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Pesquisa : G01.906.595.850 [Categoria DeCS]
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[PMID]:29297914
[Au] Autor:Swadling JB; Ishii K; Tahara T; Kitao A
[Ad] Endereço:School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, M6-13, Meguro, Tokyo 152-8550, Japan. akitao@bio.titech.ac.jp.
[Ti] Título:Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation.
[So] Source:Phys Chem Chem Phys;20(5):2990-3001, 2018 Jan 31.
[Is] ISSN:1463-9084
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structure formation and stability. We use large parallel temperature replica exchange molecular dynamics ensembles to sample the full conformational landscape of these hairpin molecules so that we can identify the stable structures formed by the hairpin sequence. Our simulations show RNA adopts a narrower distribution of folded structures compared to DNA at room temperature, which forms both hairpins and many unfolded conformations. RNA is capable of forming twice as many hydrogen bonds than DNA which results in a higher melting temperature. We see that local chemical differences lead to emergent molecular properties such as increased persistence length in RNA that is weakly temperature dependant. These discoveries provide fundamental insight into how RNA forms complex folded tertiary structures which confer enzymatic-like function in ribozymes, whereas DNA retains structural motifs in order to facilitate function such as translation of sequence.
[Mh] Termos MeSH primário: DNA/química
Simulação de Dinâmica Molecular
RNA/química
[Mh] Termos MeSH secundário: Transferência Ressonante de Energia de Fluorescência
Ligações de Hidrogênio
Sequências Repetidas Invertidas/genética
Conformação de Ácido Nucleico
Termodinâmica
Temperatura de Transição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
63231-63-0 (RNA); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180104
[St] Status:MEDLINE
[do] DOI:10.1039/c7cp06355e


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[PMID]:29413989
[Au] Autor:Marques RA; Gomes AOCV; de Brito MV; Dos Santos ALP; da Silva GS; de Lima LB; Nunes FM; de Mattos MC; de Oliveira FCE; do Ó Pessoa C; de Moraes MO; de Fátima Â; Franco LL; Silva MM; Dantas MDA; Santos JCC; Figueiredo IM; da Silva-Júnior EF; de Aquino TM; de Araújo-Júnior JX; de Oliveira MCF; Leslie Gunatilaka AA
[Ad] Endereço:Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Ceará, Brazil; Northern Educational Union - UNINORTE, Rio Branco, Acre, Brazil.
[Ti] Título:Annonalide and derivatives: Semisynthesis, cytotoxic activities and studies on interaction of annonalide with DNA.
[So] Source:J Photochem Photobiol B;179:156-166, 2018 Feb.
[Is] ISSN:1873-2682
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:The cytotoxic activity of the pimarane diterpene annonalide (1) and nine of its semisynthetic derivatives (2-10) was investigated against the human tumor cell lines HL-60 (leukemia), PC-3 (prostate adenocarcinoma), HepG2 (hepatocellular carcinoma), SF-295 (glioblastoma) and HCT-116 (colon cancer), and normal mouse fibroblast (L929) cells. The preparation of 2-10 involved derivatization of the side chain of 1 at C-13. Except for 2, all derivatives are being reported for the first time. Most of the tested compounds presented IC s below 4.0 µM, being considered potential antitumor agents. The structures of all new compounds were elucidated by spectroscopic analyses including 2D NMR and HRMS. Additionally, the interaction of annonalide (1) with ctDNA was evaluated using spectroscopic techniques, and the formation of a supramolecular complex with the macromolecule was confirmed. Competition assays with fluorescent probes (Hoechst and ethidium bromide) and theoretical studies confirmed that 1 interacts preferentially via DNA intercalation with stoichiometric ratio of 1:1 (1:ctDNA). The ΔG value was calculated as -28.24 kJ mol , and indicated that the interaction process occurs spontaneously. Docking studies revealed that van der Walls is the most important interaction in 1-DNA and EB-DNA complexes, and that both ligands (1 and EB) interact with the same DNA residues (DA6, DA17 and DT19).
[Mh] Termos MeSH primário: Ciclo-Octanos/química
DNA/química
Cetonas/química
[Mh] Termos MeSH secundário: Animais
Sítios de Ligação
Bovinos
Linhagem Celular Tumoral
Sobrevivência Celular
Ciclo-Octanos/síntese química
Ciclo-Octanos/toxicidade
DNA/metabolismo
Ensaios de Seleção de Medicamentos Antitumorais
Seres Humanos
Cetonas/síntese química
Cetonas/toxicidade
Simulação de Acoplamento Molecular
Conformação de Ácido Nucleico
Espectrofotometria
Eletricidade Estática
Termodinâmica
Temperatura de Transição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cyclooctanes); 0 (Ketones); 502-49-8 (cyclooctanone); 9007-49-2 (DNA); 91080-16-9 (calf thymus DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180223
[Lr] Data última revisão:
180223
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180208
[St] Status:MEDLINE


