Kinetics and Mechanism of In Situ Metallization of Bulk DNA Films.
Ontology highlight
ABSTRACT:
SUBMITTER: Shi ZH
PROVIDER: S-EPMC8787019 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The inherent specificity of DNA sequence hybridization has been extensively exploited to develop bioengineering applications. Nevertheless, the structural potential of DNA has been far less explored for creating non-canonical DNA-based reactions. Here we develop a DNA origami-enabled highly localized metallization reaction for intrinsic metallization patterning with 10-nm resolution. Both theoretical and experimental studies reveal that low-valence metal ions (Cu2+ and Ag+) strongly coordinate with DNA bases in protruding clustered DNA (pcDNA) prescribed on two-dimensional DNA origami, which results in effective attraction within flexible pcDNA strands for site-specific pcDNA condensation. We find that the metallization reactions occur selectively on prescribed sites while not on origami substrates. This strategy is generically applicable for free-style metal painting of alphabet letters, digits and geometric shapes on all-DNA substrates with near-unity efficiency. We have further fabricated single- and double-layer nanoscale printed circuit board (nano-PCB) mimics, shedding light on bio-inspired fabrication for nanoelectronic and nanophotonic applications.
| S-EPMC6897912 | biostudies-literature
Project description:Understanding and controlling the crystallization of organic-inorganic perovskite materials is important for their function in optoelectronic applications. This control is particularly delicate in scalable single-step thermal annealing methods. In this work, the crystallization mechanisms of flash infrared-annealed perovskite films, grown on substrates with lithographically patterned Au nucleation seeds, are investigated. The patterning enables the in situ observation to study the crystallization kinetics and the precise control of the perovskite nucleation and domain growth, while retaining the characteristic polycrystalline micromorphology with larger crystallites at the boundaries of the crystal domains, as shown by electron backscattering diffraction. Time-resolved photoluminescence measurements reveal longer charge carrier lifetimes in regions with large crystallites on the domain boundaries, relative to the domain interior. By increasing the nucleation site density, the proportion of larger crystallites is increased. This study shows that the combination of rapid thermal annealing with nucleation control is a promising approach to improve perovskite crystallinity and thereby ultimately the performance of optoelectronic devices.
| S-EPMC8437338 | biostudies-literature
Project description:Nucleotide excision repair (NER) protects cells against diverse types of DNA damage, principally UV irradiation. In Escherichia coli, damage is recognized by 2 key enzymes: UvrA and UvrB. Despite extensive investigation, the role of UvrA's 2 ATPase domains in NER remains elusive. Combining single-molecule fluorescence microscopy and classic biochemical methods, we have investigated the role of nucleotide binding in UvrA's kinetic cycle. Measurement of UvrA's steady-state ATPase activity shows it is stimulated upon binding DNA ( kcat 0.71-1.07/s). Despite UvrA's ability to discriminate damage, we find UV-damaged DNA does not alter the steady-state ATPase. To understand how damage affects UvrA, we studied its binding to DNA under various nucleotide conditions at the single molecule level. We have found that both UV damage and nucleotide cofactors affect the attached lifetime of UvrA. In the presence of ATP and UV damage, the lifetime is significantly greater compared with undamaged DNA. To reconcile these observations, we suggest that UvrA uses negative cooperativity between its ATPase sites that is gated by damage recognition. Only in the presence of damage is the second site activated, most likely in a sequential manner.-Barnett, J. T., Kad, N. M. Understanding the coupling between DNA damage detection and UvrA's ATPase using bulk and single molecule kinetics.
