Base de dados : MEDLINE
Pesquisa : G02.111.570.820.486.100 [Categoria DeCS]
Referências encontradas : 7042 [refinar]
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  1 / 7042 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


  2 / 7042 MEDLINE  
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[PMID]:29345270
[Au] Autor:Chawla M; Autiero I; Oliva R; Cavallo L
[Ad] 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.
[Ti] Título:Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair.
[So] Source:Phys Chem Chem Phys;20(5):3699-3709, 2018 Jan 31.
[Is] ISSN:1463-9084
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] 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.
[Mh] Termos MeSH primário: Ftalimidas/química
Pirimidinas/química
[Mh] Termos MeSH secundário: Pareamento de Bases
DNA de Forma B/química
Ligações de Hidrogênio
Conformação Molecular
Simulação de Dinâmica Molecular
Ftalimidas/metabolismo
Pirimidinas/metabolismo
Teoria Quântica
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (4-aminophthalimide); 0 (DNA, B-Form); 0 (Phthalimides); 0 (Pyrimidines); 156-81-0 (2,4-diaminopyrimidine)
[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:180119
[St] Status:MEDLINE
[do] DOI:10.1039/c7cp07400j


  3 / 7042 MEDLINE  
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[PMID]:29260726
[Au] Autor:Agarwal T; Manjunath GP; Habib F; Lakshmi Vaddavalli P; Chatterji A
[Ad] Endereço:IISER-Pune, 900 NCL Innovation Park, Dr. Homi Bhaba Road, Pune-411008, India.
[Ti] Título:Role of special cross-links in structure formation of bacterial DNA polymer.
[So] Source:J Phys Condens Matter;30(3):034003, 2018 Jan 24.
[Is] ISSN:1361-648X
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Using data from contact maps of the DNA-polymer of Escherichia coli (E. Coli) (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. Via suitable Monte Carlo simulations, we show that the presence of these cross-links leads to a particular organization of the chain at large (micron) length scales of the DNA. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain. We find that though the polymer does get organized at the large length scales, the nature of the organization is quite different from the organization observed with cross-links at specific biologically determined positions. We used the contact map of E. Coli bacteria which has around 4.6 million base pairs in a single circular chromosome. In our coarse-grained flexible ring polymer model, we used 4642 monomer beads and observed that around 80 cross-links are enough to induce the large-scale organization of the molecule accounting for statistical fluctuations caused by thermal energy. The length of a DNA chain even of a simple bacterial cell such as E. Coli is much longer than typical proteins, hence we avoided methods used to tackle protein folding problems. We define new suitable quantities to identify the large scale structure of a polymer chain with a few cross-links.
[Mh] Termos MeSH primário: DNA Bacteriano/química
DNA/química
Polímeros/química
Dobramento de Proteína
[Mh] Termos MeSH secundário: Pareamento de Bases
Escherichia coli
Substâncias Macromoleculares
Modelos Moleculares
Método de Monte Carlo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Bacterial); 0 (Macromolecular Substances); 0 (Polymers); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180209
[Lr] Data última revisão:
180209
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171221
[St] Status:MEDLINE
[do] DOI:10.1088/1361-648X/aa9e66


