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[PMID]:29462136
[Au] Autor:Lecamwasam A; Sexton-Oates A; Carmody J; Ekinci EI; Dwyer KM; Saffery R
[Ad] Endereço:Clinical and Disease Epigenetics Group, Murdoch Childrens Research Institute, Victoria, Australia.
[Ti] Título:DNA methylation profiling of genomic DNA isolated from urine in diabetic chronic kidney disease: A pilot study.
[So] Source:PLoS One;13(2):e0190280, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:AIM: To characterise the genomic DNA (gDNA) yield from urine and quality of derived methylation data generated from the widely used Illuminia Infinium MethylationEPIC (HM850K) platform and compare this with buffy coat samples. BACKGROUND: DNA methylation is the most widely studied epigenetic mark and variations in DNA methylation profile have been implicated in diabetes which affects approximately 415 million people worldwide. METHODS: QIAamp Viral RNA Mini Kit and QIAamp DNA micro kit were used to extract DNA from frozen and fresh urine samples as well as increasing volumes of fresh urine. Matched buffy coats to the frozen urine were also obtained and DNA was extracted from the buffy coats using the QIAamp DNA Mini Kit. Genomic DNA of greater concentration than 20µg/ml were used for methylation analysis using the HM850K array. RESULTS: Irrespective of extraction technique or the use of fresh versus frozen urine samples, limited genomic DNA was obtained using a starting sample volume of 5ml (0-0.86µg/mL). In order to optimize the yield, we increased starting volumes to 50ml fresh urine, which yielded only 0-9.66µg/mL A different kit, QIAamp DNA Micro Kit, was trialled in six fresh urine samples and ten frozen urine samples with inadequate DNA yields from 0-17.7µg/mL and 0-1.6µg/mL respectively. Sufficient genomic DNA was obtained from only 4 of the initial 41 frozen urine samples (10%) for DNA methylation profiling. In comparison, all four buffy coat samples (100%) provided sufficient genomic DNA. CONCLUSION: High quality data can be obtained provided a sufficient yield of genomic DNA is isolated. Despite optimizing various extraction methodologies, the modest amount of genomic DNA derived from urine, may limit the generalisability of this approach for the identification of DNA methylation biomarkers of chronic diabetic kidney disease.
[Mh] Termos MeSH primário: Metilação de DNA
DNA/urina
Complicações do Diabetes/urina
Insuficiência Renal Crônica/urina
[Mh] Termos MeSH secundário: Seres Humanos
Projetos Piloto
Insuficiência Renal Crônica/complicações
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180221
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190280


  2 / 262552 MEDLINE  
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[PMID]:29412476
[Au] Autor:Bakela K; Dimakopoulou M; Batsou P; Manidakis N; Athanassakis I
[Ad] Endereço:Laboratory of Immunology, Department of Biology, University of Crete, Heraklion, Crete, Greece.
[Ti] Título:Soluble MHC class II-driven therapy for a systemic lupus erythematosus murine experimental in vitro and in vivo model.
[So] Source:Scand J Immunol;87(3), 2018 Mar.
[Is] ISSN:1365-3083
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Taking into consideration the multiparametric nature of systemic lupus erythematosus (SLE), the severity and variability of symptoms and the lack of effective therapeutic approaches, this study took advantage of the recently described role of soluble major histocompatibility complex class II (sMHCII) molecules in maintaining tolerance to the organism and attempted to apply sMHCII proteins as a treatment to murine SLE experimental models in vitro as well as in vivo. After breaking tolerance to DNA in vitro, which was accompanied by development of specific anti-dsDNA antibodies, syngeneic or allogeneic sMHCII molecules, purified from healthy mouse serum, could significantly reduce the specific antibody levels and drive the system towards immunosuppression, as assessed by specific marker analysis on T cells and cytokine production by flow cytometry and ELISA, respectively. The in vivo experimental model consisted of pristane-induced SLE symptoms to BALB/c mice, which developed maximal levels of anti-dsDNA 2 months after pristane inoculation. Syngeneic or allogeneic sMHCII administration could alleviate pristane-induced symptoms, significantly decrease specific anti-dsDNA antibody production and develop immunosuppression to the host, as manifested by increase of CD4 + CTLA-4 +  and CD4 + CD25 +  cell populations in the spleen. Thus, the results presented in this study introduced the ability of sMHCII proteins to suppress specific autoantigen response, opening new areas of research and offering novel therapeutic approaches to SLE with expanding features to other autoimmune diseases.