| S-EPMC6355085 | biostudies-literature
Project description:High-entropy multimetallic nanopatterns with controlled morphology, composition and uniformity hold great potential for developing nanoelectronics, nanophotonics and catalysis. Nevertheless, the lack of general methods for patterning multiple metals poses a limit. Here, we develop a DNA origami-based metallization reaction system to prescribe multimetallic nanopatterns with peroxidase-like activities. We find that strong coordination between metal elements and DNA bases enables the accumulation of metal ions on protruding clustered DNA (pcDNA) that are prescribed on DNA origami. As a result of the condensation of pcDNA, these sites can serve as nucleation site for metal plating. We have synthesized multimetallic nanopatterns composed of up to five metal elements (Co, Pd, Pt, Ag and Ni), and obtained insights on elemental uniformity control at the nanoscale. This method provides an alternative pathway to construct a library of multimetallic nanopatterns.
| S-EPMC10060391 | biostudies-literature
Project description:Radical electrons tend to localize on individual molecules, resulting in an insulating (Mott-Hubbard) bandgap in the solid state. Herein, we report the crystal structure and intrinsic electronic properties of the first single crystal of a π-radical metal, tetrathiafulvalene-extended dicarboxylate (TED). The electrical conductivity is up to 30 000 S cm-1 at 2 K and 2300 S cm-1 at room temperature. Temperature dependence of resistivity obeys a T 3 power-law above T > 100 K, indicating a new type of metal. X-ray crystallographic analysis clarifies the planar TED molecule, with a symmetric intramolecular hydrogen bond, is stacked along longitudinal (the a-axis) and transverse (the b-axis) directions. The π-orbitals are distributed to avoid strong local interactions. First-principles electronic calculations reveal the origin of the metallization giving rise to a wide bandwidth exceeding 1 eV near the Fermi level. TED demonstrates the effect of two-dimensional stacking of π-orbitals on electron delocalization, where a high carrier mobility of 31.6 cm2 V-1 s-1 (113 K) is achieved.
| S-EPMC8162741 | biostudies-literature
Project description:Experimental discovery of ultralarge elastic deformation in nanoscale diamond and machine learning of its electronic and phonon structures have created opportunities to address new scientific questions. Can diamond, with an ultrawide bandgap of 5.6 eV, be completely metallized, solely under mechanical strain without phonon instability, so that its electronic bandgap fully vanishes? Through first-principles calculations, finite-element simulations validated by experiments, and neural network learning, we show here that metallization/demetallization as well as indirect-to-direct bandgap transitions can be achieved reversibly in diamond below threshold strain levels for phonon instability. We identify the pathway to metallization within six-dimensional strain space for different sample geometries. We also explore phonon-instability conditions that promote phase transition to graphite. These findings offer opportunities for tailoring properties of diamond via strain engineering for electronic, photonic, and quantum applications.
| S-EPMC7547227 | biostudies-literature
Project description:The p53 tumour suppressor gene, the most frequently mutated gene in human cancer, encodes a transcription factor that contains sequence-specific DNA binding and homo-tetramerization domains. Interestingly, the affinities of p53 for specific and non-specific DNA sites differ by only one order of magnitude, making it hard to understand how this protein recognizes its specific DNA targets in vivo. We describe here the structure of a p53 polypeptide containing both the DNA binding and oligomerization domains in complex with DNA. The structure reveals that sequence-specific DNA binding proceeds via an induced fit mechanism that involves a conformational switch in loop L1 of the p53 DNA binding domain. Analysis of loop L1 mutants demonstrated that the conformational switch allows DNA binding off-rates to be regulated independently of affinities. These results may explain the universal prevalence of conformational switching in sequence-specific DNA binding proteins and suggest that proteins like p53 rely more on differences in binding off-rates, than on differences in affinities, to recognize their specific DNA sites.
