Base de dados : MEDLINE
Pesquisa : D13.444.308.574 [Categoria DeCS]
Referências encontradas : 261 [refinar]
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  1 / 261 MEDLINE  
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[PMID]:28470278
[Au] Autor:Nakamura S; Yang H; Hirata C; Kersaudy F; Fujimoto K
[Ad] Endereço:School of Materials Science, Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, Japan. kenzo@jaist.ac.jp.
[Ti] Título:Development of F-NMR chemical shift detection of DNA B-Z equilibrium using F-NMR.
[So] Source:Org Biomol Chem;15(24):5109-5111, 2017 Jun 28.
[Is] ISSN:1477-0539
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on F-NMR chemical shift change.
[Mh] Termos MeSH primário: DNA de Forma B/análise
DNA de Forma B/química
DNA de Cadeia Simples/análise
DNA de Cadeia Simples/química
DNA Forma Z/análise
DNA Forma Z/química
[Mh] Termos MeSH secundário: Flúor
Espectroscopia de Ressonância Magnética/normas
Conformação de Ácido Nucleico
Padrões de Referência
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, B-Form); 0 (DNA, Single-Stranded); 0 (DNA, Z-Form); 284SYP0193 (Fluorine)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1039/c7ob00706j


  2 / 261 MEDLINE  
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[PMID]:29185909
[Au] Autor:Phromsiri P; Gerling RR; Blose JM
[Ad] Endereço:a The College at Brockport , State University of New York, Department of Chemistry and Biochemistry , Brockport , NY.
[Ti] Título:The effects of a neutral cosolute on the B to Z transition for DNA duplexes incorporating both CG and CA steps.
[So] Source:Nucleosides Nucleotides Nucleic Acids;36(11):690-703, 2017 Nov 02.
[Is] ISSN:1532-2335
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In the cell, nearly 40% of the volume is occupied by macromolecular crowding agents and smaller osmolytes accumulate in response to environmental stresses. Of particular interest is the influence of osmolytes on the transition of the right-handed B-DNA to the left-handed Z-DNA. Due to the correlation between Z-DNA formation potential and regions of active transcription, Z-DNA is believed to serve a vital role in the transcription process, and changes in osmolyte concentration may influence transcription as a part of the stress response. We utilized circular dichroism spectroscopy to monitor changes in conformation of DNA duplexes containing a full-turn of Z-DNA in the presence and absence of PEG 200. We used PEG 200 as a model neutral cosolute. Sodium ion titrations revealed that PEG 200 influenced the folding of Z-DNA compared to dilute solution conditions by decreasing the free energy of folding, increasing folding cooperativity, and decreasing the in vitro [Na ] and Δn required for folding for all sequences tested, even those that included 40% CA steps instead of the classic CG repeats. Moreover, the presence of 40% PEG 200 induced the Z-form conformation in sequences that would not fully adopt the Z-form structure even in 5 M NaCl. These results suggest that osmolytes may play a significant role in supporting the transient formation of Z-DNA in vivo, and that sequences containing a significant amounts of CA instead of CG repeats may more favorably adopt the Z-conformation as a part of binding and regulatory processes than had been previously considered.
[Mh] Termos MeSH primário: DNA de Forma B/química
DNA Forma Z/química
Conformação de Ácido Nucleico
[Mh] Termos MeSH secundário: Conformação de Ácido Nucleico/efeitos dos fármacos
Polietilenoglicóis/farmacologia
Soluções
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, B-Form); 0 (DNA, Z-Form); 0 (Solutions); 30IQX730WE (Polyethylene Glycols)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180101
[Lr] Data última revisão:
180101
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171130
[St] Status:MEDLINE
[do] DOI:10.1080/15257770.2017.1388395