[Mh] Termos MeSH primário: Anticorpos Antinucleares/imunologia
Autoantígenos/imunologia
Antígenos de Histocompatibilidade Classe II/imunologia
Tolerância Imunológica/imunologia
Imunoterapia/métodos
Lúpus Eritematoso Sistêmico/imunologia
Lúpus Eritematoso Sistêmico/terapia
Linfócitos T/imunologia
[Mh] Termos MeSH secundário: Animais
Antígenos CD4/metabolismo
Antígeno CTLA-4/metabolismo
Células Cultivadas
DNA/imunologia
Modelos Animais de Doenças
Imunossupressão
Subunidade alfa de Receptor de Interleucina-2/metabolismo
Lúpus Eritematoso Sistêmico/induzido quimicamente
Camundongos
Camundongos Endogâmicos BALB C
Baço/citologia
Baço/imunologia
Terpenos/efeitos adversos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antibodies, Antinuclear); 0 (Autoantigens); 0 (CD4 Antigens); 0 (CTLA-4 Antigen); 0 (Histocompatibility Antigens Class II); 0 (Il2ra protein, mouse); 0 (Interleukin-2 Receptor alpha Subunit); 0 (Terpenes); 26HZV48DT1 (pristane); 9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180208
[St] Status:MEDLINE
[do] DOI:10.1111/sji.12644


  3 / 262552 MEDLINE  
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[PMID]:29378242
[Au] Autor:Wang X; Xue M; Zhao M; He F; Li C; Li X
[Ad] Endereço:Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
[Ti] Título:Identification of a novel mutation (Ala66Thr) of SRY gene causes XY pure gonadal dysgenesis by affecting DNA binding activity and nuclear import.
[So] Source:Gene;651:143-151, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Sex-determining region of the Y chromosome (SRY) gene plays a crucial role in male sexual differentiation and development. Several mutations in the SRY gene have been reported in the high mobility group (HMG) box domain and can cause gonadal dysgenesis symptoms. In this study, we report that a novel missense mutation in the SRY gene, a G to A transition within the HMG box, causes the Ala66Thr amino acid substitution in a female patient presenting 46,XY karyotype with pure gonadal dysgenesis. The G to A base transition was not found in the SRY sequence after the screening of 100 normal males. Furthermore, Ala66Thr mutation drastically reduced the binding capacity of SRY to DNA sequences, whereas wild-type SRY protein showed the normal binding capacity to DNA sequences in vitro. We also found that the mutant SRY protein was partly localized in cytoplasm, whereas wild-type SRY protein was strictly localized in cell nucleus. In addition, we analyzed the three-dimensional structure of SRY protein by homology modeling methods. In conclusion, we identified a novel SRY mutation in a 46,XY female patient with pure gonadal dysgenesis, demonstrating the importance of the Ala66Thr mutation in DNA binding activity and nuclear transport.
