 (EIF2C2 protein, human); 0 (MIRN488 microRNA, human); 0 (MicroRNAs); 0 (Oligoribonucleotides); 0 (PVT1 long-non-coding RNA, human); 0 (RNA, Long Noncoding); EC 1.13.12.- (Luciferases)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170920
[Lr] Data última revisão:
170920
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170519
[St] Status:MEDLINE
[do] DOI:10.1089/dna.2017.3678


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[PMID]:28436683
[Au] Autor:Wang Q; She Y; Bi X; Zhao B; Ruan X; Tan Y
[Ad] Endereço:1 Department of Anesthesiology, The First Affiliated Hospital of Jinan University , Guangzhou, China .
[Ti] Título:Dexmedetomidine Protects PC12 Cells from Lidocaine-Induced Cytotoxicity Through Downregulation of COL3A1 Mediated by miR-let-7b.
[So] Source:DNA Cell Biol;36(7):518-528, 2017 Jul.
[Is] ISSN:1557-7430
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Safety concerns of some local anesthetics, such as lidocaine, have been raised in recent years due to potential neurological impairment. Dexmedetomidine may protect humans from neurotoxicity, and miR-let-7b is activated by nerve injury; however, the roles of miR-let-7b and its target gene in lidocaine-induced cytotoxicity are not well known. Through bioinformatics and a luciferase reporter assay, COL3A1 was suggested as a direct target gene of miR-let-7b. Here, we confirmed by measuring mRNA and protein levels that miR-let-7b was downregulated and COL3A1 was upregulated in lidocaine-treated cells, an observation that was reversed by dexmedetomidine. Similar to miR-let-7b mimics or knockdown of COL3A1, dexmedetomidine treatment reduced the expression of COL3A1, suppressed cell apoptosis and cell migration/invasion ability, and induced cell cycle progression and cell proliferation in PC12 cells, effects that were reversed by the miR-let-7b inhibitor. Meanwhile, proteins involved in cell apoptosis, such as Bcl2 and caspase 3, were impacted as well. Taken together, dexmedetomidine may protect PC12 cells from lidocaine-induced cytotoxicity through miR-let-7b and COL3A1, while also increasing Bcl2 and inhibiting caspase 3. Therefore, miR-let-7b and COL3A1 might play critical roles in neuronal injury, and they are potential therapeutic targets.
[Mh] Termos MeSH primário: Agonistas de Receptores Adrenérgicos alfa 2/farmacologia
Colágeno Tipo III/genética
Dexmedetomidina/farmacologia
Lidocaína/toxicidade
MicroRNAs/genética
Fármacos Neuroprotetores/farmacologia
Bloqueadores do Canal de Sódio Disparado por Voltagem/toxicidade
[Mh] Termos MeSH secundário: Animais
Apoptose/efeitos dos fármacos
Caspase 3/genética
Caspase 3/metabolismo
Movimento Celular/efeitos dos fármacos
Proliferação Celular/efeitos dos fármacos
Colágeno Tipo III/antagonistas & inibidores
Colágeno Tipo III/metabolismo
Biologia Computacional
Regulação da Expressão Gênica
Genes Reporter
Lidocaína/antagonistas & inibidores
Luciferases/genética
Luciferases/metabolismo
MicroRNAs/antagonistas & inibidores
MicroRNAs/metabolismo
Oligorribonucleotídeos/genética
Oligorribonucleotídeos/metabolismo
Células PC12
Ligação Proteica
Proteínas Proto-Oncogênicas c-bcl-2/genética
Proteínas Proto-Oncogênicas c-bcl-2/metabolismo
RNA Interferente Pequeno/genética
RNA Interferente Pequeno/metabolismo
Ratos
Transdução de Sinais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Adrenergic alpha-2 Receptor Agonists); 0 (Bcl2 protein, rat); 0 (COL3A1 protein, rat); 0 (Collagen Type III); 0 (MIRNLET7 microRNA, rat); 0 (MicroRNAs); 0 (Neuroprotective Agents); 0 (Oligoribonucleotides); 0 (Proto-Oncogene Proteins c-bcl-2); 0 (RNA, Small Interfering); 0 (Voltage-Gated Sodium Channel Blockers); 67VB76HONO (Dexmedetomidine); 98PI200987 (Lidocaine); EC 1.13.12.- (Luciferases); EC 3.4.22.- (Casp3 protein, rat); EC 3.4.22.- (Caspase 3)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170920
[Lr] Data última revisão:
170920
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170425
[St] Status:MEDLINE
[do] DOI:10.1089/dna.2016.3623