  4 / 7042 MEDLINE  
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[PMID]:29242886
[Au] Autor:Romero EE; Hernandez FE
[Ad] Endereço:Department of Chemistry, University of Central Florida, P. O. Box 162366, Orlando, Florida 32816-2366, USA. florencio.hernandez@ucf.edu.
[Ti] Título:Solvent effect on the intermolecular proton transfer of the Watson and Crick guanine-cytosine and adenine-thymine base pairs: a polarizable continuum model study.
[So] Source:Phys Chem Chem Phys;20(2):1198-1209, 2018 Jan 03.
[Is] ISSN:1463-9084
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Herein we present our results on the study of the double proton transfer (DPT) mechanism in the adenine-thymine (AT) and guanine-cytosine (GC) base pairs, both in gas phase and in solution. The latter was modeled using the polarizable continuum method (PCM) in different solvents. According to our DFT calculations, the DPT may occur for both complexes in a stepwise mechanism in condensate phase. In gas phase only the GC base pair exhibits a concerted DPT mechanism. Using the Wigner's tunneling corrections to the transition state theory we demonstrate that such corrections are important for the prediction of the rate constants of both systems in gas and in condensate phase. We also show that (i) as the polarity of the medium decreases the equilibrium constant of the DPT reaction increases in both complexes, and (ii) that the equilibrium constant in the GC complex is four orders of magnitude larger than in AT. This observation suggests that the spontaneous mutations in DNA base pairs are more probable in GC than in AT.
[Mh] Termos MeSH primário: Pareamento de Bases
DNA/química
Modelos Moleculares
[Mh] Termos MeSH secundário: Adenina
Citosina
Guanina
Prótons
Solventes
Timina
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Protons); 0 (Solvents); 5Z93L87A1R (Guanine); 8J337D1HZY (Cytosine); 9007-49-2 (DNA); JAC85A2161 (Adenine); QR26YLT7LT (Thymine)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180209
[Lr] Data última revisão:
180209
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1039/c7cp05356h


  5 / 7042 MEDLINE  
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[PMID]:29235442
[Au] Autor:Li S; Erdemci-Tandogan G; van der Schoot P; Zandi R
[Ad] Endereço:Department of Physics and Astronomy, University of California, Riverside, CA 92521, United States of America.
[Ti] Título:The effect of RNA stiffness on the self-assembly of virus particles.
[So] Source:J Phys Condens Matter;30(4):044002, 2018 Jan 31.
[Is] ISSN:1361-648X
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between an ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.
[Mh] Termos MeSH primário: Pareamento de Bases
Proteínas do Capsídeo/metabolismo
RNA Viral/química
Vírion/química
[Mh] Termos MeSH secundário: Capsídeo
Conformação de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Capsid Proteins); 0 (RNA, Viral)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180209
[Lr] Data última revisão:
180209
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171214
[St] Status:MEDLINE
[do] DOI:10.1088/1361-648X/aaa159


  6 / 7042 MEDLINE  
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[PMID]:29219116
[Au] Autor:O' Lee DJ
[Ad] Endereço:Department of Chemistry, Imperial College London, SW7 2AZ, London, United Kingdom.
[Ti] Título:Introducing a model of pairing based on base pair specific interactions between identical DNA sequences.
[So] Source:J Phys Condens Matter;30(7):075102, 2018 Feb 21.
[Is] ISSN:1361-648X
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model, built on this second mechanism, where both thermal stretching and twisting fluctuations are included, as well as the base pair specific helix distortions. Firstly, we consider an approximation for weak pairing interactions, or short molecules. This yields a dependence of the energy on the square root of the molecular length, which could explain recent experimental data. However, analysis suggests that this approximation is no longer valid at large DNA lengths. In a second approximation, for long molecules, we define two adaptation lengths for twisting and stretching, over which the pairing interaction can limit the accumulation of helix disorder. When the pairing interaction is sufficiently strong, both adaptation lengths are finite; however, as we reduce pairing strength, the stretching adaptation length remains finite but the torsional one becomes infinite. This second state persists to arbitrarily weak values of the pairing strength; suggesting that, if the molecules are long enough, the pairing energy scales as length. To probe differences between the two pairing mechanisms, we also construct a model of similar form. However, now, pairing between identical sequences solely relies on the intrinsic helix distortion patterns. Between the two models, we see interesting qualitative differences. We discuss our findings, and suggest new work to distinguish between the two mechanisms.
[Mh] Termos MeSH primário: Pareamento de Bases
Sequência de Bases
DNA/química
Modelos Moleculares
[Mh] Termos MeSH secundário: Ligações de Hidrogênio
Conformação de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
9007-49-2 (DNA)
[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:171209
[St] Status:MEDLINE
[do] DOI:10.1088/1361-648X/aaa043


