Linear Nanostructures Research Articles

Zeta potential of Z-DNA: A new signature to study B-Z transition in linear and branched DNA

Zeta potential is commonly referred as surface charge density and is a key factor in modulating the structural and functional properties of nucleic acids. Although the negative charge density of B-DNA is well understood, there is no prior description of the zeta potential measurement of Z-DNA. In this study, for the first time we discover the zeta potential difference between B-DNA and lanthanum chloride-induced Z-DNA. A series of linear repeat i.e. (CG)n and (GC)n DNA as well as branched DNA (bDNA) structures was used for the B-to-Z DNA transition. Herein, the positive zeta potential of Z-DNA has been demonstrated as a powerful tool to discriminate between B-form and Z-form of DNA. The generality of the approach has been validated both in linear and bDNA nanostructures. Thus, we suggest zeta potential can be used as an ideal signature for the left-handed Z-DNA.

Functional 2D Nanoplatforms Alleviate Eosinophilic Chronic Rhinosinusitis by Modulating Eosinophil Extracellular Trap Formation.

The therapeutic outcomes of patients with eosinophilic chronic rhinosinusitis (ECRS) remain unsatisfactory, largely because the underlying mechanisms of eosinophilic inflammation are uncertain. Here, it is shown that the nasal secretions of ECRS patients have high eosinophil extracellular trap (EET) and cell-free DNA (cfDNA) levels. Moreover, the cfDNA induced EET formation by activating toll-like receptor 9 (TLR9) signaling. After demonstrating that DNase I reduced eosinophilic inflammation by modulating EET formation, linear polyglycerol-amine (LPGA)-coated TiS2 nanosheets (TLPGA) as functional 2D nanoplatforms with low cytotoxicity, mild protein adsorption, and increased degradation rate is developed. Due to the more flexible linear architecture, TLPGA exhibited higher cfDNA affinity than the TiS2 nanosheets coated with dendritic polyglycerol-amine (TDPGA). TLPGA reduced cfDNA levels in the nasal secretions of ECRS patients while suppressing cfDNA-induced TLR9 activation and EET formation in vitro. TLPGA displayed exceptional biocompatibility, preferential nasal localization, and potent inflammation modulation in mice with eosinophilic inflammation. These results highlight the pivotal feature of the linear molecular architecture and 2D sheet-like nanostructure in the development of anti-inflammation nanoplatforms, which can be exploited for ECRS treatment.

Photo-controlled order-to-order host-guest self-assembly transfer for an afterglow effect with water resistance.

Due to the general incompleteness of photochemical reactions, the photostationary structure in traditional photo-controlled host-guest self-assembly transfer is usually disordered or irregular. This fact readily affects the photoregulation or improvement of related material properties. Herein, a photoexcitation-induced aggregation molecule, hydroxyl hexa(thioaryl)benzene (HB), was grafted into β-cyclodextrin to form a host-guest system. Upon irradiation, the excited state conformational change of HB can drive an order-to-order phase transition of the system, enabling the transfer of the initial linear nanostructure to a photostationary worm-like nanostructure with orderliness and crystallinity capability. Along with the photoexcitation-controlled phase transition, an afterglow effect was obtained from the films prepared by doping the host-guest system into poly(vinyl alcohol). The afterglow effect had a superior water resistance, which successfully overcame the general sensitivity of doped materials with the afterglow effect to water vapor. These results are expected to provide new insights for pushing forward chemical self-assembly from the light perspective, towards materials with superior and stable properties under light treatment.

DNA-Based Nanomaterials for Analysis of Extracellular Vesicles.

