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Pesquisa : D13.444.308.196 [Categoria DeCS]
Referências encontradas : 193 [refinar]
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  1 / 193 MEDLINE  
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PMID:29345270
Autor:Chawla M; Autiero I; Oliva R; Cavallo L
Endereço:King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia. mohitchawla.bt@gmail.com luigi.cavallo@kaust.edu.sa.
Título:Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair.
Fonte:Phys Chem Chem Phys; 20(5):3699-3709, 2018 Jan 31.
ISSN:1463-9084
País de publicação:England
Idioma:eng
Resumo:The fluorescent non-natural 4-aminophthalimide (4AP) base, when paired to the complementary 2,4-diaminopyrimidine (DAP) nucleobase, is accommodated in a B-DNA duplex being efficiently recognized and incorporated by DNA polymerases. To complement the experimental studies and rationalize the impact of the above non-natural bases on the structure, stability and dynamics of nucleic acid structures, we performed quantum mechanics (QM) calculations along with classical molecular dynamics (MD) simulations. QM calculations were initially focused on the geometry and energetics of the 4AP:DAP non-natural pair and of H-bonded base pairs between 4AP and all the natural bases in their classical Watson-Crick geometries. The QM calculations indicate that the 4AP:DAP pair, despite the fact that it can form 3 H-bonds in a classic Watson-Crick geometry, has a stability comparable to the A:T pair. Then, we extended the study to reverse Watson-Crick geometries, characteristic of parallel strands. MD simulations were carried out on two 13-mer DNA duplexes, featuring a central 4AP:DAP or A:T pair, respectively. No major structural deformation of the duplex was observed during the MD simulation. Snapshots from the MD simulations were subjected to QM calculations to investigate the 4AP:DAP interaction energy when embedded into a duplex structure, and to investigate the impact of the two non-natural bases on the stacking interactions with adjacent bases in the DNA duplex. We found a slight increase in stacking interactions involving the 4AP:DAP pair, counterbalanced by a moderate decrease in H-bonding interactions of the 4AP:DAP and of the adjacent base pairs in the duplex. The results of our study are in agreement with experimental data and complement them by providing an insight into which factors contribute positively and which factors contribute negatively to the structural compatibility of the fluorescent 4AP:DAP pair with a B-DNA structure.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (4-aminophthalimide); 0 (DNA, B-Form); 0 (Phthalimides); 0 (Pyrimidines); 156-81-0 (2,4-diaminopyrimidine)


  2 / 193 MEDLINE  
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PMID:28470278
Autor:Nakamura S; Yang H; Hirata C; Kersaudy F; Fujimoto K
Endereço:School of Materials Science, Japan Advanced Institute of Science and Technology, Asahi-dai 1-1, Nomi, Ishikawa, Japan. kenzo@jaist.ac.jp.
Título:Development of F-NMR chemical shift detection of DNA B-Z equilibrium using F-NMR.
Fonte:Org Biomol Chem; 15(24):5109-5111, 2017 Jun 28.
ISSN:1477-0539
País de publicação:England
Idioma:eng
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.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, B-Form); 0 (DNA, Single-Stranded); 0 (DNA, Z-Form); 284SYP0193 (Fluorine)


  3 / 193 MEDLINE  
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PMID:29185909
Autor:Phromsiri P; Gerling RR; Blose JM
Endereço:a The College at Brockport , State University of New York, Department of Chemistry and Biochemistry , Brockport , NY.
Título:The effects of a neutral cosolute on the B to Z transition for DNA duplexes incorporating both CG and CA steps.
Fonte:Nucleosides Nucleotides Nucleic Acids; 36(11):690-703, 2017 Nov 02.
ISSN:1532-2335
País de publicação:United States
Idioma:eng
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.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, B-Form); 0 (DNA, Z-Form); 0 (Solutions); 30IQX730WE (Polyethylene Glycols)


  4 / 193 MEDLINE  
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PMID:28988932
Autor:Chen J; Wassarman KM; Feng S; Leon K; Feklistov A; Winkelman JT; Li Z; Walz T; Campbell EA; Darst SA
Endereço:Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
Título:6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase.
Fonte:Mol Cell; 68(2):388-397.e6, 2017 Oct 19.
ISSN:1097-4164
País de publicação:United States
Idioma:eng
Resumo:Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ -holoenzyme (Eσ ) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches. Duplex RNA segments have A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture that mimics B-form promoter DNA. Our results help explain the specificity of Eco 6S RNA for Eσ and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (6S RNA); 0 (DNA, B-Form); 0 (DNA, Bacterial); 0 (Escherichia coli Proteins); 0 (RNA, Bacterial); 0 (RNA, Untranslated); 0 (Sigma Factor); EC 2.7.7.- (RNA polymerase sigma 70); EC 2.7.7.6 (DNA-Directed RNA Polymerases)


