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Pesquisa : D13.695.578.500.600 [Categoria DeCS]
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[PMID]:28615444
[Au] Autor:Qian Y; Johnson KA
[Ad] Endereço:From the Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas, Austin, Texas 78712.
[Ti] Título:The human mitochondrial single-stranded DNA-binding protein displays distinct kinetics and thermodynamics of DNA binding and exchange.
[So] Source:J Biol Chem;292(31):13068-13084, 2017 Aug 04.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The human mitochondrial ssDNA-binding protein (mtSSB) is a homotetrameric protein, involved in mtDNA replication and maintenance. Although mtSSB is structurally similar to SSB from (EcoSSB), it lacks the C-terminal disordered domain, and little is known about the biophysics of mtSSB-ssDNA interactions. Here, we characterized the kinetics and thermodynamics of mtSSB binding to ssDNA by equilibrium titrations and stopped-flow kinetic measurements. We show that the mtSSB tetramer can bind to ssDNA in two distinct binding modes: (SSB) and (SSB) , defined by DNA binding site sizes of 30 and 60 nucleotides, respectively. We found that the binding mode is modulated by magnesium ion and NaCl concentration, but unlike EcoSSB, the mtSSB does not show negative intersubunit cooperativity. Global fitting of both the equilibrium and kinetic data afforded estimates for the rate and equilibrium constants governing the formation of (SSB) and (SSB) complexes and for the transitions between the two binding modes. We found that the mtSSB tetramer binds to ssDNA with a rate constant near the diffusion limit (2 × 10 m s ) and that longer DNA (≥60 nucleotides) rapidly wraps around all four monomers, as revealed by FRET assays. We also show that the mtSSB tetramer can directly transfer from one ssDNA molecule to another via an intermediate with two DNA molecules bound to the mtSSB. In conclusion, our results indicate that human mtSSB shares many physicochemical properties with EcoSSB and that the differences may be explained by the lack of an acidic, disordered C-terminal tail in human mtSSB protein.
[Mh] Termos MeSH primário: DNA Mitocondrial/metabolismo
DNA de Cadeia Simples/metabolismo
Proteínas de Ligação a DNA/metabolismo
Proteínas de Escherichia coli/metabolismo
Proteínas Mitocondriais/metabolismo
Modelos Moleculares
[Mh] Termos MeSH secundário: Substituição de Aminoácidos
Sítios de Ligação
Calorimetria
DNA Mitocondrial/química
DNA de Cadeia Simples/química
Proteínas de Ligação a DNA/química
Proteínas de Ligação a DNA/genética
Ensaio de Desvio de Mobilidade Eletroforética
Proteínas de Escherichia coli/química
Proteínas de Escherichia coli/genética
Transferência Ressonante de Energia de Fluorescência
Corantes Fluorescentes/química
Seres Humanos
Cinética
Proteínas Mitocondriais/química
Proteínas Mitocondriais/genética
Mutação
Poli T/química
Poli T/metabolismo
Domínios e Motivos de Interação entre Proteínas
Multimerização Proteica
Proteínas Recombinantes/química
Proteínas Recombinantes/metabolismo
Termodinâmica
Titulometria
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Mitochondrial); 0 (DNA, Single-Stranded); 0 (DNA-Binding Proteins); 0 (Escherichia coli Proteins); 0 (Fluorescent Dyes); 0 (Mitochondrial Proteins); 0 (Recombinant Proteins); 0 (SSB protein, E coli); 0 (SSBP1 protein, human); 25086-81-1 (Poly T)
[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:170616
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M117.791392


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[PMID]:28256731
[Au] Autor:Tohala L; Oukacine F; Ravelet C; Peyrin E
[Ad] Endereço:DPM, UMR 5063, Université Grenoble Alpes, CNRS, Grenoble, France.
[Ti] Título:Sequence requirements of oligonucleotide chiral selectors for the capillary electrophoresis resolution of low-affinity DNA binders.
[So] Source:Electrophoresis;38(9-10):1383-1390, 2017 05.