  3 / 261 MEDLINE  
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[PMID]:28695860
[Au] Autor:Sunami T; Chatake T; Kono H
[Ad] Endereço:Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa 619-0215, Japan.
[Ti] Título:DNA conformational transitions inferred from re-evaluation of m|F | - D|F | electron-density maps.
[So] Source:Acta Crystallogr D Struct Biol;73(Pt 7):600-608, 2017 Jul 01.
[Is] ISSN:2059-7983
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies. In the present study, the m|F | - D|F | electron-density maps of double-helical DNA crystal structures were calculated at a resolution equal to or better than 1.5 Šand potential conformational transitions were found in 27% of DNA phosphates. Detailed analyses of the m|F | - D|F | peaks indicated that some of these unassigned densities correspond to ZI ↔ ZII or A/B → BI conformational transitions. A relationship was also found between ZI/ZII transitions and metal coordination in Z-DNA from the detected peaks. The present study highlights that frequent transitions of phosphate backbones occur even in crystals and that some of these transitions are affected by the local molecular environment.
[Mh] Termos MeSH primário: DNA/química
[Mh] Termos MeSH secundário: Cristalografia por Raios X/métodos
DNA Forma Z/química
Elétrons
Modelos Moleculares
Conformação de Ácido Nucleico
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Z-Form); 9007-49-2 (DNA)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170726
[Lr] Data última revisão:
170726
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170712
[St] Status:MEDLINE
[do] DOI:10.1107/S2059798317007707


  4 / 261 MEDLINE  
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[PMID]:27890616
[Au] Autor:Bhanjadeo MM; Nayak AK; Subudhi U
[Ad] Endereço:DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), New Delhi 110025, India.
[Ti] Título:Cerium chloride stimulated controlled conversion of B-to-Z DNA in self-assembled nanostructures.
[So] Source:Biochem Biophys Res Commun;482(4):916-921, 2017 Jan 22.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:DNA adopts different conformation not only because of novel base pairs but also while interacting with inorganic or organic compounds. Self-assembled branched DNA (bDNA) structures or DNA origami that change conformation in response to environmental cues hold great promises in sensing and actuation at the nanoscale. Recently, the B-Z transition in DNA is being explored to design various nanomechanical devices. In this communication we have demonstrated that Cerium chloride binds to the phosphate backbone of self-assembled bDNA structure and induce B-to-Z transition at physiological concentration. The mechanism of controlled conversion from right-handed to left-handed has been assayed by various dye binding studies using CD and fluorescence spectroscopy. Three different bDNA structures have been identified to display B-Z transition. This approach provides a rapid and reversible means to change bDNA conformation, which can be used for dynamic and progressive control at the nanoscale.
[Mh] Termos MeSH primário: Cério/química
DNA de Forma B/química
DNA Forma Z/química
Nanoestruturas/química
[Mh] Termos MeSH secundário: Sítios de Ligação
Dicroísmo Circular
Nanotecnologia/métodos
Conformação de Ácido Nucleico
Desnaturação de Ácido Nucleico
Espectrometria de Fluorescência
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, B-Form); 0 (DNA, Z-Form); 30K4522N6T (Cerium); TH8E3IE00V (cerous chloride)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170602
[Lr] Data última revisão:
170602
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161129
[St] Status:MEDLINE


  5 / 261 MEDLINE  
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[PMID]:27856245
[Au] Autor:Lee AR; Seo YJ; Choi SR; Ryu KS; Cheong HK; Lee SS; Katahira M; Park CJ; Lee JH
[Ad] Endereço:Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Gyeongnam 52828, Republic of Korea.
[Ti] Título:NMR elucidation of reduced B-Z transition activity of PKZ protein kinase at high NaCl concentration.
[So] Source:Biochem Biophys Res Commun;482(2):335-340, 2017 Jan 08.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A Z-DNA binding protein (ZBP)-containing protein kinase (PKZ) in fish species has an important role in the innate immune response. Previous structural studies of the Zα domain of the PKZ from Carassius auratus (caZα ) showed that the protein initially binds to B-DNA and induces B-Z transition of double stranded DNA in a salt concentration-dependent manner. However, the significantly reduced B-Z transition activity of caZα at high salt concentration was not fully understood. In this study, we present the binding affinity of the protein for B-DNA and Z-DNA and characterize its extremely low B-Z transition activity at 250 mM NaCl. Our results emphasize that the B-DNA-bound form of caZα can be used as molecular ruler to measure the degree of B-Z transition.
[Mh] Termos MeSH primário: DNA de Forma B/química
DNA Forma Z/química
Espectroscopia de Ressonância Magnética/métodos
Proteínas Quinases/química
Proteínas Quinases/ultraestrutura
Cloreto de Sódio/química
Proteínas de Peixe-Zebra/química
Proteínas de Peixe-Zebra/ultraestrutura
[Mh] Termos MeSH secundário: Sítios de Ligação
DNA de Forma B/ultraestrutura
DNA Forma Z/ultraestrutura
Ativação Enzimática
Cinética
Ligação Proteica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, B-Form); 0 (DNA, Z-Form); 0 (Zebrafish Proteins); 451W47IQ8X (Sodium Chloride); EC 2.7.- (PKZ protein, zebrafish); EC 2.7.- (Protein Kinases)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170522
[Lr] Data última revisão:
170522
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161119
[St] Status:MEDLINE