  5 / 193 MEDLINE  
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PMID:28949808
Autor:Izanloo C
Endereço:a Department of Chemistry, Bojnourd Branch , Islamic Azad University , Bojnourd , Iran.
Título:Effect of gold nanoparticle on stability of the DNA molecule: A study of molecular dynamics simulation.
Fonte:Nucleosides Nucleotides Nucleic Acids; 36(9):571-582, 2017 Sep 02.
ISSN:1532-2335
País de publicação:United States
Idioma:eng
Resumo:An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ∼1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule. Because of peeling and untwisting states that are occur at end of DNA, the nucleotide base lies flat on the surface of GNP. The configuration entropy is estimated using the covariance matrix of atom-positional fluctuations for different bases. The results show that when a gold nanoparticle has interaction with DNA, entropy increases. The results of conformational energy and the hydrogen bond numbers for DNA indicated that DNA becomes unstable in the vicinity of a gold nanoparticle. The radial distribution function was calculated for water hydrogen-phosphate oxygen pairs. Almost for all nucleotide, the presence of a nanoparticle around DNA caused water molecules to be released from the DNA duplex and cations were close to the DNA.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, B-Form); 7440-57-5 (Gold)


  6 / 193 MEDLINE  
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PMID:28825294
Autor:Adeniran C; Hamelberg D
Endereço:Department of Chemistry and the Center for Diagnostics & Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.
Título:Redox-Specific Allosteric Modulation of the Conformational Dynamics of κB DNA by Pirin in the NF-κB Supramolecular Complex.
Fonte:Biochemistry; 56(37):5002-5010, 2017 Sep 19.
ISSN:1520-4995
País de publicação:United States
Idioma:eng
Resumo:The molecular basis of gene regulation by Nuclear Factor-κB (NF-κB) transcription factors and their coregulators is not well understood. This family of transcription factors controls a number of essential subcellular processes. Human Pirin, a nonheme iron (Fe) binding protein, has been shown to modulate the binding affinity between p65 homodimeric NF-κB and κB DNA. However, the allosteric effect of the active Fe(III) form of Pirin on the DNA has not been established. Here, we use multiple microsecond-long molecular dynamics simulations to explore the conformational dynamics of the free DNA, the p65-DNA complex, and the Pirin-p65-DNA supramolecular complex. We show that only the Fe(III) form of Pirin enhances the affinity between p65 and the DNA in the Pirin-p65-DNA supramolecular complex, in agreement with experiments. Additionally, the results provide atomistic details of the effect of the active Fe(III) form of Pirin on the DNA upon binding to the p65-DNA complex. In general, unlike the Fe(II) form of Pirin, binding of the Fe(III) form of Pirin to the p65-DNA complex significantly alters both the conformational dynamics of the DNA and the interactions between p65 and the DNA. The results provide atomic level understanding of the modulation of the DNA as a result of a redox-specific Fe(II)/Fe(III) coregulation of NF-κB by Pirin, knowledge that is necessary to fully understand normal and aberrant subcellular processes and the role of a subtle single electron redox process in gene regulation.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, B-Form); 0 (RELA protein, human); 0 (Transcription Factor RelA); EC 1.13.11.- (Dioxygenases); EC 1.13.11.24 (quercetin 2,3-dioxygenase)


  7 / 193 MEDLINE  
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PMID:28576665
Autor:Kulkarni M; Mukherjee A
Endereço:Department of Chemistry, Indian Institute of Science Education and Research, Pune, 411008, Maharashtra, India.
Título:Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition.
Fonte:Prog Biophys Mol Biol; 128:63-73, 2017 Sep.
ISSN:1873-1732
País de publicação:England
Idioma:eng
Resumo:The right-handed DNA helix exhibits two major conformations, A-DNA and B-DNA, depending on the environmental conditions. The B-DNA to A-DNA (B→A) transition is sequence specific, cooperative, and reversible. The reduced water activity due to the addition of solvents like ethanol or the presence of protein or drug molecules causes B→A transition. In several biological cases, B→A transition occurs at a local level where small fragments of a long DNA sequence undergoes B→A transition. In this review, we have discussed various aspects of B→A transition such as the role of water, sequence specificity, mechanism of B→A transition, etc. The review primarily focuses on the B→A mechanism involved at a local level, and finally its connection to the global transition in theoretical and experimental studies.
Tipo de publicação: JOURNAL ARTICLE; REVIEW
Nome de substância:0 (DNA, A-Form); 0 (DNA, B-Form); 0 (Solvents)