[Is] ISSN:1522-2683
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:We recently reported that a great variety of DNA oligonucleotides (ONs) used as chiral selectors in partial-filling capillary electrophoresis (CE) exhibited interesting enantioresolution properties toward low-affinity DNA binders. Herein, the sequence prerequisites of ONs for the CE enantioseparation process were studied. First, the chiral resolution properties of a series of homopolymeric sequences (Poly-dT) of different lengths (from 5 to 60-mer) were investigated. It was shown that the size increase-dependent random coil-like conformation of Poly-dT favorably acted on the apparent selectivity and resolution. The base-unpairing state constituted also an important factor in the chiral resolution ability of ONs as the switch from the single-stranded to double-stranded structure was responsible for a significant decrease in the analyte selectivity range. Finally, the chemical diversity enhanced the enantioresolution ability of single-stranded ONs. The present work could lay the foundation for the design of performant ON chiral selectors for the CE separation of weak DNA binder enantiomers.
[Mh] Termos MeSH primário: Eletroforese Capilar/métodos
Oligonucleotídeos/química
[Mh] Termos MeSH secundário: Oligonucleotídeos/análise
Oligonucleotídeos/isolamento & purificação
Poli T/análise
Poli T/química
Poli T/isolamento & purificação
Estereoisomerismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Oligonucleotides); 25086-81-1 (Poly T)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171106
[Lr] Data última revisão:
171106
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170304
[St] Status:MEDLINE
[do] DOI:10.1002/elps.201600516


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[PMID]:27566394
[Au] Autor:Chi BZ; Liang RP; Qiu WB; Yuan YH; Qiu JD
[Ad] Endereço:College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, China.
[Ti] Título:Direct fluorescence detection of microRNA based on enzymatically engineered primer extension poly-thymine (EPEPT) reaction using copper nanoparticles as nano-dye.
[So] Source:Biosens Bioelectron;87:216-221, 2017 Jan 15.
[Is] ISSN:1873-4235
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:A new strategy based on enzymatically engineered primer extension poly-thymine (EPEPT) and nanomaterials in situ generation technology is reported for direct detection of microRNA (miRNA) in a fluorescence turn-on format using the sequential and complementary reactions catalyzed by Klenow Fragment exo (KFexo ) and terminal deoxynucleotidyl transferase (TdTase). The short miRNA can be efficiently converted into long poly-thymine (polyT) sequences, which function as template for in situ formation of fluorescence copper nanoparticles (CuNPs) as nano-dye for detecting miRNA. The polyT-CuNPs can effectively form and emit intense red fluorescence under the 340nm excitation. For the proof of concept, microRNA-21 (miR-21) was selected as the model target to testify this strategy as a versatile assay platform. By directly using miR-21 as the primer, the simple, rapid and sensitive miRNA detection was successfully achieved with a good linearity between 1pM and 1nM and a detection limit of 100fM. Thus, the EPEPT strategy holds great potential in biochemical sensing research as an efficient and universal platform.
[Mh] Termos MeSH primário: Técnicas Biossensoriais/métodos
Cobre/química
Corantes Fluorescentes/química
Nanopartículas Metálicas/química
MicroRNAs/análise
Poli T/química
[Mh] Termos MeSH secundário: Células A549
DNA Nucleotidilexotransferase/química
DNA Polimerase I/química
Fluorescência
Seres Humanos
Limite de Detecção
Células MCF-7
Espectrometria de Fluorescência/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Fluorescent Dyes); 0 (MIRN21 microRNA, human); 0 (MicroRNAs); 25086-81-1 (Poly T); 789U1901C5 (Copper); EC 2.7.7.- (DNA Polymerase I); EC 2.7.7.31 (DNA Nucleotidylexotransferase)
[Em] Mês de entrada:1702
[Cu] Atualização por classe:170816
[Lr] Data última revisão:
170816
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160828
[St] Status:MEDLINE


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[PMID]:27710901
[Au] Autor:Shin JH; Hwang YM; Jang YJ; Kim SK
[Ad] Endereço:Department of Chemistry, Yeungnam University, 212 Dae-dong, Gyeongsan City, Gyeong-buk 712-749, Republic of Korea.
[Ti] Título:Length and sequence effect on the B-Z transition of [d(A-T) ] oligonucleotide induced by a cationic porphyrin.
[So] Source:Biophys Chem;219:38-42, 2016 Dec.
[Is] ISSN:1873-4200
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:trans-BMPyP induced the B-Z transition for alternated AT oligonucleotides as it was evident by inversed CD spectrum. The transition occurred simultaneously with appearance of the extensive stacking of porphyrin. Complete B-Z transition required at least 14 base-pairs long. Insertion of one or two GC base pairs prevented the B-Z transition.
