Chiroplasmonic DNA Scaffolded "Fusilli" Structures.

DNA is an ideal template for the design of nanoarchitectures with molecular-like features. Here, we present an optimized assembly strategy for the concatenation of DNA quasi-rings into long scaffolds. Ionic strength, which played a major role during self-assembly, produced the expected high quality only at 15 mM MgCl2. Atomic force microscopy (AFM) characterization showed several micrometer long tubular structures that were used as templates for the positioning of plasmonic nanoparticles (NPs) along a three-dimensional helical path using DNA tethers. As imaged by high-resolution scanning transmission electron microscopy (HR-STEM) and modeled by theoretical calculations, the NPs distributed into a "fusilli" fashion (i.e., a helical pasta shape), displaying chiroptical activity as revealed by a bisignated CD absorption, centered at the plasmon resonance wavelength. The present structures contribute to enrich the ever-developing arena of chiroplasmonic DNA-based nanomaterials and demonstrate that large assemblies are attainable for their future application to develop metamaterials.

Rational design of hybrid DNA-RNA triplex structures as modulators of transcriptional activity in vitro.

Triplex nanostructures can be formed in vitro in the promoter region of DNA templates, and it is commonly accepted that these assemblies inhibit the transcription of the downstream genes. Herein, a proof of concept highlighting the possibility of the up- or downregulation of RNA transcription is presented. Hybrid DNA-RNA triplex nanostructures were rationally designed to produce bacterial transcription units with switchable promoters. The rate of RNA production was measured using the signal of a transcribed fluorescent RNA aptamer (i.e. Broccoli). Indeed, several designed bacterial promoters showed the ability of induced transcriptional inhibition, while other properly tailored sequences demonstrated switchable enhancement of transcriptional activity, representing an unprecedented feature to date. The use of RNA-regulated transcription units and fluorescent RNA aptamers as readouts will allow the realization of biocomputation circuits characterized by a strongly reduced set of components. Triplex forming RNA oligonucleotides are proposed as smart tools for transcriptional modulation and represent an alternative to current methods for producing logic gates using protein-based components.

Acidic Shift of Optimum pH of Bovine Serum Amine Oxidase upon Immobilization onto Nanostructured Ferric Tannates.

Protein-nanoparticle hybrids represent entities characterized by emerging biological properties that can significantly differ from those of the parent components. Herein, bovine serum amine oxidase (i.e., BSAO) was immobilized onto a magnetic nanomaterial constituted of surface active maghemite nanoparticles (i.e., SAMNs, the core), surface-modified with tannic acid (i.e., TA, the shell), to produce a biologically active ternary hybrid (i.e., SAMN@TA@BSAO). In comparison with the native enzyme, the secondary structure of the immobilized BSAO responded to pH variations sensitively, resulting in a shift of its optimum activity from pH 7.2 to 5.0. Conversely, the native enzyme structure was not influenced by pH and its activity was affected at pH 5.0, i.e., in correspondence with the best performances of SAMN@TA@BSAO. Thus, an extensive NMR study was dedicated to the structure-function relationship of native BSAO, confirming that its low activity below pH 6.0 was ascribable to minimal structural modifications not detected by circular dichroism. The generation of cytotoxic products, such as aldehydes and H2O2, by the catalytic activity of SAMN@TA@BSAO on polyamine oxidation is envisaged as smart nanotherapy for tumor cells. The present study supports protein-nanoparticle conjugation as a key for the modulation of biological functions.

DNA-driven dynamic assembly of MoS2 nanosheets.

Controlling the assembly of molybdenum disulfide (MoS2) layers into static and dynamic superstructures can impact on their use in optoelectronics, energy, and drug delivery. Toward this goal, we present a strategy to drive the assembly of MoS2 layers via the hybridization of complementary DNA linkers. By functionalizing the MoS2 surface with thiolated DNA, MoS2 nanosheets were assembled into mulitlayered superstructures, and the complementary DNA strands were used as linkers. A disassembly process was triggered by the formation of an intramolecular i-motif structure at a cystosine-rich sequence in the DNA linker at acidic pH values. We tested the versatility of our approach by driving the disassembly of the MoS2 superstructures through a different DNA-based mechanism, namely strand displacement. This study demonstrates how DNA can be employed to drive the static and dynamic assembly of MoS2 nanosheets in aqueous solution.