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[PMID]:28470260
[Au] Autor:Han Y; Zhang Z; Smith GS; Do C
[Ad] Endereço:Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. doc1@ornl.gov.
[Ti] Título:Effect of nucleoside analogue antimetabolites on the structure of PEO-PPO-PEO micelles investigated by SANS.
[So] Source:Phys Chem Chem Phys;19(24):15686-15692, 2017 Jun 21.
[Is] ISSN:1463-9084
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The effect of three nucleoside analogue antimetabolites (5-fluorouracil, floxuridine, and gemcitabine) on the structure of Pluronic L62 copolymer micelles was investigated using small-angle neutron scattering. These antimetabolites used for cancer chemotherapy have analogous molecular structures but different molecular sizes and aqueous solubilities. It was found that the addition of the three antimetabolites slightly reduced the micellar size and aggregation number, and the micellar anisotropy. The added antimetabolites also changed the internal molecular distribution of the micelles as measured by the scattering length densities, resulting in enhanced hydration of the hydrophobic core region of the micelle. The strength of the effect was found to correlate with the molecular properties of the model drugs, i.e. a larger molecular size and a higher aqueous solubility lead to enhanced hydration of the micellar core.
[Mh] Termos MeSH primário: Antimetabólitos/química
Micelas
Difração de Nêutrons
Polietilenoglicóis/química
Propilenoglicóis/química
Espalhamento a Baixo Ângulo
[Mh] Termos MeSH secundário: Desoxicitidina/análogos & derivados
Desoxicitidina/química
Floxuridina/química
Fluoruracila/química
Poloxâmero/química
Temperatura de Transição
Água/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antimetabolites); 0 (Micelles); 0 (PEO-PPO-PEO); 0 (Propylene Glycols); 039LU44I5M (Floxuridine); 059QF0KO0R (Water); 0W860991D6 (Deoxycytidine); 106392-12-5 (Poloxamer); 30IQX730WE (Polyethylene Glycols); B76N6SBZ8R (gemcitabine); U3P01618RT (Fluorouracil)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1039/c7cp02028g


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[PMID]:29304068
[Au] Autor:Drake AC; Lee Y; Burgess EM; Karlsson JOM; Eroglu A; Higgins AZ
[Ad] Endereço:School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, United States of America.
[Ti] Título:Effect of water content on the glass transition temperature of mixtures of sugars, polymers, and penetrating cryoprotectants in physiological buffer.
[So] Source:PLoS One;13(1):e0190713, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Long-term storage of viable mammalian cells is important for applications ranging from in vitro fertilization to cell therapy. Cryopreservation is currently the most common approach, but storage in liquid nitrogen is relatively costly and the requirement for low temperatures during shipping is inconvenient. Desiccation is an alternative strategy with the potential to enable viable cell preservation at more convenient storage temperatures without the need for liquid nitrogen. To achieve stability during storage in the dried state it is necessary to remove enough water that the remaining matrix forms a non-crystalline glassy solid. Thus, the glass transition temperature is a key parameter for design of cell desiccation procedures. In this study, we have investigated the effects of moisture content on the glass transition temperature (Tg) of mixtures of sugars (trehalose or raffinose), polymers (polyvinylpyrrolidone or Ficoll), penetrating cryoprotectants (ethylene glycol, propylene glycol, or dimethyl sulfoxide), and phosphate buffered saline (PBS) solutes. Aqueous solutions were dried to different moisture contents by equilibration with saturated salt solutions, or by baking at 95°C. The glass transition temperatures of the dehydrated samples were then measured by differential scanning calorimetry. As expected, Tg increased with decreasing moisture content. For example, in a desiccation medium containing 0.1 M trehalose in PBS, Tg ranged from about 360 K for a completely dry sample to about 220 K at a water mass fraction of 0.4. Addition of polymers to the solutions increased Tg, while addition of penetrating cryoprotectants decreased Tg. Our results provide insight into the relationship between relative humidity, moisture content and glass transition temperature for cell desiccation solutions containing sugars, polymers and penetrating cryoprotectants.
[Mh] Termos MeSH primário: Crioprotetores/química
Polímeros/química
Açúcares/química
Temperatura de Transição
Água/química
[Mh] Termos MeSH secundário: Tampões (Química)
Varredura Diferencial de Calorimetria
Criopreservação/métodos
Dessecação/métodos
Dimetil Sulfóxido/química
Etilenoglicol/química
Ficoll/química
Vidro/química
Modelos Teóricos
Povidona/química
Propilenoglicol/química
Rafinose/química
Soluções/química
Trealose/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Buffers); 0 (Cryoprotective Agents); 0 (Polymers); 0 (Solutions); 0 (Sugars); 059QF0KO0R (Water); 25702-74-3 (Ficoll); 6DC9Q167V3 (Propylene Glycol); B8WCK70T7I (Trehalose); FC72KVT52F (Ethylene Glycol); FZ989GH94E (Povidone); N5O3QU595M (Raffinose); YOW8V9698H (Dimethyl Sulfoxide)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180205
[Lr] Data última revisão:
180205
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180106
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190713