[Mh] Termos MeSH primário: Conformação de Ácido Nucleico/efeitos dos fármacos
Oligonucleotídeos/química
Porfirinas/farmacologia
[Mh] Termos MeSH secundário: Sequência de Bases
Cátions
Dicroísmo Circular
DNA de Forma B
DNA Forma Z
Poli A/química
Poli T/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cations); 0 (DNA, B-Form); 0 (DNA, Z-Form); 0 (Oligonucleotides); 0 (Porphyrins); 24937-83-5 (Poly A); 25086-81-1 (Poly T); 27156-07-6 (poly A-T)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170515
[Lr] Data última revisão:
170515
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161007
[St] Status:MEDLINE


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[PMID]:27192828
[Au] Autor:Surovaya AN; Bazhulina NP; Lepehina SY; Andronova VL; Galegov GA; Moiseeva ED; Grokhovsky SL; Gursky GV
[Ti] Título:[Interaction of Dystamycin Dimeric Analog with Poly(dA) x poly(dT), Poly[d(A-T)] x poly[d(A-T)] and Duplex O23 at Origin of Replication of the Herpes Simplex Virus].
[So] Source:Biofizika;61(2):270-6, 2016 Mar-Apr.
[Is] ISSN:0006-3029
[Cp] País de publicação:Russia (Federation)
[La] Idioma:rus
[Ab] Resumo:The binding of distamycin dimeric analog (Pt-bis-Dst) to poly[d(A-T)] x poly[d(A-T)1, poly(dA) x poly(dT) and duplex O23 with the sequence 5'-GCCAATATATATATATTATTAGG-3' which is present at the origin of replication of herpes simplex virus OriS is investigated with the use of UV and CD spectroscopy. The distinction of the synthetic polyamide from a natural antibiotic lies in the fact that in the synthetic polyamide there are two distamycin moieties bound via a glycine cis-diamino platinum group. It was shown that the binding of Pt-bis-Dst to poly[d(A-T)] x poly[d(A-T)] and poly(dA) x poly(dT) reaches saturation if one molecule of the ligand occurs at approximately every 8 bp. With further increase in the ratio of the added ligand to the base pairs in CD spectra of complexes with poly[d(A-T)] x poly[d(A-T)], we observed that the maximum wavelength band tend to be shifted towards longer wavelengths, while in the spectral region of 290-310 nm a "shoulder", that was absent in the spectra of the complexes obtained at low polymer coverages by the ligand, appeared. At high molar concentration ratios of ligand to oligonucleotide Pt-bis-Dst can bind to poly[d(A-T)] x poly[d(A-T)] in the form of hairpins or may form associates by the interaction between the distamycin moieties of neighboring molecules of Pt-bis-Dst. The structure of the complexes is stabilized by interactions between pirrolcarboxamide moieties of two molecules of Pt-bis-Dst adsorbed on adjacent overlapping binding sites. These interactions are probably also responsible for the concentration-dependent spectral changes observed during the formation of a complex between Pt-bis-Dst and poly[d(A-T)] x poly[d(A-T)]. Spectral changes are almost absent in binding of Pt-bis-Dst to poly(dA) x poly(dT). Binding of Pt-bis-Dst to duplex O23 reaches saturation if two ligand molecules occur in a duplex that contains a cluster of 18 AT pairs. With increasing the molar concentration ratio of the ligand to the duplex CD spectra undergo concentration-dependent changes similar to those observed during binding of Pt-bis-Dst to poly [d(A-T)] x poly[d(A-T)]. Testing for antiviral efficacy of Pt-bis-Dst showed that the concentration, at which the cytopathic effect produced by the herpes simplex virus in cell culture Vero E6 halved, is equal to 1.5 µg/ml and the selectivity index for evaluating antiviral activity is 65 at a relatively low cytotoxicity. The concentration of Pt-bis-Dst, at which approximately half the cells are killed, is equal to 100 µg/ml.
[Mh] Termos MeSH primário: Replicação do DNA/genética
Origem de Replicação/genética
Simplexvirus/química
[Mh] Termos MeSH secundário: Dicroísmo Circular
Conformação de Ácido Nucleico
Oligonucleotídeos/química
Poli A/química
Poli A/genética
Poli T/química
Poli T/genética
[Pt] Tipo de publicação:ENGLISH ABSTRACT; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Oligonucleotides); 24937-83-5 (Poly A); 25086-81-1 (Poly T); 25191-20-2 (poly(dA))
[Em] Mês de entrada:1606
[Cu] Atualização por classe:160519
[Lr] Data última revisão:
160519
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160520
[St] Status:MEDLINE


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[PMID]:26818653
[Au] Autor:Tremblay M; Brisson D; Gaudet D
[Ad] Endereço:Lipidology Unit, Community Genomic Medicine Center, Department of Medicine, Université de Montréal, Chicoutimi, Québec, Canada.
