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1.
J Phys Chem Lett ; 10(10): 2386-2392, 2019 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-31010285

RESUMO

Molecular excitons are used in a variety of applications including light harvesting, optoelectronics, and nanoscale computing. Controlled aggregation via covalent attachment of dyes to DNA templates is a promising aggregate assembly technique that enables the design of extended dye networks. However, there are few studies of exciton dynamics in DNA-templated dye aggregates. We report time-resolved excited-state dynamics measurements of two cyanine-based dye aggregates, a J-like dimer and an H-like tetramer, formed through DNA-templating of covalently attached dyes. Time-resolved fluorescence and transient absorption indicate that nonradiative decay, in the form of internal conversion, dominates the aggregate ground state recovery dynamics, with singlet exciton lifetimes on the order of tens of picoseconds for the aggregates versus nanoseconds for the monomer. These results highlight the importance of circumventing nonradiative decay pathways in the future design of DNA-templated dye aggregates.


Assuntos
Carbocianinas/química , DNA/química , Corantes Fluorescentes/química , Espectrometria de Fluorescência , Fatores de Tempo
2.
Chem Rev ; 119(10): 6326-6369, 2019 05 22.
Artigo em Inglês | MEDLINE | ID: mdl-30714375

RESUMO

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

3.
ACS Nano ; 13(3): 2986-2994, 2019 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-30758934

RESUMO

The excitonic circuitry found in photosynthetic organisms suggests an alternative to electronic circuits, but the assembly of optically active molecules to fabricate even simple excitonic devices has been hampered by the limited availability of suitable molecular scale assembly technologies. Here we have designed and operated a hybrid all-optical excitonic switch comprised of donor/acceptor chromophores and photochromic nucleotide modulators assembled with nanometer scale precision using DNA nanotechnology. The all-optical excitonic switch was operated successfully in both liquid and solid phases, exhibiting high ON/OFF switching contrast with no apparent cyclic fatigue through nearly 200 cycles. These findings, combined with the switch's small footprint and volume, estimated low energy requirement, and potential ability to switch at speeds in the 10s of picoseconds, establish a prospective pathway forward for all-optical excitonic circuits.

4.
J Phys Chem A ; 122(46): 8989-8997, 2018 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-30380862

RESUMO

The excited state properties of cyanine dyes and the orientations of their aggregates were studied using density functional theory (DFT). The effects of exchange-correlation functional and solvent model on the absorption spectrum of Cy5 was investigated. Using the 6-31+G(d,p) basis set and B3LYP exchange-correlation functional with IEF-PCM (water) solvent, the predicted spectrum achieved a maximum absorbance within 0.007 eV of experiment. An in-house program based on the theoretical model of Kühn, Renger, and May (KRM), which predicts the orientation of dyes within an aggregate from its absorbance and circular dichroism (CD) spectra or vice versa, was used to investigate the orientation of an experimentally observed dimer. The absorbance spectrum predicted using the KRM model of the dimer structure optimized with the 6-31+G(d,p) basis set, ωB97XD exchange-correlation functional, and IEF-PCM solvent agrees with experimental data.

5.
J Phys Chem A ; 122(8): 2086-2095, 2018 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-29420037

RESUMO

Exciton delocalization in dye aggregate systems is a phenomenon that is revealed by spectral features, such as Davydov splitting, J- and H-aggregate behavior, and fluorescence suppression. Using DNA as an architectural template to assemble dye aggregates enables specific control of the aggregate size and dye type, proximal and precise positioning of the dyes within the aggregates, and a method for constructing large, modular two- and three-dimensional arrays. Here, we report on dye aggregates, organized via an immobile Holliday junction DNA template, that exhibit large Davydov splitting of the absorbance spectrum (125 nm, 397.5 meV), J- and H-aggregate behavior, and near-complete suppression of the fluorescence emission (∼97.6% suppression). Because of the unique optical properties of the aggregates, we have demonstrated that our dye aggregate system is a viable candidate as a sensitive absorbance and fluorescence optical reporter. DNA-templated aggregates exhibiting exciton delocalization may find application in optical detection and imaging, light-harvesting, photovoltaics, optical information processing, and quantum computing.