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[PMID]:28470825
[Au] Autor:Börner T; Rämisch S; Bartsch S; Vogel A; Adlercreutz P; Grey C
[Ad] Endereço:Department of Chemistry and Biotechnology, Institute of Materials Science, Nestlé Research Center, Route du Jorat 57, 1000, Lausanne 26, Switzerland.
[Ti] Título:Three in One: Temperature, Solvent and Catalytic Stability by Engineering the Cofactor-Binding Element of Amine Transaminase.
[So] Source:Chembiochem;18(15):1482-1486, 2017 08 04.
[Is] ISSN:1439-7633
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Amine transaminase (ATA) catalyse enantioselectively the direct amination of ketones, but insufficient stability during catalysis limits their industrial applicability. Recently, we revealed that ATAs suffer from substrate-induced inactivation mechanism involving dissociation of the enzyme-cofactor intermediate. Here, we report on engineering the cofactor-ring-binding element, which also shapes the active-site entrance. Only two point mutations in this motif improved temperature and catalytic stability in both biphasic media and organic solvent. Thermodynamic analysis revealed a higher melting point for the enzyme-cofactor intermediate. The high cofactor affinity eliminates the need for pyridoxal 5'-phosphate supply, thus making large-scale reactions more cost effective. This is the first report on stabilising a tetrameric ATA by mutating a single structural element. As this structural "hotspot" is a common feature of other transaminases it could serve as a general engineering target.
[Mh] Termos MeSH primário: Transaminases/química
[Mh] Termos MeSH secundário: Sítios de Ligação
Dimetil Sulfóxido/química
Estabilidade Enzimática
Propilaminas/química
Engenharia de Proteínas
Estrutura Quaternária de Proteína
Fosfato de Piridoxal/química
Piridoxamina/análogos & derivados
Piridoxamina/química
Solventes/química
Temperatura Ambiente
Temperatura de Transição
Água/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Propylamines); 0 (Solvents); 059QF0KO0R (Water); 5V5IOJ8338 (Pyridoxal Phosphate); 6466NM3W93 (Pyridoxamine); EC 2.6.1.- (Transaminases); P8W26T4MTD (2-propylamine); QWW7V29814 (pyridoxamine phosphate); YOW8V9698H (Dimethyl Sulfoxide)
[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.201700236


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[PMID]:29177444
[Au] Autor:Huguet JM; Ribezzi-Crivellari M; Bizarro CV; Ritort F
[Ad] Endereço:Condensed Matter Physics Department, University of Barcelona, C/Marti i Franques s/n, 08028 Barcelona, Spain.
[Ti] Título:Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments.
[So] Source:Nucleic Acids Res;45(22):12921-12931, 2017 Dec 15.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections.
[Mh] Termos MeSH primário: DNA/química
Magnésio/química
Termodinâmica
Temperatura de Transição
[Mh] Termos MeSH secundário: Algoritmos
Composição de Bases
Pareamento de Bases
DNA/genética
DNA/metabolismo
Cinética
Magnésio/metabolismo
Modelos Químicos
Conformação de Ácido Nucleico
Hibridização de Ácido Nucleico/métodos
Sódio/química
Sódio/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
9007-49-2 (DNA); 9NEZ333N27 (Sodium); I38ZP9992A (Magnesium)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180115
[Lr] Data última revisão:
180115
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx1161