[Ti] Título:Association between a polymorphic poly-T repeat sequence in the promoter of the somatostatin gene and hypertension.
[So] Source:Hypertens Res;39(6):467-74, 2016 Jun.
[Is] ISSN:1348-4214
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Despite the numerous common pathways connecting blood pressure regulation to somatostatin (SST) metabolism, the SST gene has never been seen as a significant blood pressure modulator. The aim of this study was to evaluate the association between a poly-T repeat sequence (rs34872250) in the promoter of the SST gene and blood pressure, according to the obesity status. We genotyped 1918 French-Canadian subjects from a founder population. Analyses were performed according to the length of the poly-T repeat sequence on both alleles and divided into two groups, the 13/13-13/14 group and the 13/15-13/16 group. The effect of age, gender, body mass index, antihypertensive drugs and diabetic status were considered. Systolic, diastolic and mean blood pressures are significantly higher among the 13/15-13/16 group in the whole sample (P<0.05). Whereas the differences remain significant in women, they turn to be non-significant when men are considered alone. The risk of hypertension is increased in the 13/15-13/16 group, particularly among overweight/obese subjects. Systolic blood pressure is significantly higher among overweight/obese carriers of the 13/15-13/16 alleles in the whole sample (P<0.001), in men (P=0.006) and in women (P=0.002), even after correction for age and antihypertensive drugs. These results suggest that the poly-T repeat sequence polymorphism in the promoter of the SST gene is associated with significant variations of blood pressure and could modulate the risk of hypertension, particularly among women.
[Mh] Termos MeSH primário: Pressão Sanguínea/genética
Hipertensão/genética
Poli T/genética
Polimorfismo Genético
Regiões Promotoras Genéticas
Somatostatina/genética
[Mh] Termos MeSH secundário: Adulto
Alelos
Feminino
Estudos de Associação Genética
Predisposição Genética para Doença
Genótipo
Seres Humanos
Hipertensão/complicações
Masculino
Meia-Idade
Sobrepeso/complicações
Sobrepeso/genética
Fatores de Risco
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
25086-81-1 (Poly T); 51110-01-1 (Somatostatin)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170817
[Lr] Data última revisão:
170817
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160129
[St] Status:MEDLINE
[do] DOI:10.1038/hr.2016.4


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[PMID]:26756745
[Au] Autor:Lindqvist D; Prokopenko I; Londos E; Middleton L; Hansson O
[Ad] Endereço:Division of Psychiatry, Department of Clinical Sciences, Lund University, Lund, Sweden.
[Ti] Título:Associations between TOMM40 Poly-T Repeat Variants and Dementia in Cases with Parkinsonism.
[So] Source:J Parkinsons Dis;6(1):99-108, 2016.
[Is] ISSN:1877-718X
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Mitochondrial dysfunction has been implicated in the pathophysiology of Parkinson's disease (PD)-related pathologies. OBJECTIVE: To investigate the role of the Translocase of the Outer Mitochondrial Membrane 40 homolog (TOMM40) variants in PD without dementia (PDND), PD with dementia (PDD) and in Dementia with Lewy bodies (DLB). METHODS: 248 individuals, including 92 PDND, 55 PDD, and 101 DLB, were included. The rs10524523 locus in the TOMM40 gene (TOMM40 poly-T repeat) is characterized by a variable number of T residues that were classified into three groups based on length; short (S), long (L), and very long (VL). We tested log-additive genetic model of association with dementia and adjusted for age, sex, and APOEÉ›4 carrier status. We analyzed cerebrospinal fluid (CSF) levels of Aß42 and Tau, biomarkers related to Alzheimer's disease (AD). RESULTS: PDD/DBL status and abnormal CSF AD biomarkers (Aß42 and Aß42/Tau ratio) were both associated with the APOEÉ›4 allele (p <  0.014) and the L allele of TOMM40 poly-T repeat (p <  0.008). The VL allele was less frequently observed in the PDD/DLB group (p = 0.013). In APOE-É›4 adjusted analyses, the relationships between the L and VL alleles and dementia status as well as CSF AD biomarkers were not significant. When adjusting for APOE-É›4, however, there were associations between S carrier status and PDD/DLB (p = 0.019) and abnormal CSF levels of Aß42/Tau ratio (p = 0.037) although these were not significant after adjustment for multiple comparisons. CONCLUSION: Our results do not support the notion that TOMM40 poly-T repeat variants have independent effects on PDD and DLB pathology. This relationship seems to be driven by APOE-É›4.