Toward the Specificity of Bare Nanomaterial Surfaces for Protein Corona Formation.

Aiming at creating smart nanomaterials for biomedical applications, nanotechnology aspires to develop a new generation of nanomaterials with the ability to recognize different biological components in a complex environment. It is common opinion that nanomaterials must be coated with organic or inorganic layers as a mandatory prerequisite for applications in biological systems. Thus, it is the nanomaterial surface coating that predominantly controls the nanomaterial fate in the biological environment. In the last decades, interdisciplinary studies involving not only life sciences, but all branches of scientific research, provided hints for obtaining uncoated inorganic materials able to interact with biological systems with high complexity and selectivity. Herein, the fragmentary literature on the interactions between bare abiotic materials and biological components is reviewed. Moreover, the most relevant examples of selective binding and the conceptualization of the general principles behind recognition mechanisms were provided. Nanoparticle features, such as crystalline facets, density and distribution of surface chemical groups, and surface roughness and topography were encompassed for deepening the comprehension of the general concept of recognition patterns.

Controlling Chirality across Length Scales using DNA.

Nano-objects with chiral properties attract growing interest due to their relevance for a wide variety of technological applications. For example, chiral nano-objects may be used in characterization platforms that involve chiral molecular recognition of proteins or in the fabrication of nanomechanical devices such as screw-gears or nanoswimmers. Spatial ordering of emitters of circularly polarized light might greatly benefit from the utilization of chiral shapes. Tools developed in DNA nanotechnology now allow precise tailoring of the chiral properties of molecules and materials at various length scales. Among others, they have already been applied to control the handedness of helical shapes (configurational chirality) or the chiral positioning of different-sized nanoparticles at the vertices of tetrahedra (compositional chirality). This work covers some of the key advances and recent developments in the field of chiral DNA nanoarchitectures and discusses their future perspectives and potential applications.

Cu2+ -Modified Metal-Organic Framework Nanoparticles: A Peroxidase-Mimicking Nanoenzyme.

The synthesis and characterization of UiO-type metal-organic framework nanoparticles (NMOFs) composed of Zr4+ ions bridged by 2,2'-bipyridine-5,5'-dicarboxylic acid ligands and the postmodification of the NMOFs with Cu2+ ions are described. The resulting Cu2+ -modified NMOFs, Cu2+ -NMOFs, exhibit peroxidase-like catalytic activities reflected by the catalyzed oxidation of Amplex-Red to the fluorescent Resorufin by H2 O2 , the catalyzed oxidation of dopamine to aminochrome by H2 O2 , and the catalyzed generation of chemiluminescence in the presence of luminol/H2 O2 . Also, the Cu2+ -NMOFs mimic NADH peroxidase functions and catalyze the oxidation of dihydronicotinamide adenine dinucleotide, NADH, to nicotinamide adenine dinucleotide, NAD+ , in the presence of H2 O2 . The Cu2+ -NMOFs-catalyzed generation of chemiluminescence in the presence of luminol/H2 O2 is used to develop a glucose sensor by monitoring the H2 O2 formed by the aerobic oxidation of glucose to gluconic acid in the presence of glucose oxidase. Furthermore, loading the Cu2+ -NMOFs with fluorescein and activating the catalyzed generation of chemiluminescence in the presence of luminol/H2 O2 yield an efficient chemiluminescence resonance energy transfer (CRET) process to the fluorescein reflected by the activation of the fluorescence of the dye (λ = 520 nm, CRET efficiency 35%).

Mimicking Peroxidase Activities with Prussian Blue Nanoparticles and Their Cyanometalate Structural Analogues.

Nanoparticles composed of Prussian Blue, PB, and the cyanometalate structural analogues, CuFe, FeCoFe, and FeCo, are examined as inorganic clusters that mimic the functions of peroxidases. PB acts as a superior catalyst for the oxidation of dopamine to aminochrome by H2O2. The oxidation of dopamine by H2O2 in the presence of PB is 6-fold faster than in the presence of CuFe. The cluster FeCo does not catalyze the oxidation of dopamine to aminochrome. The most efficient catalyst for the generation of chemiluminescence by the oxidation of luminol by H2O2 is, however, FeCo, and PB lacks any catalytic activity toward the generation of chemiluminescence. The order of catalyzed chemiluminescence generation is FeCo ≫ CuFe > FeCoFe. The clusters PB, CuFe, FeCoFe, and FeCo mimic the functions of NADH peroxidase. The catalyzed oxidation of NADH by H2O2 to form NAD+ follows the order PB ≫ CuFe ∼ FeCoFe, FeCo. The efficient generation of chemiluminescence by the FeCo-catalyzed oxidation of luminol by H2O2 is used to develop a glucose sensor. The aerobic oxidation of glucose in the presence of glucose oxidase, GOx, yields gluconic acid and H2O2. The chemiluminescence intensities formed by the GOx-generated H2O2 relate to the concentration of glucose, thus providing a quantitative readout signal for the concentrations of glucose.