Assuntos
Carbocianinas/química , DNA Cruciforme/química , Fluorescência , Corantes Fluorescentes/química , Modelos Moleculares , Moldes Genéticos
6.
Sci Rep ; 7(1): 7382, 2017 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-28785065

RESUMO

DNA nanostructures represent the confluence of materials science, computer science, biology, and engineering. As functional assemblies, they are capable of performing mechanical and chemical work. In this study, we demonstrate global twisting of DNA nanorails made from two DNA origami six-helix bundles. Twisting was controlled using ethidium bromide or SYBR Green I as model intercalators. Our findings demonstrate that DNA nanorails: (i) twist when subjected to intercalators and the amount of twisting is concentration dependent, and (ii) twisting saturates at elevated concentrations. This study provides insight into how complex DNA structures undergo conformational changes when exposed to intercalators and may be of relevance when exploring how intercalating drugs interact with condensed biological structures such as chromatin and chromosomes, as well as chromatin analogous gene expression devices.


Assuntos
DNA/síntese química , Substâncias Intercalantes/química , Nanoestruturas/química , DNA/química , Etídio/química , Modelos Moleculares , Conformação de Ácido Nucleico , Compostos Orgânicos/química
7.
J Phys Chem A ; 121(37): 6905-6916, 2017 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-28813152

RESUMO

Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temperature are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. Here, we report on a simple dye system templated by DNA that exhibits tunable optical properties. At low salt and DNA concentrations, a DNA duplex with two internally functionalized Cy5 dyes (i.e., dimer) persists and displays predominantly J-aggregate behavior. Increasing the salt and/or DNA concentrations was found to promote coupling between two of the DNA duplexes via branch migration, thus forming a four-armed junction (i.e., tetramer) with H-aggregate behavior. This H-tetramer aggregate exhibits a surprisingly large Davydov splitting in its absorbance spectrum that produces a visible color change of the solution from cyan to violet and gives clear evidence of coherent exciton delocalization.


Assuntos
Carbocianinas/química , DNA/química , Corantes Fluorescentes/química , Materiais Biomiméticos/química , Materiais Biomiméticos/efeitos da radiação , Carbocianinas/efeitos da radiação , DNA/efeitos da radiação , Transferência de Energia , Corantes Fluorescentes/efeitos da radiação , Cinética , Luz , Cloreto de Magnésio/química , Modelos Químicos , Temperatura , Termodinâmica
8.
J Phys Chem B ; 121(12): 2594-2602, 2017 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-28256835

RESUMO

Locked nucleic acids (LNAs) are conformationally restricted RNA nucleotides. Their increased thermal stability and selectivity toward their complements make them well-suited for diagnostic and therapeutic applications. Although the structural and thermodynamic properties of LNA-LNA, LNA-RNA, and LNA-DNA hybridizations are known, the kinetic effects of incorporating LNA nucleotides into DNA strand displacement systems are not. Here, we thoroughly studied the strand displacement kinetics as a function of the number and position of LNA nucleotides in DNA oligonucleotides. When compared to that of an all-DNA control, with an identical sequence, the leakage rate constant was reduced more than 50-fold, to an undetectable level, and the invasion rate was preserved for a hybrid DNA/LNA system. The total performance enhancement ratio also increased more than 70-fold when calculating the ratio of the invading rate to the leakage rate constants for a hybrid system. The rational substitution of LNA nucleotides for DNA nucleotides preserves sequence space while improving the signal-to-noise ratio of strand displacement systems. Hybrid DNA/LNA systems offer great potential for high-performance chemical reaction networks that include catalyzed hairpin assemblies, hairpin chain reactions, motors, walkers, and seesaw gates.


Assuntos
DNA/química , Oligonucleotídeos/química , Cinética , Modelos Moleculares , Conformação de Ácido Nucleico
9.
ACS Synth Biol ; 6(1): 84-93, 2017 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-26875531

RESUMO

DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.


Assuntos
DNA/química , Pareamento Incorreto de Bases , Computadores Moleculares , DNA/genética , DNA/metabolismo , Cinética , Nanotecnologia , Conformação de Ácido Nucleico , Hibridização de Ácido Nucleico , Biologia Sintética
10.
Proc Natl Acad Sci U S A ; 112(45): E6086-95, 2015 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-26504222