  7 / 7042 MEDLINE  
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[PMID]:29240425
[Au] Autor:Chakraborty D; Wales DJ
[Ad] Endereço:Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.
[Ti] Título:Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.
[So] Source:J Phys Chem Lett;9(1):229-241, 2018 Jan 04.
[Is] ISSN:1948-7185
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.
[Mh] Termos MeSH primário: Pareamento de Bases
DNA/química
[Mh] Termos MeSH secundário: Sequência de Bases
Modelos Moleculares
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180207
[Lr] Data última revisão:
180207
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171215
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jpclett.7b01933


  8 / 7042 MEDLINE  
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[PMID]:29211987
[Au] Autor:Liu Y; Lilley DMJ
[Ad] Endereço:Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, United Kingdom.
[Ti] Título:Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA.
[So] Source:Biophys J;113(11):2336-2343, 2017 Dec 05.
[Is] ISSN:1542-0086
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The indodicarbocyanine fluorophores Cy3 and Cy5 are extensively used as donor-acceptor pairs in fluorescence resonance energy transfer experiments, especially those involving single molecules. When terminally attached to double-stranded nucleic acids via the 5' phosphate group these fluorophores stack onto the ends of the molecule. Knowledge of the positions of the fluorophores is critical to the interpretation of fluorescence resonance energy transfer data. The positions have been demonstrated for double-stranded (ds) DNA using NMR spectroscopy. Here, we have used x-ray crystallography to analyze the location of Cy3 and Cy5 on dsRNA, using complexes of an RNA stem-loop bound to L5 protein determined at 2.4 Å resolution. This confirms the tendency of both fluorophores to stack on the free end of RNA, with the long axis of the fluorophores approximately parallel to that of the terminal basepair. However, the manner of interaction of both Cy3 and Cy5 with the terminus of the dsRNA is significantly different from that deduced for dsDNA using NMR. The fluorophores are stacked on the terminal basepair such that their indole nitrogen atoms lie on the major groove side, and thus their pendant methyl groups are on the minor groove side.
[Mh] Termos MeSH primário: Carbocianinas/química
Corantes Fluorescentes/química
RNA de Cadeia Dupla/química
[Mh] Termos MeSH secundário: Proteínas de Bactérias/química
Proteínas de Bactérias/metabolismo
Pareamento de Bases
Cristalografia por Raios X
Modelos Moleculares
Conformação Proteica
RNA de Cadeia Dupla/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Carbocyanines); 0 (Fluorescent Dyes); 0 (RNA, Double-Stranded)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180120
[Lr] Data última revisão:
180120
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171207
[St] Status:MEDLINE


  9 / 7042 MEDLINE  
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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


  10 / 7042 MEDLINE  
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[PMID]:29242317
[Au] Autor:Srinivas N; Parkin J; Seelig G; Winfree E; Soloveichik D
[Ad] Endereço:Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA. niranjan@dna.caltech.edu david.soloveichik@utexas.edu.
[Ti] Título:Enzyme-free nucleic acid dynamical systems.
[So] Source:Science;358(6369), 2017 12 15.
[Is] ISSN:1095-9203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Chemistries exhibiting complex dynamics-from inorganic oscillators to gene regulatory networks-have been long known but either cannot be reprogrammed at will or rely on the sophisticated enzyme chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? Abstract chemical reaction networks have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems by identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base-pairing interactions alone suffice for complex chemical dynamics and that autonomous molecular systems can be designed via molecular programming languages.
[Mh] Termos MeSH primário: Pareamento de Bases
DNA/química
Linguagens de Programação
[Mh] Termos MeSH secundário: Sequência de Bases
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180112
[Lr] Data última revisão:
180112
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE



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