[Mh] Termos MeSH primário: Demência/genética
Doença por Corpos de Lewy/genética
Proteínas de Membrana Transportadoras/genética
Transtornos Parkinsonianos/genética
Poli T/genética
[Mh] Termos MeSH secundário: Idoso
Apolipoproteínas E/genética
Biomarcadores/líquido cefalorraquidiano
Demência/patologia
Feminino
Genótipo
Seres Humanos
Doença por Corpos de Lewy/patologia
Masculino
Transtornos Parkinsonianos/patologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (ApoE protein, human); 0 (Apolipoproteins E); 0 (Biomarkers); 0 (Membrane Transport Proteins); 0 (TOMM40 protein, human); 25086-81-1 (Poly T)
[Em] Mês de entrada:1701
[Cu] Atualização por classe:170117
[Lr] Data última revisão:
170117
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160113
[St] Status:MEDLINE
[do] DOI:10.3233/JPD-150693


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[PMID]:26742581
[Au] Autor:Raveendran D; Raghavan SC
[Ad] Endereço:Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012, India.
[Ti] Título:Biochemical Characterization of Nonamer Binding Domain of RAG1 Reveals its Thymine Preference with Respect to Length and Position.
[So] Source:Sci Rep;6:19091, 2016 Jan 08.
[Is] ISSN:2045-2322
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:RAG complex consisting of RAG1 and RAG2 is a site-specific endonuclease responsible for the generation of antigen receptor diversity. It cleaves recombination signal sequence (RSS), comprising of conserved heptamer and nonamer. Nonamer binding domain (NBD) of RAG1 plays a central role in the recognition of RSS. To investigate the DNA binding properties of the domain, NBD of murine RAG1 was cloned, expressed and purified. Electrophoretic mobility shift assays showed that NBD binds with high affinity to nonamer in the context of 12/23 RSS or heteroduplex DNA. NBD binding was specific to thymines when single stranded DNA containing poly A, C, G or T were used. Biolayer interferometry studies showed that poly T binding to NBD was robust and comparable to that of 12RSS. More than 23 nt was essential for NBD binding at homothymidine stretches. On a double-stranded DNA, NBD could bind to A:T stretches, but not G:C or random sequences. Although NBD is indispensable for sequence specific activity of RAGs, external supplementation of purified nonamer binding domain to NBD deleted cRAG1/cRAG2 did not restore its activity, suggesting that the overall domain architecture of RAG1 is important. Therefore, we define the sequence requirements of NBD binding to DNA.
[Mh] Termos MeSH primário: DNA de Cadeia Simples/química
Proteínas de Ligação a DNA/química
Proteínas de Homeodomínio/química
Poli T/química
Receptores de Antígenos/química
[Mh] Termos MeSH secundário: Animais
Linfócitos B/citologia
Linfócitos B/imunologia
Linfócitos B/metabolismo
Sequência de Bases
Sítios de Ligação
Clonagem Molecular
DNA de Cadeia Simples/genética
Proteínas de Ligação a DNA/genética
Escherichia coli/genética
Escherichia coli/metabolismo
Expressão Gênica
Proteínas de Homeodomínio/genética
Camundongos
Poli A/química
Poli C/química
Poli G/química
Ligação Proteica
Domínios Proteicos
Sinais Direcionadores de Proteínas
Receptores de Antígenos/genética
Receptores de Antígenos/imunologia
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Linfócitos T/citologia
Linfócitos T/imunologia
Linfócitos T/metabolismo
Recombinação V(D)J
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Single-Stranded); 0 (DNA-Binding Proteins); 0 (Homeodomain Proteins); 0 (Protein Sorting Signals); 0 (Rag2 protein, mouse); 0 (Receptors, Antigen); 0 (Recombinant Proteins); 128559-51-3 (RAG-1 protein); 24937-83-5 (Poly A); 25086-81-1 (Poly T); 25191-14-4 (Poly G); 30811-80-4 (Poly C)
[Em] Mês de entrada:1612
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160109
[St] Status:MEDLINE
[do] DOI:10.1038/srep19091


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[PMID]:26685711
[Au] Autor:Del Bonis-O'Donnell JT; Pennathur S; Fygenson DK
[Ad] Endereço:Department of Mechanical Engineering, ‡Department of Physics, and §Program in Biomolecular Science & Engineering, University of California , Santa Barbara 93106, United States.