Controlling the Catalytic Functions of DNAzymes within Constitutional Dynamic Networks of DNA Nanostructures.

Mimicking complex cellular dynamic chemical networks being up-regulated or down-regulated by external triggers is one of the challenges in systems chemistry. Constitutional dynamic networks (CDNs), composed of exchangeable components that respond to environmental triggers by self-adaption, provide general means to mimic biosystems. We use the structural and functional information encoded in nucleic acid nanostructures to construct effector (input)-triggered constitutional dynamic networks that reveal adaptable catalytic properties. Specifically, CDNs composed of four exchangeable constituents, AA', BA', AB', and BB', are constructed. In the presence of an effector (input) that controls the stability of one of the constituents, the input-guided up-regulation or down-regulation of the CDN's constituents proceeds. As effectors we apply the fuel-strand stabilization of one of the CDN constituents by the formation of the T-A·T triplex structure, or by the K+-ion-induced stabilization of one of the CDN constituents, via the formation of a K+-ion-stabilized G-quadruplex. Energetic stabilization of one of the CDN constituents leads to a new dynamically adapted network composed of up-regulated and down-regulated constituents. By applying counter triggers to the effector units, e.g., an antifuel strand or 18-crown-6-ether, reconfiguration to the original CDNs is demonstrated. The performance of the CDNs is followed by the catalytic activities of the constituents and by complementary quantitative gel electrophoresis experiments. The orthogonal triggered and switchable operation of the CDNs is highlighted.

Triplex DNA Nanostructures: From Basic Properties to Applications.

Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.

Recent Advances in the Synthesis and Functions of Reconfigurable Interlocked DNA Nanostructures.

Interlocked circular DNA nanostructures, e.g., catenanes or rotaxanes, provide functional materials within the area of DNA nanotechnology. Specifically, the triggered reversible reconfiguration of the catenane or rotaxane structures provides a means to yield new DNA switches and to use them as dynamic scaffolds for controlling chemical functions and positioning functional cargoes. The synthesis of two-ring catenanes and their switchable reconfiguration by pH, metal ions, or fuel/anti-fuel stimuli are presented, and the functions of these systems, as pendulum or rotor devices or as switchable catalysts, are described. Also, the synthesis of three-, five-, and seven-ring catenanes is presented, and their switchable reconfiguration using fuel/anti-fuel strands is addressed. Implementation of the dynamically reconfigured catenane structures for the programmed organization of Au nanoparticle (NP) assemblies, which allows the plasmonic control of the fluorescence properties of Au NP/fluorophore loads associated with the scaffold, and for the operation of logic gates is discussed. Interlocked DNA rotaxanes and their different synthetic approaches are presented, and their switchable reconfiguration by means of fuel/anti-fuel strands or photonic stimuli is described. Specifically, the use of the rotaxane as a scaffold to organize Au NP assemblies, and the control of the fluorescence properties with Au NP/fluorophore hybrids loaded on the rotaxane scaffold, are introduced. The future prospectives and challenges in the field of interlocked DNA nanostructures and the possible applications are discussed.

DNA Scaffolds for the Dictated Assembly of Left-/Right-Handed Plasmonic Au NP Helices with Programmed Chiro-Optical Properties.

Within the broad interest of assembling chiral left- and right-handed helices of plasmonic nanoparticles (NPs), we introduce the DNA-guided organization of left- or right-handed plasmonic Au NPs on DNA scaffolds. The method involves the self-assembly of stacked 12 DNA quasi-rings interlinked by 30 staple-strands. By the functionalization of one group of staple units with programmed tether-nucleic acid strands and additional staple elements with long nucleic acid chains, acting as promoter strands, the promoter-guided assembly of barrels modified with 12 left- or right-handed tethers is achieved. The subsequent hybridization of Au NPs functionalized with single nucleic acid tethers yields left- or right-handed structures of plasmonic NPs. The plasmonic NP structures reveal CD spectra at the plasmon absorbance, and the NPs are imaged by HR-TEM. Using geometrical considerations corresponding to the left- and right-handed helices of the Au NPs, the experimental CD spectra of the plasmonic Au NPs are modeled by theoretical calculations.