[Mh] Termos MeSH primário: Disgenesia Gonadal 46 XY/genética
Mutação de Sentido Incorreto
Proteína da Região Y Determinante do Sexo/genética
[Mh] Termos MeSH secundário: Transporte Ativo do Núcleo Celular
Adolescente
Adulto
Alanina
DNA/metabolismo
Feminino
Células HEK293
Seres Humanos
Cariotipagem
Masculino
Ligação Proteica
Conformação Proteica
Análise de Sequência de DNA
Proteína da Região Y Determinante do Sexo/química
Proteína da Região Y Determinante do Sexo/metabolismo
Treonina
Adulto Jovem
[Pt] Tipo de publicação:CASE REPORTS; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Sex-Determining Region Y Protein); 2ZD004190S (Threonine); 9007-49-2 (DNA); OF5P57N2ZX (Alanine)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180130
[St] Status:MEDLINE


  4 / 262552 MEDLINE  
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[PMID]:29372577
[Au] Autor:Mansouri F; Heydarzadeh R; Yousefi S
[Ad] Endereço:Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
[Ti] Título:The association of interferon-gamma, interleukin-4 and interleukin-17 single-nucleotide polymorphisms with susceptibility to tuberculosis.
[So] Source:APMIS;126(3):227-233, 2018 Mar.
[Is] ISSN:1600-0463
[Cp] País de publicação:Denmark
[La] Idioma:eng
[Ab] Resumo:Susceptibility to tuberculosis and progression of the disease depend on interactions between the bacterial agent, host immune system, and environmental and genetic factors. In this case-controlled study, we aimed to determine the role of single-nucleotide polymorphisms of interferon-gamma, interleukin-4 and interleukin-17 in susceptibility to tuberculosis. Genomic DNA was extracted from peripheral blood samples of patients and controls. The association of single-nucleotide polymorphisms in interleukin-4 (-590C/T), interleukin-17 (-152A/G) and interferon-gamma (+874T/A) was investigated by polymerase chain reaction (PCR)-restriction fragment length polymorphism and amplification refractory mutation system-PCR. A total of 76 tuberculosis patients and 119 healthy individuals were included in this study. The interferon-gamma (+874T/A) TA genotype was significantly associated with susceptibility to tuberculosis in patients compared to controls (OR = 1.76; 95%CI = 0.84-3.71; p = 0.007), while the interferon-gamma (+874T/A) TT genotype (OR = 0.51; 95%CI = 0.19-1.36; p = 0.007) had protective effects against tuberculosis and was related to a low risk of tuberculosis development. The difference between allelic and genotypic frequencies of interleukin-4 (-590C/T) between patients and controls was not significant (p = 0.46). Multivariate logistic regression analysis revealed that the interleukin-17 (-152A/G) AG genotype (OR = 2.27; 95%CI = 1.19-4.34; p = 0.03) and AA genotype (OR = 1.03; 95%CI = 0.43-2.44; p = 0.03) were significantly different between patients and controls. In conclusion, single-nucleotide mutations in different cytokine genes may have protective effects or increase the risk of tuberculosis.
[Mh] Termos MeSH primário: Predisposição Genética para Doença
Interferon gama/genética
Interleucina-17/genética
Interleucina-4/genética
Tuberculose Pulmonar/genética
[Mh] Termos MeSH secundário: Adulto
Alelos
Estudos de Casos e Controles
DNA/genética
Feminino
Frequência do Gene/genética
Genótipo
Seres Humanos
Masculino
Meia-Idade
Mycobacterium tuberculosis/imunologia
Técnicas de Amplificação de Ácido Nucleico
Polimorfismo de Fragmento de Restrição
Polimorfismo de Nucleotídeo Único/genética
Tuberculose Pulmonar/microbiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (IL17A protein, human); 0 (IL4 protein, human); 0 (Interleukin-17); 207137-56-2 (Interleukin-4); 82115-62-6 (Interferon-gamma); 9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180127
[St] Status:MEDLINE
[do] DOI:10.1111/apm.12810


  5 / 262552 MEDLINE  
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[PMID]:29364930
[Au] Autor:Tang M; Zhang M; Yan S; Xia L; Yang Z; Du C; Cui HL; Wei D
[Ad] Endereço:Chongqing Key laboratory of Multi-Scale manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.