Extracellular vesicles (EVs) are cell-derived nanovesicles comprising a myriad of molecular cargo such as proteins and nucleic acids, playing essential roles in intercellular communication and physiological and pathological processes. EVs have received substantial attention as noninvasive biomarkers for disease diagnosis and prognosis. Owing to their ability to recognize protein and nucleic acid targets, DNA-based nanomaterials with excellent programmability and modifiability provide a promising tool for the sensitive and accurate detection of molecular cargo carried by EVs. In this perspective, recent advancements in EV analysis using a variety of DNA-based nanomaterials are summarized, which can be broadly classified into three categories: linear DNA probes, DNA nanostructures, and hybrid DNA nanomaterials. The design, construction, advantages, and disadvantages of different types of DNA nanomaterials, as well as their performance for detecting EVs are reviewed. The challenges and opportunities in the field of EV analysis by DNA nanomaterials are also discussed.

Sensing the DNA-mismatch tolerance of catalytically inactive Cas9 via barcoded DNA nanostructures in solid-state nanopores.

Single-molecule quantification of the strength and sequence specificity of interactions between proteins and nucleic acids would facilitate the probing of protein-DNA binding. Here we show that binding events between the catalytically inactive Cas9 ribonucleoprotein and any pre-defined short sequence of double-stranded DNA can be identified by sensing changes in ionic current as suitably designed barcoded linear DNA nanostructures with Cas9-binding double-stranded DNA overhangs translocate through solid-state nanopores. We designed barcoded DNA nanostructures to study the relationships between DNA sequence and the DNA-binding specificity, DNA-binding efficiency and DNA-mismatch tolerance of Cas9 at the single-nucleotide level. Nanopore-based sensing of DNA-barcoded nanostructures may help to improve the design of efficient and specific ribonucleoproteins for biomedical applications, and could be developed into sensitive protein-sensing assays.

Disclosing Early Excited State Relaxation Events in Prototypical Linear Carbon Chains.

One-dimensional (1D) linear nanostructures comprising sp-hybridized carbon atoms, as derivatives of the prototypical allotrope known as carbyne, are predicted to possess outstanding mechanical, thermal, and electronic properties. Despite recent advances in their synthesis, their chemical and physical properties are still poorly understood. Here, we investigate the photophysics of a prototypical polyyne (i.e., 1D chain with alternating single and triple carbon bonds) as the simplest model of finite carbon wire and as a prototype of sp-carbon-based chains. We perform transient absorption experiments with high temporal resolution (<30 fs) on monodispersed hydrogen-capped hexayne H─(C≡C)6─H synthesized by laser ablation in liquid. With the support of computational studies based on ground state density functional theory (DFT) and excited state time-dependent (TD)-DFT calculations, we provide a comprehensive description of the excited state relaxation processes at early times following photoexcitation. We show that the internal conversion from a bright high-energy singlet excited state to a low-lying singlet dark state is ultrafast and takes place with a 200 fs time constant, followed by thermalization on the picosecond time scale and decay of the low-energy singlet state with hundreds of picoseconds time constant. We also show that the time scale of these processes does not depend on the end groups capping the sp-carbon chain. The understanding of the primary photoinduced events in polyynes is of key importance both for fundamental knowledge and for potential optoelectronic and light-harvesting applications of low-dimensional nanostructured carbon-based materials.

MicroRNA Imaging Encounters Rolling Circle Amplification: Intracellular Na+-Fueled Linear Programmable DNAzyme Nanostructure.

DNAzyme motors are widely used for the sensitive detection of intracellular miRNAs due to their excellent signal response. Generally, the addition of exogenous mental ions to DNAzyme motors is crucial for the efficient operation of the system. Moreover, the position of the DNAzyme relative to the substrate has a significant impact on the cleavage rate during the reaction. Herein, we proposed a highly loaded Na+-fueled linear programmable DNAzyme nanostructure (LPDN) composed of long, single-strand DNA produced by rolling circle amplification reactions that served as binding partners for Na+-specific DNAyme and substrate. In the meantime, the long, programmable scaffolds can precisely control the position of the DNAzyme and substrate for the optimal effect. During the assay, miR-21 and endogenous Na+ can specifically trigger multiple adjacent substrate-cleaving reactions, resulting in a significant recovery of the Cy3 fluorescence signal in living cells. This method could enable in situ real-time imaging and biocompatibility-enhancing evaluation of intracellular miR-21-level changes. Furthermore, LPDN's ability to distinguish normal cells from cancer cells makes it a promising candidate for early cancer diagnosis and imaging analysis of cancer.