Orthogonal Dual-Triggered Shape-Memory DNA-Based Hydrogels.

DNA-based shape-memory hydrogels revealing switchable shape recovery in the presence of two orthogonal triggers are described. In one system, a shaped DNA/acrylamide hydrogel is stabilized by duplex nucleic acids and pH-responsive cytosine-rich, i-motif, bridges. Separation of the i-motif bridges at pH 7.4 transforms the hydrogel into a quasi-liquid, shapeless state, that includes the duplex bridges as permanent shape-memory elements. Subjecting the quasi-liquid state to pH 5.0 or Ag(+) ions recovers the hydrogel shape, due to the stabilization of the hydrogel by i-motif or C-Ag(+) -C bridged i-motif. The cysteamine-induced transformation of the duplex/C-Ag(+) -C bridged i-motif hydrogel into a quasi-liquid shapeless state results in the recovery of the shaped hydrogel in the presence of H(+) or Ag(+) ions as triggers. In a second system, a shaped DNA/acrylamide hydrogel is generated by DNA duplexes and bridging Pb(2+) or Sr(2+) ions-stabilized G-quadruplex subunits. Subjecting the shaped hydrogel to the DOTA or KP ligands eliminates the Pb(2+) or Sr(2+) ions from the respective hydrogels, leading to shapeless, memory-containing, quasi-liquid states that restore the original shapes with Pb(2+) or Sr(2+) ions.

Integration of Switchable DNA-Based Hydrogels with Surfaces by the Hybridization Chain Reaction.

A novel method to assemble acrylamide/acrydite DNA copolymer hydrogels on surfaces, specifically gold-coated surfaces, is introduced. The method involves the synthesis of two different copolymer chains consisting of hairpin A, HA, modified acrylamide copolymer and hairpin B, HB, acrylamide copolymer. In the presence of a nucleic acid promoter monolayer associated with the surface, the hybridization chain reaction between the two hairpin-modified polymer chains is initiated, giving rise to the cross-opening of hairpins HA and HB and the formation of a cross-linked hydrogel on the surface. By the cofunctionalization of the HA- and HB-modified polymer chains with G-rich DNA tethers that include the G-quadruplex subunits, hydrogels of switchable stiffness are generated. In the presence of K(+)-ions, the hydrogel associated with the surface is cooperatively cross-linked by duplex units of HA and HB, and K(+)-ion-stabilized G-quadruplex units, giving rise to a stiff hydrogel. The 18-crown-6-ether-stimulated elimination of the K(+)-ions dissociates the bridging G-quadruplex units, resulting in a hydrogel of reduced stiffness. The duplex/G-quadruplex cooperatively stabilized hydrogel associated with the surface reveals switchable electrocatalytic properties. The incorporation of hemin into the G-quadruplex units electrocatalyzes the reduction of H2O2. The 18-crown-6-ether stimulated dissociation of the hemin/G-quadruplex bridging units leads to a catalytically inactive hydrogel.

Switchable Reconfiguration of a Seven-Ring Interlocked DNA Catenane Nanostructure.

The synthesis, purification, and structure characterization of a seven-ring interlocked DNA catenane is described. The design of the seven-ring catenane allows the dynamic reconfiguration of any of the four rings (R1, R3, R4, and R6) on the catenane scaffold, or the simultaneous switching of any combination of two, three, or all four rings to yield 16 different isomeric states of the catenane. The dynamic reconfiguration across the states is achieved by implementing the strand-displacement process in the presence of appropriate fuel/antifuel strands and is probed by fluorescence spectroscopy. Each of the 16 isomers of the catenane can be transformed into any of the other isomers, thus allowing for 240 dynamic transitions within the system.

Dual switchable CRET-induced luminescence of CdSe/ZnS quantum dots (QDs) by the hemin/G-quadruplex-bridged aggregation and deaggregation of two-sized QDs.