  8 / 193 MEDLINE  
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PMID:28501432
Autor:Le BH; Koo JC; Joo HN; Seo YJ
Endereço:Department of Bioactive Material Sciences, Chonbuk National University, Jeonju 54896, South Korea.
Título:Diverse size approach to incorporate and extend highly fluorescent unnatural nucleotides into DNA.
Fonte:Bioorg Med Chem; 25(14):3591-3596, 2017 Jul 15.
ISSN:1464-3391
País de publicação:England
Idioma:eng
Resumo:We have prepared a series of size-diverse unnatural nucleotides containing fluorescent (dApyrTP, dUpyrTP, dUantTP, dUthiTP) and quencher (dUazoTP) units, as well as nucleotides presenting small functional groups (dAethTP, dAoctTP, dUethTP, dUiodTP), all based on deoxyadenosine and deoxyuridine, and examined their suitability for use in enzymatic incorporation and extension into DNA. We observed a size-dependence of the incorporation and extension capability (following the order dUiodTP=dUethTP=dUthiTP>dUazoTP>dUpyrTP>dUantTP) during primer extension. This result was supported by circular dichroism (CD) spectra, which revealed a trend in the different B-form DNA structures depending on the size of the unit at the 5-position of the deoxyuridine (dUiodTP>dUethTP>dUthiTP>dUpyrTP), obtained from the PCR products. Interestingly, dUthiTP could be incorporated and extended into long DNA strands during primer extension and even PCR amplification, with CD spectroscopy confirming a stable secondary B-form duplex DNA structure. We observed full-length extension products even when combining dUthiTP with a template containing 24 continuous dA units during the primer extension. Thus, we believe that dUthiTP is a promising fluorescent nucleotide for a diverse range of biological applications requiring multiple incorporation and extension directly without disruption of B-form DNA structures.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, B-Form); 0 (Fluorescent Dyes); 0 (Nucleotides); 0 (Pyrenes); 9007-49-2 (DNA); 9E0T7WFW93 (pyrene)


  9 / 193 MEDLINE  
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PMID:28363908
Autor:Tao J; Zhang XW; Jin J; Du XX; Lian T; Yang J; Zhou X; Jiang Z; Su XD
Endereço:State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
Título:Nonspecific DNA Binding of cGAS N Terminus Promotes cGAS Activation.
Fonte:J Immunol; 198(9):3627-3636, 2017 May 01.
ISSN:1550-6606
País de publicação:United States
Idioma:eng
Resumo:The cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS) mediates innate immune responses against invading pathogens, or against self-dsDNA, which causes autoimmune disorders. Upon nonspecific binding of cytosolic B-form DNA, cGAS synthesizes the second messenger 2'3'-cGAMP and triggers STING-dependent signaling to produce type I IFNs. The cGAS comprises less-conserved N-terminal residues and highly conserved nucleotidyltransferase/Mab21 domains. The function and structure of the well-conserved domains have been extensively studied, whereas the physiological function of the N-terminal domain of cGAS is largely uncharacterized. In this study we used a single-molecule technique combined with traditional biochemical and cellular assays to demonstrate that binding of nonspecific dsDNA by the N-terminal domain of cGAS promotes its activation. We have observed that the N terminus of human cGAS ( cGAS-N160) undergoes secondary structural change upon dsDNA binding in solution. Furthermore, we showed that the cGAS-N160 helps full length cGAS to expand the binding range on λDNA and facilitates its binding efficiency to dsDNA compared with cGAS without the 160 N-terminal residues ( cGAS-d160). More importantly, cGAS-N160 endows full length cGAS relatively higher enzyme activity and stronger activation of STING/IRF3-mediated cytosolic DNA signaling. These findings strongly indicate that the N-terminal domain of cGAS plays an important role in enhancing its function.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, B-Form); 0 (IRF3 protein, human); 0 (Interferon Regulatory Factor-3); 0 (Interferon Type I); 0 (MPYS protein, human); 0 (Membrane Proteins); EC 2.7.7.- (MB21D1 protein, human); EC 2.7.7.- (Nucleotidyltransferases)


  10 / 193 MEDLINE  
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PMID:28334906
Autor:Dehez F; Gattuso H; Bignon E; Morell C; Dumont E; Monari A
Endereço:CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.
Título:Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates.
Fonte:Nucleic Acids Res; 45(7):3654-3662, 2017 Apr 20.
ISSN:1362-4962
País de publicação:England
Idioma:eng
Resumo:DNA photolesions constitute a particularly deleterious class of molecular defects responsible for the insurgence of a vast majority of skin malignant tumors. Dimerization of two adjacent thymines or cytosines mostly gives rise to cyclobutane pyrimidine dimers (CPD) and pyrimidine(6-4)pyrimidone 64-PP as the most common defects. We perform all-atom classical simulations, up to 2 µs, of CPD and 64-PP embedded in a 16-bp duplex, which reveal the constrasted behavior of the two lesions. In particular we evidence a very limited structural deformation induced by CPD while 64-PP is characterized by a complex structural polymorphism. Our simulations also allow to unify the contrasting experimental structural results obtained by nuclear magnetic resonance or Förster Resonant Energy Transfer method, showing that both low and high bent structures are indeed accessible. These contrasting behaviors can also explain repair resistance or the different replication obstruction, and hence the genotoxicity of these two photolesions.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, B-Form); 0 (Pyrimidine Dimers); 0 (pyrimidine-pyrimidone dimer)



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