DNA Mold-Based Fabrication of Palladium Nanostructures.

DNA origami molds allow a shape-controlled growth of metallic nanoparticles. So far, this approach is limited to gold and silver. Here, the fabrication of linear palladium nanostructures with controlled lengths and patterns is demonstrated. To obtain nucleation centers for a seeded growth, a synthesis procedure of palladium nanoparticles (PdNPs) using Bis(p-sulfonatophenyl)phenylphosphine (BSPP) both as reductant and stabilizer is developed to establish an efficient functionalization protocol of the particles with single-stranded DNA. Attaching the functionalized particles to complementary DNA strands inside DNA mold cavities supports subsequently a highly specific seeded palladium deposition. This provides rod-like PdNPs with diameters of 20-35nm of grainy morphology. Using an annealing procedure and a post-reduction step with hydrogen, homogeneous palladium nanostructures can be obtained. With the adaptation of the procedure to palladium the capabilities of the mold-based tool-box are expanded. In the future, this may allow a facile adaptation of the mold approach to less noble metals including magnetic materials such as Ni and Co.

Synthesis of Linear Black Gold Nanostructures Processable as Sunlight and Low-Energy Light Collecting Films for Photo-Thermoelectricity.

As one of the effort to cope with the energy crisis and carbon neutrality, utilization of low-grade energy generated indoors (e.g., light) is imperative because this saves building and house energy, which accounts for ≈40% of total energy consumption. Although photovoltaic devices could contribute to energy savings, it is also necessary to harvest heat from indoor lights to generate electricity because the light absorbed by materials is mostly transformed into heat. For daily life uses, materials should not only have high absorptance and low emittance but also be easily processed into various forms. To this end, this work synthesizes black aqueous suspensions containing winding and bent linear gold nanostructures with diameters of 3-5nm and length-to-diameter ratios of ≈4-10. Their optical and photo-thermal characteristicsareunderstood through experimental and theoretical investigations. Black gold nanostructures are conveniently processed into metal-dielectric films on metal, glass, and flexible substrates. The film on copper has an absorptance of 0.97 and an emittance of 0.08. Under simulated sunlight and indoor LED light illumination, the film has equivalent photo-thermal and photo-thermoelectric performances to a top-tier sunlight-collecting film. This work attempts to modify the film structure to generate more usable electricity from low-energy indoor light.

Two-dimensional self-assembly and co-assembly of two tetracarboxylic acid derivatives investigated by STM.

In this work, the two-dimensional self-assembly and co-assembly behaviors of two tetracarboxylic acid derivatives (H4BDETP and H4BTB) were investigated by scanning tunneling microscopy (STM). H4BDETP molecules self-assembled into linear nanostructures, and H4BTB molecules formed lamellar and tetragonal nanostructures. The formation of a H4BDETP/H4BTB co-assembly nanostructure was closely related to the deposition sequence of H4BDETP and H4BTB on highly oriented pyrolytic graphite (HOPG). The introduction of H4BTB into the self-assembly system of H4BDETP resulted in the emergence of the H4BDETP/H4BTB nanostructure, while the addition of H4BDETP had no effect on the self-assembly system of H4BTB and a H4BDETP/H4BTB co-assembly nanostructure was not obtained.

Scan direction of circularly polarized laser beam determines the orientation of laser-induced periodic surface structures (LIPSSs) on silicon

Upon irradiation of a silicon surface with circularly polarized green nanosecond laser pulses, the formation of linear periodic nanostructures is observed. Due to the lack of inherent directional anisotropy by the laser polarization, no 1D-laser-induced periodic surface structures (LIPSSs) formation is expected. The orientation of the formed surface modulation depends on the laser scan direction. Silicon wafers, which are often used in LIPSS studies, are commonly considered inert substrates. This assumption needs to be reconsidered. Our finding is not explained by the current LIPSS theories.