| S-EPMC3117648 | biostudies-literature
Project description:Gene regulatory networks are multistable dynamical systems in which attractor states represent cell phenotypes. Spontaneous, noise-induced transitions between these states are thought to underlie critical cellular processes, including cell developmental fate decisions, phenotypic plasticity in fluctuating environments, and carcinogenesis. As such, there is increasing interest in the development of theoretical and computational approaches that can shed light on the dynamics of these stochastic state transitions in multistable gene networks. We applied a numerical rare-event sampling algorithm to study transition paths of spontaneous noise-induced switching for a ubiquitous gene regulatory network motif, the bistable toggle switch, in which two mutually repressive genes compete for dominant expression. We find that the method can efficiently uncover detailed switching mechanisms that involve fluctuations both in occupancies of DNA regulatory sites and copy numbers of protein products. In addition, we show that the rate parameters governing binding and unbinding of regulatory proteins to DNA strongly influence the switching mechanism. In a regime of slow DNA-binding/unbinding kinetics, spontaneous switching occurs relatively frequently and is driven primarily by fluctuations in DNA-site occupancies. In contrast, in a regime of fast DNA-binding/unbinding kinetics, switching occurs rarely and is driven by fluctuations in levels of expressed protein. Our results demonstrate how spontaneous cell phenotype transitions involve collective behavior of both regulatory proteins and DNA. Computational approaches capable of simulating dynamics over many system variables are thus well suited to exploring dynamic mechanisms in gene networks.
| S-EPMC4624158 | biostudies-literature
Project description:Optoelectronic devices based on metal halide perovskites continue to show a improved performance, and solution-based coating techniques pave the way for large-area applications. However, not all parameters influencing the thin film formation process of metal halide perovskites are identified and entirely rationalised over their full compositional range, thus hampering optimised thin film fabrication. Furthermore, while the perovskite deposition via spin-coating and annealing is an easily accessible technique, more profound insights into the chemical formation process are still lacking. Varying the precursor solution concentration is commonly used to vary the resulting thin film thickness. This study shows that varying the precursor solution concentration also affects the thin film morphology and optoelectronic quality. Hence, we herein investigate the influence of the precursor solution concentration on the formation process of a pure bromide-based triple cation perovskite (Cs0.05MA0.10FA0.85PbBr3) by fiber-based optical in situ measurement. During the spin-coating process, in situ UV-vis and PL measurements reveal formation kinetics are strongly dependent on the concentration. Furthermore, we identify delayed nucleation and retarded growth kinetics for more concentrated precursor solutions. In addition, we quantify the shifting chemical equilibrium of colloidal pre-coordination in the precursor solution depending on concentration. Namely, colloids are pre-organised to a higher degree and higher-coordination lead-bromide complexes tend to form in more concentrated precursor solutions. Thus, the modified solution chemistry rationalises retarded perovskite formation kinetics and highlights the precursor concentration as an influential and optimisable parameter for solution-based thin film deposition.
| S-EPMC9664315 | biostudies-literature
Project description:The DNA mismatch repair system (MMR) identifies replication errors and damaged bases in DNA and functions to preserve genomic integrity. MutS performs the task of locating mismatched base pairs, loops and lesions and initiating MMR, and the fundamental question of how this protein targets specific sites in DNA is unresolved. To address this question, we examined the interactions between Saccharomyces cerevisiae Msh2-Msh6, a eukaryotic MutS homolog, and DNA in real time. The reaction kinetics reveal that Msh2-Msh6 binds a variety of sites at similarly fast rates (k (ON) approximately 10(7) M(-1) s(-1)), and its selectivity manifests in differential dissociation rates; e.g., the protein releases a 2-Aminopurine:T base pair approximately 90-fold faster than a G:T mismatch. On releasing the 2-Ap:T site, Msh2-Msh6 is able to move laterally on DNA to locate a nearby G:T site. The long-lived Msh2-Msh6.G:T complex triggers the next step in MMR--formation of an ATP-bound clamp--more effectively than the short-lived Msh2-Msh6.2-Ap:T complex. Mutation of Glu in the conserved Phe-X-Glu DNA binding motif stabilizes Msh2-Msh6(E339A).2-Ap:T complex, and the mutant can signal 2-Ap:T repair as effectively as wild-type Msh2-Msh6 signals G:T repair. These findings suggest a targeting mechanism whereby Msh2-Msh6 scans DNA, interrogating base pairs by transient contacts and pausing at potential target sites, and the longer the pause the greater the likelihood of MMR.
| S-EPMC2818965 | biostudies-literature