RESUMO

Quantifying the mechanical forces produced by fluid flows within the ocean is critical to understanding the ocean's environmental phenomena. Such forces may have been instrumental in the origin of life by driving a primitive form of self-replication through fragmentation. Among the intense sources of hydrodynamic shear encountered in the ocean are breaking waves and the bursting bubbles produced by such waves. On a microscopic scale, one expects the surface-tension-driven flows produced during bubble rupture to exhibit particularly high velocity gradients due to the small size scales and masses involved. However, little work has examined the strength of shear flow rates in commonly encountered ocean conditions. By using DNA nanotubes as a novel fluid flow sensor, we investigate the elongational rates generated in bursting films within aqueous bubble foams using both laboratory buffer and ocean water. To characterize the elongational rate distribution associated with a bursting bubble, we introduce the concept of a fragmentation volume and measure its form as a function of elongational flow rate. We find that substantial volumes experience surprisingly large flow rates: during the bursting of a bubble having an air volume of 10 mm(3), elongational rates at least as large as [Formula: see text] s(-1) are generated in a fragmentation volume of [Formula: see text] [Formula: see text]. The determination of the elongational strain rate distribution is essential for assessing how effectively fluid motion within bursting bubbles at the ocean surface can shear microscopic particles and microorganisms, and could have driven the self-replication of a protobiont.


Assuntos
Aerossóis/análise , DNA/química , Nanotubos/química , Água do Mar/química , California , Hidrodinâmica , Lasers , Microscopia de Fluorescência
11.
Nanoscale ; 7(23): 10382-90, 2015 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-25959862

RESUMO

DNA nanotechnology holds the potential for enabling new tools for biomedical engineering, including diagnosis, prognosis, and therapeutics. However, applications for DNA devices are thought to be limited by rapid enzymatic degradation in serum and blood. Here, we demonstrate that a key aspect of DNA nanotechnology-programmable molecular shape-plays a substantial role in device lifetimes. These results establish the ability to operate synthetic DNA devices in the presence of endogenous enzymes and challenge the textbook view of near instantaneous degradation.


Assuntos
Computadores Moleculares , DNA/química , DNA/ultraestrutura , Soro/química , Espectrometria de Fluorescência/métodos , Humanos , Nanotecnologia/métodos , Conformação de Ácido Nucleico
12.
ACS Photonics ; 2(3): 398-404, 2015 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-25839049

RESUMO

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.

13.
Chem Sci ; 6(4): 2252-2267, 2015 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-29308139

RESUMO

DNA nanotubes provide a programmable architecture for molecular self-assembly and can serve as model systems for one-dimensional biomolecular assemblies. While a variety of DNA nanotubes have been synthesized and employed as models for natural biopolymers, an extensive investigation of DNA nanotube kinetics and thermodynamics has been lacking. Using total internal reflection microscopy, DNA nanotube polymerization was monitored in real time at the single filament level over a wide range of free monomer concentrations and temperatures. The measured polymerization rates were subjected to a global nonlinear fit based on polymerization theory in order to simultaneously extract kinetic and thermodynamic parameters. For the DNA nanotubes used in this study, the association rate constant is (5.99 ± 0.15) × 105 M-1 s-1, the enthalpy is 87.9 ± 2.0 kcal mol-1, and the entropy is 0.252 ± 0.006 kcal mol-1 K-1. The qualitative and quantitative similarities between the kinetics of DNA nanotubes, actin filaments, and microtubules polymerization highlight the prospect of building complex dynamic systems from DNA molecules inspired by biological architecture.

14.
Nanoscale ; 6(23): 14153-7, 2014 Nov 06.
Artigo em Inglês | MEDLINE | ID: mdl-25350569

RESUMO

The specific recognition and programmable assembly properties make DNA a potential material for nanodevices. However, the more intelligent the nanodevice is, the more complicated the structure of the nanodevice is, which limits the speed of DNA assembly. Herein, to address this problem, we investigate the performance of DNA Strand Displacement Reaction (DSDR) in a mixture of polar organic solvents and aqueous buffer and demonstrate that the organic polar solvent can speed up DNA self-assembly efficiently. Taking DSDR in 20% ethanol as an example, first we have demonstrated that the DSDR is highly accelerated in the beginning of the reaction and it can complete 60% of replacement reactions (160% enhancement compared with aqueous buffer) in the first 300 seconds. Secondly, we calculated that the ΔΔG of the DSDR in 20% ethanol (-18.2 kcal mol(-1)) is lower than that in pure aqueous buffer (-32.6 kcal mol(-1)), while the activation energy is lowered by introducing ethanol. Finally, we proved that the DSDR on the electrode surface can also be accelerated using this simple strategy. More importantly, to test the efficacy of this approach in nanodevices with a complicated and slow DNA self-assembly process, we apply this strategy in the hybridization chain reaction (HCR) and prove the acceleration is fairly obvious in 20% ethanol, which demonstrates the feasibility of the proposed strategy in DNA nanotechnology and DNA-based biosensors.