In situ imaging miRNAs using multifunctional linear DNA nanostructure

The microRNAs (miRNAs) play a critical role in many biological processes and are essential biomarkers for diagnosing disease. However, the sensitive and specific quantification of microRNAs (miRNAs) expression in living cells still faces a huge challenge. Our study designed a multifunctional linear DNA nanostructure (MLN) as a carrier of molecular beacons (MB-21) for detecting and intracellular imaging miRNA-21. The MLN-MB consists of three parts: aptamer, MLN, and MB-21. The aptamer (AS1411) could media MLN-MB enter live cells without additional transfection reagents. Once inside the cells, the intracellular miRNA-21 could hybridize the MB-21s, resulting in significantly enhanced fluorescence signals. The whole process was enzyme-free, autonomous, and continuous, which avoided the necessity of adding external fuel strands or enzymes. We demonstrated that the MLN-MB could be used to screen the miRNA-21 with a detection limit of 320 pM in a short time (10 min) and show high specificity toward miRNA-21 against other miRNAs. Moreover, the proposed MLN-MB could detect the miRNA-21 in complex matrixes stably. With its outstanding stability, dual recognition, and biocompatibility, MLN-MB is capable of delivering into living cells to identify specific cancer cells. Therefore, our sensing approach, with high sensitivity, specificity, and simplicity advantages, holds great potential for early cancer diagnosis.

Chain-Length- and Concentration-Dependent Isomerization of Bithiophenyl-Based Diaminotriazine Derivatives in Two-Dimensional Polymorphic Self-Assembly§.

Bithiophenyl-based diaminotriazine derivatives (2TDT-n, n = 10, 12, 16, and 18) with different chain lengths display colhex/p6mm mesophases. Their supramolecular self-assembled mechanism is investigated using scanning tunneling microscopy (STM) at the 1-octanoic acid/graphite interface at various concentrations. The chain length effect on the two-dimensional adlayers is observed in this system, and 2TDT-n molecules show a structural phase transition from the four-leaf arrangement to the two-row linear nanostructure accompanied by the emergence of molecular isomerization with the increase of the side-chain length. The self-assembled structure of 2TDT-10 is composed of a four-leaf pattern with uniform s-cis conformers. In 2TDT-12, three kinds of nanostructures (bamboo-like, two-row linear pattern-I, and flower-like) are observed. These nanostructures are randomly constituted by cis and trans conformers, and the ratios of the s-cis conformer in three kinds of patterns are 55.7, 42.3, and 62.5%, respectively. Furthermore, when n = 16 and 18, the ratio of the s-cis conformer further decreases to 19.0 and 4.3%, respectively. Those molecules mainly form linear nanostructures consisting of s-trans conformers. Therefore, it is reasonable to conclude that the side-chain length has a great effect on the self-assembled patterns and the molecular conformation of bithiophenyl-based diaminotriazine derivatives. Density functional theory calculations are applied to optimize molecular conformers and assess their single-point energies, showing that the s-cis conformation has higher energy than the s-trans conformer. We speculate that the ratio of two conformers in nanostructures might be similar to that of the liquid crystalline phase.

Programmable binary crystallization behaviors assisted by hydrogen bond on HOPG surface