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[PMID]:28426093
[Au] Autor:Choi YJ; Gibala KS; Ayele T; Deventer KV; Resendiz MJE
[Ad] Endereço:Department of Chemistry, University of Colorado Denver, Science Building 1151 Arapahoe St, Denver, CO 80204, USA.
[Ti] Título:Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA-a study of duplex, hairpins and the aptamer for preQ1 as models.
[So] Source:Nucleic Acids Res;45(4):2099-2111, 2017 Feb 28.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:8-10: A better understanding of the effects that oxidative lesions have on RNA is of importance to understand their role in the development/progression of disease. 8-oxo-7,8-dihydroguanine was incorporated into RNA to understand its structural and functional impact on RNA:RNA and RNA:DNA duplexes, hairpins and pseudoknots. One to three modifications were incorporated into dodecamers of RNA [AAGA GGG AUGAC] resulting in thermal destabilization (Δ T m - 10°C per lesion). Hairpins with tetraloops c-UUCG*-g* ( ), a-ACCG-g* ( ), c-UUG*G*-g* ( ) and c-ACG*G*-g* ( ) were modified and used to determine thermal stabilities, concluding that: (i) modifying the stem leads to destabilization unless adenosine is the opposing basepair of 8-oxoGua; (ii) modification at the loop is position- and sequence-dependent and varies from slight stabilization to large destabilization, in some cases leading to formation of other secondary structures (hairpin→duplex). Functional effects were established using the aptamer for preQ 1 as model. Modification at G5 disrupted the stem P1 and inhibited recognition of the target molecule 7-methylamino-7-deazaguanine (preQ 1 ). Modifying G11 results in increased thermal stability, albeit with a K d 4-fold larger than its canonical analog. These studies show the capability of 8-oxoG to affect structure and function of RNA, resulting in distinct outcomes as a function of number and position of the lesion.
[Mh] Termos MeSH primário: Guanina/análogos & derivados
Conformação de Ácido Nucleico
Oligorribonucleotídeos/química
Oligorribonucleotídeos/metabolismo
[Mh] Termos MeSH secundário: Aptâmeros de Nucleotídeos
DNA/química
DNA/metabolismo
Guanina/química
Guanina/metabolismo
Sequências Repetidas Invertidas
Espectroscopia de Ressonância Magnética
Pirimidinonas
Pirróis
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (7-(aminomethyl)-7-deazaguanine); 0 (Aptamers, Nucleotide); 0 (Oligoribonucleotides); 0 (Pyrimidinones); 0 (Pyrroles); 5614-64-2 (8-hydroxyguanine); 5Z93L87A1R (Guanine); 9007-49-2 (DNA)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171002
[Lr] Data última revisão:
171002
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170421
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkw885