  6 / 261 MEDLINE  
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[PMID]:27841753
[Au] Autor:Drozdzal P; Gilski M; Jaskolski M
[Ad] Endereço:Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
[Ti] Título:Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations.
[So] Source:Acta Crystallogr D Struct Biol;72(Pt 11):1203-1211, 2016 11 01.
[Is] ISSN:2059-7983
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The self-complementary d(CGCGCG) hexanucleotide was synthesized with both D-2'-deoxyribose (the natural enantiomer) and L-2'-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form with C2/c symmetry that diffracted X-rays to 0.78 Šresolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to an R factor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg sites. The crystal structure is comprised of both left-handed (D-form) and right-handed (L-form) Z-DNA duplexes and shows an unexpectedly high degree of structural disorder, which is manifested by the presence of alternate conformations along the DNA backbone chains as well as at four nucleobases (including one base pair) modelled in double conformations. The crystal packing of the presented D/L-DNA-Mg structure exhibits novel DNA hydration patterns and an unusual arrangement of the DNA helices in the unit cell. The paper describes the structure in detail, concentrating on the mode of disorder, and compares the crystal packing of the racemic d(CGCGCG) duplex with those of other homochiral and heterochiral Z-DNA structures.
[Mh] Termos MeSH primário: DNA Forma Z/química
[Mh] Termos MeSH secundário: Pareamento de Bases
Sequência de Bases
Cristalografia por Raios X
Modelos Moleculares
Conformação de Ácido Nucleico
Oligonucleotídeos/química
Estereoisomerismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Z-Form); 0 (Oligonucleotides)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171117
[Lr] Data última revisão:
171117
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161115
[St] Status:MEDLINE


  7 / 261 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


  8 / 261 MEDLINE  
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[PMID]:27481249
[Au] Autor:Pittman KJ; Cervantes PW; Knoll LJ
[Ad] Endereço:Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA.
[Ti] Título:Z-DNA Binding Protein Mediates Host Control of Toxoplasma gondii Infection.
[So] Source:Infect Immun;84(10):3063-70, 2016 Oct.
[Is] ISSN:1098-5522
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Intrinsic to Toxoplasma gondii infection is the parasite-induced modulation of the host immune response, which ensures establishment of a chronic lifelong infection. This manipulation of the host immune response allows T. gondii to not only dampen the ability of the host to eliminate the parasite but also trigger parasite differentiation to the slow-growing, encysted bradyzoite form. We previously used RNA sequencing (RNA-seq) to profile the transcriptomes of mice and T. gondii during acute and chronic stages of infection. One of the most abundant host transcripts during acute and chronic infection was Z-DNA binding protein 1 (ZBP1). In this study, we determined that ZBP1 functions to control T. gondii growth. In activated macrophages isolated from ZBP1 deletion (ZBP1(-/-)) mice, T. gondii has an increased rate of replication and a decreased rate of degradation. We also identified a novel function for ZBP1 as a regulator of nitric oxide (NO) production in activated macrophages, even in the absence of T. gondii infection. Upon stimulation, T. gondii-infected ZBP1(-/-) macrophages display increased proinflammatory cytokines compared to wild-type macrophages under the same conditions. These in vitro phenotypes were recapitulated in vivo, with ZBP1(-/-) mice having increased susceptibility to oral challenge, higher cyst burdens during chronic infection, and elevated inflammatory cytokine responses. Taken together, these results highlight a role for ZBP1 in assisting host control of T. gondii infection.
[Mh] Termos MeSH primário: Proteínas de Ligação a DNA/fisiologia
Interações Hospedeiro-Parasita/fisiologia
Toxoplasma/patogenicidade
Toxoplasmose Animal/microbiologia
[Mh] Termos MeSH secundário: Doença Aguda
Animais
Doença Crônica
Citocinas/metabolismo
DNA Forma Z
Proteínas de Ligação a DNA/metabolismo
Modelos Animais de Doenças
Perfilação da Expressão Gênica
Macrófagos/metabolismo
Macrófagos/parasitologia
Camundongos
Camundongos Endogâmicos C57BL
Camundongos Knockout
Óxido Nítrico/metabolismo
Análise de Sequência de RNA
Toxoplasma/crescimento & desenvolvimento
Toxoplasmose Animal/imunologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cytokines); 0 (DNA, Z-Form); 0 (DNA-Binding Proteins); 31C4KY9ESH (Nitric Oxide)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170525
[Lr] Data última revisão:
170525
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160803
[St] Status:MEDLINE
[do] DOI:10.1128/IAI.00511-16