[Ti] Título:Detection of DNA oligonucleotides with base mutations by terahertz spectroscopy and microstructures.
[So] Source:PLoS One;13(1):e0191515, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:DNA oligonucleotides with a 5-base mutation at the 3'-terminus were investigated by terahertz (THz) spectroscopy in a marker-free manner. The four single-stranded oligonucleotides with 17nt have been detected with specificity on a microfluidic chip, and corroborated by spectral measurements with split-ring resonators. The number of hydrogen bonds formed between the oligonucleotide and its surrounding water molecules, deemed a key contribution to the THz absorption of biological solutions, was explored by molecular dynamics simulations to explain the experimental findings. Our work underlies the feasibility of THz spectroscopy combined with microstructures for marker-free detection of DNA, which may form the basis of a prospective diagnostic tool for studying genic mutation.
[Mh] Termos MeSH primário: DNA/química
Mutação
Espectroscopia Terahertz/métodos
[Mh] Termos MeSH secundário: DNA/genética
Microfluídica
Simulação de Dinâmica Molecular
Conformação de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180125
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191515


  6 / 262552 MEDLINE  
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[PMID]:29355528
[Au] Autor:Zhu J; Li S; Ramelot TA; Kennedy MA; Liu M; Yang Y
[Ad] Endereço:State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
[Ti] Título:Structural insights into the impact of two holoprosencephaly-related mutations on human TGIF1 homeodomain.
[So] Source:Biochem Biophys Res Commun;496(2):575-581, 2018 02 05.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Human protein TGIF1 is an essential regulator of cell fate with broad roles in different tissues, and has been implicated in holoprosencephaly (HPE) and many cancers. The function of TGIF1 in transcriptional regulation depends on its three-amino acid loop extension (TALE) type of homeodomain (HD). Two missense mutations that led to P192A and R219C substitutions in TGIF1-HD were previously found in HPE patients and suggested to be the causes for these cases. However, how these mutations affected TGIF1 function has not been investigated from a structural view. Here, we investigated the roles of P192 and R219 in TGIF1-HD structure packing through determining the NMR structure of TGIF1-HD. Surprisingly, P192 and R219 were found to play roles in packing α1 and α2 to α3 together with A190 and F215 through side-chain interactions. Circular dichroism (CD) showed that P192A and R219C mutants displayed structural change and less folding compared with wild-type TGIF1-HD, and H- N HSQC spectrum of P192A mutant exhibited chemical shift perturbations in all three helices of TGIF1-HD. Thus, it is suggested that P192A and R219C mutations led to structure disturbances of TGIF1-HD, which subsequently reduced the DNA-binding affinity of TGIF1-HD by 23-fold and 10-fold respectively, as revealed by the isothermal titration calorimetry (ITC) experiments. Our study provides structural insights of the probable pathogenesis mechanism of two TGIF1-related HPE cases, and evidences for the roles of P192 and R219 in HD folding.
[Mh] Termos MeSH primário: Holoprosencefalia/genética
Proteínas de Homeodomínio/química
Proteínas de Homeodomínio/genética
Mutação Puntual
Proteínas Repressoras/química
Proteínas Repressoras/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
DNA/metabolismo
Holoprosencefalia/metabolismo
Proteínas de Homeodomínio/metabolismo
Seres Humanos
Modelos Moleculares
Mutação de Sentido Incorreto
Ressonância Magnética Nuclear Biomolecular
Conformação Proteica
Dobramento de Proteína
Proteínas Repressoras/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Homeodomain Proteins); 0 (Repressor Proteins); 0 (TGIF1 protein, human); 9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180123
[St] Status:MEDLINE


  7 / 262552 MEDLINE  
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[PMID]:29339157
[Au] Autor:Teng Y; Pramanik S; Tateishi-Karimata H; Ohyama T; Sugimoto N
[Ad] Endereço:Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
[Ti] Título:Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition.