Assuntos
Técnicas Biossensoriais , DNA/química , Etanol/química
15.
Nanoscale ; 6(22): 13928-38, 2014 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-25311051

RESUMO

High precision, high yield, and high density self-assembly of nanoparticles into arrays is essential for nanophotonics. Spatial deviations as small as a few nanometers can alter the properties of near-field coupled optical nanostructures. Several studies have reported assemblies of few nanoparticle structures with controlled spacing using DNA nanostructures with variable yield. Here, we report multi-tether design strategies and attachment yields for homo- and hetero-nanoparticle arrays templated by DNA origami nanotubes. Nanoparticle attachment yield via DNA hybridization is comparable with streptavidin-biotin binding. Independent of the number of binding sites, >97% site-occupation was achieved with four tethers and 99.2% site-occupation is theoretically possible with five tethers. The interparticle distance was within 2 nm of all design specifications and the nanoparticle spatial deviations decreased with interparticle spacing. Modified geometric, binomial, and trinomial distributions indicate that site-bridging, steric hindrance, and electrostatic repulsion were not dominant barriers to self-assembly and both tethers and binding sites were statistically independent at high particle densities.


Assuntos
DNA/química , Nanopartículas Metálicas/química , Análise em Microsséries/instrumentação , Nanotubos/química , Sítios de Ligação , DNA/metabolismo , Ouro/química , Análise em Microsséries/estatística & dados numéricos , Microscopia de Força Atômica , Microtecnologia/métodos , Nanotecnologia/métodos , Conformação de Ácido Nucleico , Tamanho da Partícula , Probabilidade , Eletricidade Estática , Propriedades de Superfície
16.
Nat Commun ; 4: 2948, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24336125

RESUMO

Circular dichroism spectra of naturally occurring molecules and also of synthetic chiral arrangements of plasmonic particles often exhibit characteristic bisignate shapes. Such spectra consist of peaks next to dips (or vice versa) and result from the superposition of signals originating from many individual chiral objects oriented randomly in solution. Here we show that by first aligning and then toggling the orientation of DNA-origami-scaffolded nanoparticle helices attached to a substrate, we are able to reversibly switch the optical response between two distinct circular dichroism spectra corresponding to either perpendicular or parallel helix orientation with respect to the light beam. The observed directional circular dichroism of our switchable plasmonic material is in good agreement with predictions based on dipole approximation theory. Such dynamic metamaterials introduce functionality into soft matter-based optical devices and may enable novel data storage schemes or signal modulators.


Assuntos
Dicroísmo Circular , DNA/química , Nanocompostos/química , DNA de Cadeia Simples/química , Vidro , Ouro/química , Teste de Materiais , Nanopartículas Metálicas/química , Nanotecnologia , Óptica e Fotônica , Tamanho da Partícula , Processamento de Sinais Assistido por Computador , Soluções , Estereoisomerismo , Propriedades de Superfície
17.
Nucleic Acids Res ; 41(22): 10641-58, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24019238

RESUMO

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.


Assuntos
DNA/química , Algoritmos , Fenômenos Biofísicos , Cinética , Modelos Moleculares , Termodinâmica
18.
Biosens Bioelectron ; 50: 382-6, 2013 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-23891867

RESUMO

A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkage from only one target DNA strand, catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gel electrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules.


Assuntos
Técnicas Biossensoriais/métodos , DNA/análise , Ouro/química , Nanopartículas/química , Colorimetria/métodos , Hibridização de Ácido Nucleico/métodos
19.
Nano Lett ; 13(8): 3850-6, 2013 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-23841957

RESUMO

DNA origami templated self-assembly has shown its potential in creating rationally designed nanophotonic devices in a parallel and repeatable manner. In this investigation, we employ a multiscaffold DNA origami approach to fabricate linear waveguides of 10 nm diameter gold nanoparticles. This approach provides independent control over nanoparticle separation and spatial arrangement. The waveguides were characterized using atomic force microscopy and far-field polarization spectroscopy. This work provides a path toward large-scale plasmonic circuitry.


Assuntos
DNA/química , Ouro/química , Nanopartículas Metálicas/química , Tamanho da Partícula
20.
Proc Natl Acad Sci U S A ; 109(17): 6405-10, 2012 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-22493232

RESUMO

Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes. Crystal growth propagates a sequence of bits while mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chemical sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.


Assuntos
Cristalização , Replicação do DNA , Biocatálise , DNA/química , Evolução Molecular
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