  9 / 261 MEDLINE  
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[PMID]:27351554
[Au] Autor:Gulis G; Silva IC; Sousa HR; Sousa IG; Bezerra MA; Quilici LS; Maranhao AQ; Brigido MM
[Ad] Endereço:Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil.
[Ti] Título:Characterization of an In Vivo Z-DNA Detection Probe Based on a Cell Nucleus Accumulating Intrabody.
[So] Source:Mol Biotechnol;58(8-9):585-94, 2016 Sep.
[Is] ISSN:1559-0305
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Left-handed Z-DNA is a physiologically unstable DNA conformation, and its existence in vivo can be attributed to localized torsional distress. Despite evidence for the existence of Z-DNA in vivo, its precise role in the control of gene expression is not fully understood. Here, an in vivo probe based on an anti-Z-DNA intrabody is proposed for native Z-DNA detection. The probe was used for chromatin immunoprecipitation of potential Z-DNA-forming sequences in the human genome. One of the isolated putative Z-DNA-forming sequences was cloned upstream of a reporter gene expression cassette under control of the CMV promoter. The reporter gene encoded an antibody fragment fused to GFP. Transient co-transfection of this vector along with the Z-probe coding vector improved reporter gene expression. This improvement was demonstrated by measuring reporter gene mRNA and protein levels and the amount of fluorescence in co-transfected CHO-K1 cells. These results suggest that the presence of the anti-Z-DNA intrabody can interfere with a Z-DNA-containing reporter gene expression. Therefore, this in vivo probe for the detection of Z-DNA could be used for global correlation of Z-DNA-forming sequences and gene expression regulation.
[Mh] Termos MeSH primário: Núcleo Celular/genética
Sondas de DNA/metabolismo
DNA Forma Z/isolamento & purificação
[Mh] Termos MeSH secundário: Animais
Células CHO
Linhagem Celular
Imunoprecipitação da Cromatina
Cricetinae
Cricetulus
DNA Forma Z/metabolismo
Regulação da Expressão Gênica
Genes Reporter
Seres Humanos
Células MCF-7
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Probes); 0 (DNA, Z-Form)
[Em] Mês de entrada:1703
[Cu] Atualização por classe:171108
[Lr] Data última revisão:
171108
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160629
[St] Status:MEDLINE
[do] DOI:10.1007/s12033-016-9958-6


  10 / 261 MEDLINE  
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[PMID]:27303797
[Au] Autor:Malinska M; Dauter Z
[Ad] Endereço:Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.
[Ti] Título:Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.
[So] Source:Acta Crystallogr D Struct Biol;72(Pt 6):770-9, 2016 06.
[Is] ISSN:2059-7983
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.
[Mh] Termos MeSH primário: Cristalografia por Raios X/métodos
DNA Forma Z/química
Oligopeptídeos/química
Tripsina/química
[Mh] Termos MeSH secundário: Animais
Bovinos
Modelos Moleculares
Conformação de Ácido Nucleico
Conformação Proteica
Eletricidade Estática
Raios X
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., INTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Z-Form); 0 (Oligopeptides); EC 3.4.21.4 (Trypsin)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171025
[Lr] Data última revisão:
171025
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160616
[St] Status:MEDLINE
[do] DOI:10.1107/S2059798316006355



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