Crystallization behaviors of 1,3,5-tri(1H-benzo[d]imidazol-2-yl) benzene (BTIB), gallic acid derivative (A10), and their hydrogen-bonded complex BTIB/A10 on Highly Oriented Graphite(HOPG) surface were studied by scanning tunneling microscope (STM) in combination with density functional theory (DFT) calculations. Single component BTIB self-assembled into porous and linear nanostructures, and A10 aggregated into linear nanostructure. Induced by the intermolecular interactions, an ordered BTIB/A10 nanostructure with the molecular ratio of 1:3 was in situ obtained and identical to the bulk assembly structure. When 1,3,5-Tris(4-carboxyphenylethynyl) benzene (H3BTE) or 1,3,5-tris(10-carboxydecyloxy)-benzene (TCDB) instead of A10 was adopted, porous nanostructure with the molar ratio of 1:1 was in situ prepared in BTIB/H3BTE and BTIB/TCDB system respectively, which indicated the regulatory effect of the number of aromatic acids’ carboxyl groups on the co-assemblies of BTIB and aromatic acids. Simultaneously, the flexible connection groups between the three carboxyl groups and the central benzene ring in TCDB resulted in the formation of another co-assembly nanostructure in BTIB/TCDB system, which was different from the BTIB/H3BTE system. These results would be contributed to deepening the understanding of the interfacial crystal behaviors and probably providing an efficient pathway of regulating the structures of binary hydrogen-bonded crystals.

A novel targeted co-delivery system for transfer of epirubicin and antimiR-10b into cancer cells through a linear DNA nanostructure consisting of FOXM1 and AS1411 aptamers

Herein, a novel linear DNA nanostructure (LDN)-based delivery system was designed and prepared to efficiently co-deliver both epirubicin (Epi), as a chemotherapy drug, and antimiR-10b, as a therapeutic oligonucleotide, into breast cancer cells (MCF-7 and 4T1 cells). Firstly, the LDN, comprised of AS1411 aptamer (targeting agent), FOXM1 Apt (therapeutic aptamer), and complementary strand (linker), was prepared to carry both Epi and antimiR-10b. This targeted system is highly stable in serum and easy to be constructed. The Epi-loaded LDN structure showed a remarkable internalization for target cells (MCF-7 and 4T1 cells, nucleolin positive) in comparison with CHO cells (nucleolin negative, non-target). Furthermore, based on the MTT assay, the Epi-loaded LDN significantly decreased the cell viability of MCF-7 and 4T1 cells, while the non-targeted cells indicated less cytotoxicity for this structure, showing the targeting ability of Epi-loaded LDN. Moreover, the ability of tumor growth inhibition of the Epi-loaded LDN structure was significantly much more than free Epi and LDN in tumor-bearing mice, suggesting the significance of combination therapy for tumor treatment.

Ionic liquids: "normal" solvents or nanostructured fluids?

Ionic liquids (ILs) are a class of non-conventional solvents, which, for almost two decades, have continued to generate burgeoning interest in different fields of present-day chemical research with few similar precedents. Among the various aspects related to ILs, a topic worthy of in-depth analysis is their influence on organic reactivity and reaction rates. In light of this, the present short review aims to provide an overview of the literature from 2010 to the present day that addresses this issue. In particular, we herein present two main different viewpoints by which the solvent effect of ILs is explained: the first is mainly based on considering the bulk polarity of ILs and linear solvation energy relationships, while the other treats ILs as nanostructured fluids. In both cases, studies dealing with IL mixtures are also covered. Finally, literature addressing the area of supramolecular catalysis "by" or "in" ILs is also reported. This is one of the few reviews covering these specific aspects, aiming to provide a useful framework to guide future research into the effects of ILs on organic reactivity.

Design novel three-dimensional network nanostructure for lubricant infused on titanium alloys towards long-term anti-fouling

Titanium alloys, recognized as a marine material with great potential, are currently facing serious biofouling problems, which greatly limits its application range. To improve the antifouling performance of titanium alloys, three unique surface of three-dimensional network, grass-like and linear nanostructures were obtained on titanium alloys via hydrothermal treatment in this work. Further, slippery liquid-infused porous surfaces (SLIPSs) were fabricated on titanium alloys via infusing PFPE lubricant into these nanostructures. Water contact angles and sliding angles of SLIPSs were measured to evaluate the effect of nanostructures on the stability of PFPE lubricant layer. Anti-fouling capability of SLIPSs were investigated by quantifying the cells of chlorella and phaeodactylum tricornutum (P. tricornutum)adhered to titanium alloys. The results shows that all the SLIPSs exhibited remarkable inhibition capacity for the settlement of chlorella and P. tricornutum. Among them, the SLIPS with three-dimensional network nanostructure displayed the longest-term anti-fouling performance, and its reduction rate of P. tricornutum and chlorella reaching 77.2 % and 84.5 % after being cultivated for 21 days, respectively, indicating that there existed a positive correlation between the stability of lubricant layer in the artificial seawater and the antifouling effect.