The hemin/G-quadruplex-catalyzed generation of chemiluminescence through the oxidation of luminol by H2O2 stimulates the chemiluminescence resonance energy transfer (CRET) to CdSe/ZnS quantum dots (QDs), resulting in the luminescence of the QDs. By the cyclic K(+)-ion-induced formation of the hemin/G-quadruplex linked to the QDs, and the separation of the G-quadruplex in the presence of 18-crown-6-ether, the ON-OFF switchable CRET-induced luminescence of the QDs is demonstrated. QDs were modified with nucleic acids consisting of the G-quadruplex subunits sequences and of programmed domains that can be cross-linked through hybridization, using an auxiliary scaffold. In the presence of K(+)-ions, the QDs aggregate through the cooperative stabilization of K(+)-ion-stabilized G-quadruplex bridges and duplex domains between the auxiliary scaffold and the nucleic acids associated with the QDs. In the presence of 18-crown-6-ether, the K(+)-ions are eliminated from the G-quadruplex units, leading to the separation of the aggregated QDs. By the cyclic treatment of the QDs with K(+)-ions/18-crown-6-ether, the reversible aggregation/deaggregation of the QDs is demonstrated. The incorporation of hemin into the K(+)-ion-stabilized G-quadruplex leads to the ON-OFF switchable CRET-stimulated luminescence of the QDs. By the mixing of appropriately modified two-sized QDs, emitting at 540 and 610 nm, the dual ON-OFF activation of the luminescence of the QDs is demonstrated.

Metal nanoparticle-functionalized DNA tweezers: from mechanically programmed nanostructures to switchable fluorescence properties.

DNA tweezers are modified with two 10-nm sized Au NPs and one 5-nm sized Au NP. Upon treatment of the tweezers with fuel and antifuel nucleic acid strands, the switchable closure and opening of the tweezers proceed, leading to the control of programmed nanostructures of the tethered NPs. The tweezers are further modified with a single 10-nm sized nanoparticle, and a fluorophore unit (Cy3), positioned at different distinct sites of the tweezers. The reversible and cyclic fluorescence quenching or fluorescence enhancement phenomena, upon the dynamic opening/closure of the different tweezers, are demonstrated.

Au nanoparticle/DNA rotaxane hybrid nanostructures exhibiting switchable fluorescence properties.

The preparation of a DNA rotaxane consisting of a circular nucleic acid interlocked, through hybridization, on a nucleic acid axle and stoppered by two 10-nm-sized Au nanoparticles (NPs) is described. By the tethering of 5-nm- or 15-nm-sized Au NPs on the ring, the supramolecular structure of the rotaxane is confirmed. Using nucleic acids as "fuels" and "anti-fuels", the cyclic and reversible transition of the rotaxane ring across two states is demonstrated. By the functionalization of the ring with fluorophore-modified nucleic acids in different orientations, the transitions of the rings between the sites are followed by fluorescence quenching or surface-enhanced fluorescence. The experimental results are supported by theoretical modeling.

A three-station DNA catenane rotary motor with controlled directionality.

The assembly of DNA machines represents a central effort in DNA nanotechnology. We report on the first DNA rotor system composed of a two-ring catenane. The DNA rotor ring rotates in dictated directions along a wheel, and it occupies three distinct sites. Hg(2+)/cysteine or pH (H(+)/OH(-)) act as fuels or antifuels in positioning the rotor ring. Analysis of the kinetics reveals directional clockwise or anticlockwise population of the target-sites (>85%), and the rotor's direction is controlled by the shortest path on the wheel.

Switchable reconfiguration of an interlocked DNA olympiadane nanostructure.

Interlocked DNA rings (catenanes) are interesting reconfigurable nanostructures. The synthesis of catenanes with more than two rings is, however, hampered, owing to low yields of these systems. We report a new method for the synthesis of catenanes with a controlled number of rings in satisfactory yields. Our approach is exemplified by the synthesis of a five-ring DNA catenane that exists in four different configurations. By the use of nucleic acids as "fuels" and "antifuels", the cyclic reconfiguration of the system across four states is demonstrated. One of the states, olympiadane, corresponds to the symbol of the Olympic Games. The five-ring catenane was implemented as a mechanical scaffold for the reconfiguration of Au NPs. The advantages of DNA catenanes over supramolecular catenanes include the possibility of generating highly populated defined states and the feasibility of tethering nanoobjects to the catenanes, which act as a mechanical scaffold to reconfigure the nanoobjects.