[So] Source:Biochem Biophys Res Commun;496(2):601-607, 2018 02 05.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The trinucleotide repeat d(CXG) (X = A, C, G or T) is the most common sequence causing repeat expansion disorders. The formation of non-canonical structures, such as hairpin structures with X-X mismatches, has been proposed to affect gene expression and regulation, which are important in pathological studies of these devastating neurological diseases. However, little information is available regarding the thermodynamics of the repeat sequence under crowded cellular conditions where many non-canonical structures such as G-quadruplexes are highly stabilized, while duplexes are destabilised. In this study, we investigated the different stabilities of X-X mismatches in the context of internal d(CXG) self-complementary sequences in an environment with a high concentration of cosolutes to mimic the crowding conditions in cells. The stabilities of full-matched duplexes and duplexes with A-A, G-G, and T-T mismatched base pairs under molecular crowding conditions were notably decreased compared to under dilute conditions. However, the stability of the DNA duplex with a C-C mismatch base pair was only slightly destabilised. Investigating different stabilities of X-X mismatches in d(CXG) sequences is important for improving our understanding of the formation and transition of multiple non-canonical structures in trinucleotide repeat diseases, and may provide insights for pathological studies and drug development.
[Mh] Termos MeSH primário: Pareamento Incorreto de Bases
DNA/genética
Repetições de Trinucleotídeos
[Mh] Termos MeSH secundário: Sequência de Bases
DNA/química
Quadruplex G
Conformação de Ácido Nucleico
Polietilenoglicóis/química
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
30IQX730WE (Polyethylene Glycols); 9007-49-2 (DNA)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180118
[St] Status:MEDLINE


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[PMID]:28465725
[Au] Autor:McEwen LM; Morin AM; Edgar RD; MacIsaac JL; Jones MJ; Dow WH; Rosero-Bixby L; Kobor MS; Rehkopf DH
[Ad] Endereço:Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada.
[Ti] Título:Differential DNA methylation and lymphocyte proportions in a Costa Rican high longevity region.
[So] Source:Epigenetics Chromatin;10:21, 2017.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The Nicoya Peninsula in Costa Rica has one of the highest old-age life expectancies in the world, but the underlying biological mechanisms of this longevity are not well understood. As DNA methylation is hypothesized to be a component of biological aging, we focused on this malleable epigenetic mark to determine its association with current residence in Nicoya versus elsewhere in Costa Rica. Examining a population's unique DNA methylation pattern allows us to differentiate hallmarks of longevity from individual stochastic variation. These differences may be characteristic of a combination of social, biological, and environmental contexts. METHODS: In a cross-sectional subsample of the Costa Rican Longevity and Healthy Aging Study, we compared whole blood DNA methylation profiles of residents from Nicoya ( = 48) and non-Nicoya (other Costa Rican regions,  = 47) using the Infinium HumanMethylation450 microarray. RESULTS: We observed a number of differences that may be markers of delayed aging, such as bioinformatically derived differential CD8+ T cell proportions. Additionally, both site- and region-specific analyses revealed DNA methylation patterns unique to Nicoyans. We also observed lower overall variability in DNA methylation in the Nicoyan population, another hallmark of younger biological age. CONCLUSIONS: Nicoyans represent an interesting group of individuals who may possess unique immune cell proportions as well as distinct differences in their epigenome, at the level of DNA methylation.
[Mh] Termos MeSH primário: Metilação de DNA
Longevidade/genética
Linfócitos/metabolismo
[Mh] Termos MeSH secundário: Idoso
Idoso de 80 Anos ou mais
Linfócitos T CD4-Positivos/citologia
Linfócitos T CD4-Positivos/metabolismo
Linfócitos T CD8-Positivos/citologia
Linfócitos T CD8-Positivos/metabolismo
Costa Rica
Ilhas de CpG
Estudos Transversais
DNA/química
DNA/isolamento & purificação
DNA/metabolismo
Epigenômica
Feminino
Seres Humanos
Linfócitos/citologia
Masculino
Meia-Idade
Células T Matadoras Naturais/citologia
Células T Matadoras Naturais/metabolismo
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170504
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0128-2


  9 / 262552 MEDLINE  
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[PMID]:28453010
[Au] Autor:Sethi S; Ooe M; Sakamoto T; Fujimoto K
[Ad] Endereço:School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan. kenzo@jaist.ac.jp.