Lighting Up CircRNA Using a Linear DNA Nanostructure.

Accurate analysis of circular RNA (circRNA) is essential for the elucidation of circRNA-mediated signaling pathways and its association with diseases. Here we present a new tool, namely, linear DNA nanostructure (LDN), for efficient assay of circRNA. In this assay, target circRNA initiates cascade displacement reaction between two hairpin probes sequentially assembled along the LDN and finally lights up the whole LDN. Meanwhile, the target circRNA can be recycled and serve as a catalyst for multiple LDNs lighting, leading to the signal switch from "OFF" to "ON". Systematic studies reveal that our LDN-based method can strictly recognize and rapid respond to circRNA with high signal gain. Furthermore, by using human tumor cells it has been verified that the LDN-based method can also be used for easy and high-sensitive imaging of intracellular circRNA, which provides a useful platform for assaying low-abundance circRNA in cells.

One Dimensional AuAg Nanostructures as Anodic Catalysts in the Ethylene Glycol Oxidation.

Direct alcohol fuel cells are highly promising as efficient power sources for various mobile and portable applications. However, for the further advancement of fuel cell technology it is necessary to develop new, cost-effective Pt-free electrocatalysts that could provide efficient alcohol oxidation and also resist cross-over poisoning. Here, we report new electrocatalytic materials for ethylene glycol oxidation, which are based on AuAg linear nanostructures. We demonstrate a low temperature tunable synthesis that enables the preparation of one dimensional (1D) AuAg nanostructures ranging from nanowires to a new nano-necklace-like structure. Using a two-step method, we showed that, by aging the initial reaction mixture at various temperatures, we produced ultrathin AuAg nanowires with a diameter of 9.2 ± 2 and 3.8 ± 1.6 nm, respectively. These nanowires exhibited a high catalytic performance for the electro-oxidation of ethylene glycol with remarkable poisoning resistance. These results highlight the benefit of 1D metal alloy-based nanocatalysts for fuel cell applications and are expected to make an important contribution to the further development of fuel cell technology.

Self-Assembly of Gold Nanoparticles with Oppositely Charged, Long, Linear Chains of Periodic Copolymers.

We studied the assembly of nanoparticles (NPs) with oppositely charged linear and periodic copolymers (CPs), alternating ionic and polar sequences, in the dilute range of polymer concentration. For the first time, we considered CPs displaying a contour length much higher than the gold NP (AuNP) perimeter. We assumed that such CPs will enable the collection of a finite number of NPs into linear nanostructures with a gain of colloidal stability and a better structural control compared to electrostatic complexes obtained with homopolyelectrolytes. As a case study, we synthesized anionic AuNPs and CPs consisting of alternated cationic poly-l-lysine (PLL) blocks and polar sequences of poly(ethylene glycol) (PEG). We showed that complexation of AuNPs with CPs is quite similar to that observed with homo PLL. In that respect, finite size nanometric clusters, of less than 30 NPs, are formed outside the electroneutrality domain and a fast phase separation occurs at the electroneutrality. Nevertheless, the presence of PEG blocks allowed us to highlight some specific effects. First, the global charge of the positively charged clusters was found to be always lower for CP-based clusters than for homo PLL with a dependence of the charge with the number and the mass of the PEG blocks. Second, in spite of this effect which should have promoted the formation of a dense structure, the fractal dimension characterizing the structure of the clusters in bulk was found to be always below 1.8. Finally, we showed that PEG blocks influence the interparticle distance by disfavoring plasmon delocalization when the clusters are dispersed in water and collapse around the NPs when the clusters are deposited on the substrate.