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[PMID]:28890237
[Au] Autor:Reddy ST; Swamy MJ
[Ad] Endereço:School of Chemistry, University of Hyderabad, Hyderabad 500 046, India.
[Ti] Título:Molecular structure, supramolecular organization and thermotropic phase behavior of N-acylglycine alkyl esters with matched acyl and alkyl chains.
[So] Source:Chem Phys Lipids;208:43-51, 2017 Nov.
[Is] ISSN:1873-2941
[Cp] País de publicação:Ireland
[La] Idioma:eng
[Ab] Resumo:N-Acylglycines (NAGs), the endogenous single-tailed lipids present in rat brain and other mammalian tissues, play significant roles in cell physiology and exhibit interesting pharmacological properties. In the present study, a homologous series of N-acylglycine alkyl esters (NAGEs) with matched chains were synthesized and characterized. Results of differential scanning calorimetric studies revealed that all NAGEs exhibit a single sharp phase transition and that the transition enthalpy and entropy show a linear dependence on the N-acyl and ester alkyl chain length. The structure of N-myristoylglycine myristyl ester (NMGME), solved by single-crystal X-ray diffraction, showed that the molecule adopts a linear geometry and revealed that the structure of N-myristoyl glycyl moiety in NMGME is identical to that in N-myristoylglycine. The molecules are packed in layers with the polar functional groups of the ester and amide functionalities located at the center of the layer. The crystal packing is stabilized by NH⋯O hydrogen bonds between the amide CO and NH groups of adjacent molecules as well as by CH⋯O hydrogen bonds between the amide carbonyl and the methylene CH adjacent to the ester carbonyl of neighboring molecules as well as between ester carbonyl and methylene group of the glycine moiety of adjacent molecules. Powder X-ray diffraction studies showed a linear dependence of the d-spacings on the acyl chain length, suggesting that all NAGEs adopt a structure similar to the packing exhibited in the crystal lattice of NMGME.
[Mh] Termos MeSH primário: Ésteres/química
Glicina/análogos & derivados
Ácidos Mirísticos/química
Temperatura de Transição
[Mh] Termos MeSH secundário: Entropia
Glicina/química
Modelos Moleculares
Conformação Molecular
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Esters); 0 (Myristic Acids); 14246-55-0 (N-myristoylglycine); TE7660XO1C (Glycine)
[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:170912
[St] Status:MEDLINE


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[PMID]:28888939
[Au] Autor:Takahashi H; Jojiki K
[Ad] Endereço:Biophysics Laboratory, Division of Pure and Applied Science, Graduate School of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan. Electronic address: hirotakahashi@gunma-u.ac.jp.
[Ti] Título:Water isotope effect on the lipidic cubic phase: Heavy water-Induced interfacial area reduction of monoolein-Water system.
[So] Source:Chem Phys Lipids;208:52-57, 2017 Nov.
[Is] ISSN:1873-2941
[Cp] País de publicação:Ireland
[La] Idioma:eng
[Ab] Resumo:Heavy water (D O) affects various functions of cells and living things. In order to gain fundamental insight into the molecular mechanism on biological effects of heavy water, D O-effects on fully hydrated monoolein (MO) systems were investigated from the structural viewpoints. At room temperature, the MO fully hydrated by pure light water (H O) forms a bicontinuous cubic (Pn3m) phase, and then, the Pn3m cubic phase transforms into an inverted hexagonal (H ) phase at about 90°C. Temperature-scan X-ray diffraction measurements showed that substitution of D O for H O lowers the Pn3m-to-H phase transition temperature and reduces the lattice constants of both phases. The structural analysis of the Pn3m phase using the diffraction intensity data indicated that D O reduces the surface occupied area of MO at the interface by 12% in comparison with H O. This change is probably due to the difference of the strength of hydrogen bond.
[Mh] Termos MeSH primário: Óxido de Deutério/química
Glicerídeos/química
[Mh] Termos MeSH secundário: Propriedades de Superfície
Temperatura de Transição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Glycerides); C4YAD5F5G6 (monoolein); J65BV539M3 (Deuterium Oxide)
[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:170911
[St] Status:MEDLINE