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[PMID]:28383118
[Au] Autor:Shaik MM; Bhattacharjee N; Feliks M; Ng KK; Field MJ
[Ad] Endereço:Division of Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, 02115.
[Ti] Título:Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences.
[So] Source:Proteins;85(8):1435-1445, 2017 Aug.
[Is] ISSN:1097-0134
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Norovirus (NV) RNA-dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer-template duplex was investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the post-incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435-1445. © 2017 Wiley Periodicals, Inc.
[Mh] Termos MeSH primário: Cobre/química
Manganês/química
Norovirus/química
Oligorribonucleotídeos/química
RNA Replicase/química
Proteínas Virais/química
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Sítios de Ligação
Domínio Catalítico
Cátions Bivalentes
Cobalto/química
Cristalografia por Raios X
Ferro/química
Cinética
Simulação de Dinâmica Molecular
Níquel/química
Norovirus/enzimologia
Ligação Proteica
Conformação Proteica em alfa-Hélice
Conformação Proteica em Folha beta
Domínios e Motivos de Interação entre Proteínas
Teoria Quântica
RNA Replicase/genética
RNA Replicase/metabolismo
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Especificidade por Substrato
Termodinâmica
Proteínas Virais/genética
Proteínas Virais/metabolismo
Zinco/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cations, Divalent); 0 (Oligoribonucleotides); 0 (Recombinant Proteins); 0 (Viral Proteins); 3G0H8C9362 (Cobalt); 42Z2K6ZL8P (Manganese); 789U1901C5 (Copper); 7OV03QG267 (Nickel); E1UOL152H7 (Iron); EC 2.7.7.48 (RNA Replicase); J41CSQ7QDS (Zinc)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170825
[Lr] Data última revisão:
170825
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170407
[St] Status:MEDLINE
[do] DOI:10.1002/prot.25304


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[PMID]:28334903
[Au] Autor:Liu N; Zhou KI; Parisien M; Dai Q; Diatchenko L; Pan T
[Ad] Endereço:Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.
[Ti] Título:N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein.
[So] Source:Nucleic Acids Res;45(10):6051-6063, 2017 Jun 02.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA), and affects almost every stage of the mRNA life cycle. The YTH-domain proteins can specifically recognize m6A modification to control mRNA maturation, translation and decay. m6A can also alter RNA structures to affect RNA-protein interactions in cells. Here, we show that m6A increases the accessibility of its surrounding RNA sequence to bind heterogeneous nuclear ribonucleoprotein G (HNRNPG). Furthermore, HNRNPG binds m6A-methylated RNAs through its C-terminal low-complexity region, which self-assembles into large particles in vitro. The Arg-Gly-Gly repeats within the low-complexity region are required for binding to the RNA motif exposed by m6A methylation. We identified 13,191 m6A sites in the transcriptome that regulate RNA-HNRNPG interaction and thereby alter the expression and alternative splicing pattern of target mRNAs. Low-complexity regions are pervasive among mRNA binding proteins. Our results show that m6A-dependent RNA structural alterations can promote direct binding of m6A-modified RNAs to low-complexity regions in RNA binding proteins.
[Mh] Termos MeSH primário: Adenosina/análogos & derivados
Ribonucleoproteínas Nucleares Heterogêneas/metabolismo
Conformação de Ácido Nucleico
RNA/metabolismo
[Mh] Termos MeSH secundário: Adenosina/química
Processamento Alternativo
Sequência Conservada
Técnicas de Silenciamento de Genes
Células HEK293
Células HeLa
Seres Humanos
Metiltransferases/antagonistas & inibidores
Metiltransferases/genética
Oligorribonucleotídeos/síntese química
Oligorribonucleotídeos/química
Oligorribonucleotídeos/metabolismo
Filogenia
Ligação Proteica
RNA/química
Interferência de RNA
RNA Longo não Codificante/metabolismo
RNA Interferente Pequeno/genética
Análise de Sequência de RNA
Transcriptoma
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Heterogeneous-Nuclear Ribonucleoproteins); 0 (MALAT1 long non-coding RNA, human); 0 (Oligoribonucleotides); 0 (RNA, Long Noncoding); 0 (RNA, Small Interfering); 0 (heterogeneous nuclear ribonucleoprotein G, human); 1867-73-8 (N(6)-methyladenosine); 63231-63-0 (RNA); EC 2.1.1.- (METTL4 protein, human); EC 2.1.1.- (Methyltransferases); EC 2.1.1.62 (METTL3 protein, human); K72T3FS567 (Adenosine)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171002
[Lr] Data última revisão:
171002
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170324
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx141



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