[Ti] Título:Changes in Spectra and Conformation of Hairpin DNA-Stabilized Silver Nanoclusters Induced by Stem Sequence Perturbations.
[So] Source:Langmuir;32(2):569-76, 2016 Jan 19.
[Is] ISSN:1520-5827
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:It is well-known that even small perturbations of the DNA sequence can drastically and unpredictably disrupt or alter the fluorescence of DNA-stabilized silver nanoclusters (DNA-AgNCs). Understanding how the structure of DNA affects the nanocluster that it stabilizes is the key to rationalizing such effects. We approach this challenge by strategically modifying the stem sequence of a hairpin DNA that hosts a spectrally pure, red-emitting nanocluster. Most of our modifications (base composition, sequence orientation, and loop location) reduce AgNC fluorescence in purity and shift it in wavelength, but one modification (appending poly(thymidine) to the 3' end of the stem) is inert with respect to fluorescence. Microfluidic capillary electrophoresis reveals that all of the modifications induce conformational changes of the DNA and that the original, spectrally pure nanocluster exists in two structurally distinct conformations. Interestingly, appending five or more thymidines, despite having no effect on fluorescence, eliminates this structural degeneracy. To explain this result, we propose that the original spectrally pure cluster is stabilized by a pair of hairpins whose stems can arrange in either a cis or trans orientation. Finally, we quantify the extent to which thymidine appendages of different lengths can be used to fine-tune the electrophoretic mobility of DNA-AgNC.
[Mh] Termos MeSH primário: DNA/química
Nanopartículas Metálicas/química
Poli T/química
Prata/química
[Mh] Termos MeSH secundário: Composição de Bases
Eletroforese Capilar
Fluorescência
Sequências Repetidas Invertidas
Dispositivos Lab-On-A-Chip
Dados de Sequência Molecular
Conformação de Ácido Nucleico
Espectrometria de Fluorescência
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
25086-81-1 (Poly T); 3M4G523W1G (Silver); 9007-49-2 (DNA)
[Em] Mês de entrada:1610
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151222
[St] Status:MEDLINE
[do] DOI:10.1021/acs.langmuir.5b03934


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[PMID]:26459910
[Au] Autor:Niu Y; Zhang L; Qiu H; Wu Y; Wang Z; Zai Y; Liu L; Qu J; Kang K; Gou D
[Ad] Endereço:Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, 518060, China.
[Ti] Título:An improved method for detecting circulating microRNAs with S-Poly(T) Plus real-time PCR.
[So] Source:Sci Rep;5:15100, 2015 Oct 13.
[Is] ISSN:2045-2322
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:We herein describe a simple, sensitive and specific method for analysis of circulating microRNAs (miRNA), termed S-Poly(T) Plus real-time PCR assay. This new method is based on our previously developed S-Poly(T) method, in which a unique S-Poly(T) primer is used during reverse-transcription to increase sensitivity and specificity. Further increased sensitivity and simplicity of S-Poly(T) Plus, in comparison with the S-Poly(T) method, were achieved by a single-step, multiple-stage reaction, where RNAs were polyadenylated and reverse-transcribed at the same time. The sensitivity of circulating miRNA detection was further improved by a modified method of total RNA isolation from serum/plasma, S/P miRsol, in which glycogen was used to increase the RNA yield. We validated our methods by quantifying miRNA expression profiles in the sera of the patients with pulmonary arterial hypertension associated with congenital heart disease. In conclusion, we developed a simple, sensitive, and specific method for detecting circulating miRNAs that allows the measurement of 266 miRNAs from 100 µl of serum or plasma. This method presents a promising tool for basic miRNA research and clinical diagnosis of human diseases based on miRNA biomarkers.
[Mh] Termos MeSH primário: Primers do DNA
MicroRNAs/genética
Poli T
[Mh] Termos MeSH secundário: Linhagem Celular
Perfilação da Expressão Gênica
Cardiopatias Congênitas/complicações
Cardiopatias Congênitas/genética
Seres Humanos
Hipertensão Pulmonar/etiologia
MicroRNAs/sangue
Reação em Cadeia da Polimerase em Tempo Real/métodos
Sensibilidade e Especificidade
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA Primers); 0 (MicroRNAs); 25086-81-1 (Poly T)
[Em] Mês de entrada:1608
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151014
[St] Status:MEDLINE
[do] DOI:10.1038/srep15100



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