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[PMID]:28825481
[Au] Autor:Mary V; Haris P; Varghese MK; Aparna P; Sudarsanakumar C
[Ad] Endereço:School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India.
[Ti] Título:Experimental Probing and Molecular Dynamics Simulation of the Molecular Recognition of DNA Duplexes by the Flavonoid Luteolin.
[So] Source:J Chem Inf Model;57(9):2237-2249, 2017 Sep 25.
[Is] ISSN:1549-960X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Luteolin (C H O ) is an important flavonoid found in many fruits, plants, medicinal herbs, and vegetables exhibiting many pharmacological properties. The anticancer, antitumor, antioxidant, and anti-inflammatory activities of luteolin have been reported. The pharmacological action of small molecules is dependent upon its interaction with biomacromolecules. The interactions of small molecules with DNA play a major role in the transcription and translation process. In this work, we explored the energetic profile of DNA-luteolin interaction by isothermal titration calorimetry (ITC). The effect of temperature and salt concentration on DNA binding was examined by UV-Vis method. The mode of interaction was further probed by UV melting temperature analysis and differential scanning calorimetry. An atomic level insight on the recognition of luteolin with DNA was achieved by employing molecular dynamics (MD) simulation on luteolin in complex with AT- and GC-rich DNA sequences. AMBER force field proves to be appropriate in providing an understanding on the binding mode and specificity of luteolin with duplex DNA. MD results suggest a minor groove binding of luteolin with DNA and the binding free energy obtained is in agreement with the experimental results.
[Mh] Termos MeSH primário: DNA/metabolismo
Luteolina/metabolismo
Simulação de Dinâmica Molecular
[Mh] Termos MeSH secundário: Animais
Bovinos
DNA/química
Ligações de Hidrogênio
Conformação de Ácido Nucleico
Desnaturação de Ácido Nucleico
Termodinâmica
Temperatura de Transição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
9007-49-2 (DNA); KUX1ZNC9J2 (Luteolin)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171010
[Lr] Data última revisão:
171010
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170822
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jcim.6b00747


  10 / 4238 MEDLINE  
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[PMID]:28793208
[Au] Autor:Carr CE; Marky LA
[Ad] Endereço:Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, Nebraska.
[Ti] Título:Investigation of the Melting Behavior of DNA Three-Way Junctions in the Closed and Open States.
[So] Source:Biophys J;113(3):529-539, 2017 Aug 08.
[Is] ISSN:1542-0086
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Intramolecular three-way junctions are commonly found in both DNA and RNA. These structures are functionally relevant in ribozymes, riboswitches, rRNA, and during replication. In this work, we present a thermodynamic description of the unfolding of DNA intramolecular three-way junctions. We used a combination of spectroscopic and calorimetric techniques to investigate the folding/unfolding thermodynamics of two three-way junctions with a closed (Closed-J) or open (Open-J) junction and their appropriate control stem-loop motifs (GAAATT-Hp, CTATC-Hp, and Dumbbell). The overall results show that both junctions are stable over a wide range of salt concentrations. However, Open-J is more stable due to a higher enthalpy contribution from the formation of a higher number of basepair stacks whereas Closed-J has a defined structure and retains the basepair stacking of all three stems. The comparison of the experimental results of Closed-J and Open-J with those of their component stem-loop motifs allowed us to be more specific about their cooperative unfolding. For instance, Closed-J sacrifices thermal stability of the Dumbbell structure to maintain an overall folded state. At higher salt concentration, the simultaneous unfolding of the above domains is lost, resulting in the unfolding of the three separate stems. In contrast, the junction of Open-J in low salt retains the thermal and enthalpic stability of the Dumbbell structure although sacrificing stability of the CTATC stem. The relative stability of Dumbbell is the primary reason for the higher ΔG° , or free energy, value seen for Open-J at low salt. Higher salt not only maintains thermal stability of the Dumbbell structure in Open-J but causes the CTATC stem to fully fold.
[Mh] Termos MeSH primário: DNA/química
[Mh] Termos MeSH secundário: Pareamento de Bases
Sequência de Bases
DNA/genética
Desnaturação de Ácido Nucleico
Temperatura de Transição
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170831
[Lr] Data última revisão:
170831
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170810
[St] Status:MEDLINE



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