[Ti] Título:Effect of nucleobase change on cytosine deamination through DNA photo-cross-linking reaction via 3-cyanovinylcarbazole nucleoside.
[So] Source:Mol Biosyst;13(6):1152-1156, 2017 Jun 01.
[Is] ISSN:1742-2051
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Photo-chemical deamination of cytosine using 3-cyanovinylcarbazole nucleoside ( K) mediated photo-cross-linking is a technique for site-directed mutagenesis. Using this technique in vivo requires the elimination of a high-temperature incubation step; instead, incubation should be carried out under physiological conditions. To improve the reactivity of K mediated photo-cross-link induced deamination of cytosine under physiological conditions, an evaluation of base pairing in cytosine was carried out with respect to its deamination. Guanine was replaced with 4 different counter bases (inosine, 2-aminopurine, 5-nitroindole, and nebularine), showing distinct hydrogen bonding patterns with target cytosine, which was incorporated at the -1 position with respect to K in the K-modified photo-responsive oligodeoxyribonucleotides to ascertain the role of hydrogen bonding in deamination under physiological conditions. Among the counter bases, inosine showed the highest acceleration towards the photo-induced deamination reaction.
[Mh] Termos MeSH primário: Citosina/química
DNA/química
Guanina/química
Nucleosídeos/química
[Mh] Termos MeSH secundário: 2-Aminopurina/química
Pareamento de Bases
Desaminação
Ligações de Hidrogênio
Indóis/química
Estrutura Molecular
Mutagênese Sítio-Dirigida
Oligodesoxirribonucleotídeos/química
Nucleosídeos de Purina/química
Ribonucleosídeos/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Indoles); 0 (Nucleosides); 0 (Oligodeoxyribonucleotides); 0 (Purine Nucleosides); 0 (Ribonucleosides); 452-06-2 (2-Aminopurine); 5Z93L87A1R (Guanine); 8J337D1HZY (Cytosine); 9007-49-2 (DNA); B8B604PS4P (nebularine); O2BHX6EDBN (5-nitroindole)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1039/c7mb00082k


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[PMID]:29286779
[Au] Autor:Chuang HM; Reifenberger JG; Cao H; Dorfman KD
[Ad] Endereço:Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA.
[Ti] Título:Sequence-Dependent Persistence Length of Long DNA.
[So] Source:Phys Rev Lett;119(22):227802, 2017 Dec 01.
[Is] ISSN:1079-7114
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Using a high-throughput genome-mapping approach, we obtained circa 50 million measurements of the extension of internal human DNA segments in a 41 nm×41 nm nanochannel. The underlying DNA sequences, obtained by mapping to the reference human genome, are 2.5-393 kilobase pairs long and contain percent GC contents between 32.5% and 60%. Using Odijk's theory for a channel-confined wormlike chain, these data reveal that the DNA persistence length increases by almost 20% as the percent GC content increases. The increased persistence length is rationalized by a model, containing no adjustable parameters, that treats the DNA as a statistical terpolymer with a sequence-dependent intrinsic persistence length and a sequence-independent electrostatic persistence length.
[Mh] Termos MeSH primário: DNA/química
DNA/genética
Modelos Químicos
Modelos Genéticos
[Mh] Termos MeSH secundário: Sequência de Bases
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Seres Humanos
Relação Estrutura-Atividade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171230
[St] Status:MEDLINE
[do] DOI:10.1103/PhysRevLett.119.227802



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