Critical assessment of interactions between ct-DNA and choline-based magnetic ionic liquids: evidences of compaction

Ionic liquids (ILs) have become an alternative green solvent for storage and for stability of DNA. However, an in-depth understanding of binding and molecular interactions between ILs and DNA is needed. In this respect, magnetic ILs (MILs) are promising due to their tunable physicochemical properties. Various spectroscopic techniques and molecular simulations have been employed to unravel the critical factors of the strength and binding mechanism of MILs with DNA. UV-vis spectra unravel the multimodal binding of MILs with DNA, and the intrusion of IL molecules into the minor groove of DNA has been observed from dye displacement studies. Fluorescence correlation spectroscopic studies and scanning electron microscopy confirm the compaction of the DNA. ITC and molecular docking studies estimate the binding affinity of DNA with MILs, of ∼7 kcal mol-1. The 1 μs long-MD simulations give insight into the structural changes in the DNA in the MIL environment. Due to strong interaction with choline ions in the close vicinity, DNA helixes bend or squeeze in length and dilate in diameter (elliptical → spherical), leading to compaction. The post-MD parameters suggest a stronger interaction with [Ch]2[Mn] IL than with [Ch][Fe] IL; hence, the former induces DNA compaction to a more significant extent. Furthermore, decompaction is observed with the addition of sodium salts and is characterized using spectroscopic methods.

Flexibility Analysis of DNA Nanotubes with Prescribed Circumferences and Their Pearl-Necklace Assemblies with Gold Nanoclusters

DNA has been demonstrated as a powerful platform for the construction of inorganic nanoparticles (NPs) into complex three-dimensional assemblies. Despite extensive research, the physical fundamental details of DNA nanostructures and their assemblies with NPs remain obscure. Here, we report the identification and quantification of the assembly details of programmable DNA nanotubes with monodisperse circumferences of a 4, 5, 6, 7, 8, or 10 DNA helix and their pearl-necklace-like assemblies with ultrasmall gold nanoparticles, Au₂₅ nanoclusters (AuNCs), liganded by -S(CH₂)_nNH₃⁺ (n = 3, 6, 11). The flexibilities of DNA nanotubes, analyzed via statistical polymer physics analysis through atomic force microscopy (AFM), demonstrate that ∼2.8 power exponentially increased with the DNA helix number. Moreover, the short-length liganded AuS(CH₂)₃NH₃⁺ NCs were observed to be able to form pearl-necklace-like DNA-AuNC assemblies stiffened than neat DNA nanotubes, while long-length liganded AuS(CH₂)₆NH₃⁺ and AuS(CH₂)₁₁NH₃⁺ NCs could fragment DNA nanotubular structures, indicating that DNA-AuNC assembling can be precisely manipulated by customizing the hydrophobic domains of the AuNC nanointerfaces. We prove the advantages of polymer science concepts in unraveling useful intrinsic information on physical fundamental details of DNA-AuNC assembling, which facilitates DNA-metal nanocomposite construction.

Rapid DNA origami nanostructure detection and classification using the YOLOv5 deep convolutional neural network

The intra-image identification of DNA structures is essential to rapid prototyping and quality control of self-assembled DNA origami scaffold systems. We postulate that the YOLO modern object detection platform commonly used for facial recognition can be applied to rapidly scour atomic force microscope (AFM) images for identifying correctly formed DNA nanostructures with high fidelity. To make this approach widely available, we use open-source software and provide a straightforward procedure for designing a tailored, intelligent identification platform which can easily be repurposed to fit arbitrary structural geometries beyond AFM images of DNA structures. Here, we describe methods to acquire and generate the necessary components to create this robust system. Beginning with DNA structure design, we detail AFM imaging, data point annotation, data augmentation, model training, and inference. To demonstrate the adaptability of this system, we assembled two distinct DNA origami architectures (triangles and breadboards) for detection in raw AFM images. Using the images acquired of each structure, we trained two separate single class object identification models unique to each architecture. By applying these models in sequence, we correctly identified 3470 structures from a total population of 3617 using images that sometimes included a third DNA origami structure as well as other impurities. Analysis was completed in under 20 s with results yielding an F1 score of 0.96 using our approach.

Self-Assembled Single-Stranded DNA Nano-Networks in Solution and at Surfaces

We studied the directed self-assembly of two types of complementary single-stranded DNA (ssDNA) strands [i.e., poly(dA) and poly(dT)] into more complex, organized, and percolating networks in dilute solutions and at surfaces. Understanding ssDNA self-assembly into 2D networks on surfaces is important for the use of such networks in the fabrication of well-defined nanotechnological devices, as, for instance, required in nanoelectronics or for biosensing. To control the formation of 2D networks on surfaces, it is important to know whether DNA assemblies are formed already in dilute solutions or only during the drying/immobilization process at the surface, where the concentration automatically increases. Fluorescence cross-correlation spectroscopy clearly shows the presence of larger DNA complexes in mixed poly(dA) and poly(dT) solutions already at very low DNA concentrations (<1 nM), that is, well below the overlap concentration. Here, we describe for the first time such supramolecular complexes in solution and how their structure depends on the ssDNA length and concentration and ionic strength. Hence, future attempts to control such networks should also focus on network precursors in solution and not only on their immobilization on surfaces.

Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters

The real motivation in the present work is to tune the synthesis variables that can result in a highly fluorescent and stable DNA copper nanocluster (CuNC) and also to understand the intricate mechanism behind this process. Here, carefully optimized concentrations of various reactants enabled the creation of a DNA-encapsulated CuNC for AT-DNA, displaying a size of <1.0 nm as confirmed by transmission electron microscopy and dynamic light scattering. The extremely small size of the AT-DNACuNC supports the discrete electronic transitions, also characterized by an exceptionally strong negative circular dichroism (CD) band around 350 nm, whose intensity is well correlated with the observed strong fluorescence emission intensity. This remarkably strong CD can open new applications in the detection and quantification of a specific DNACuNC. Further, time-dependent fluorescence analysis suggested stronger photostabilization of these DNACuNCs. The simulation study, based on Cu ion distribution, explained how AT-DNA is a better candidate for NC formation than GC-DNA. In conclusion, the better-tuned synthesis procedure has resulted in a highly compact, well-defined three-dimensional conformation that promotes a more favorable microenvironment to sequester a DNA-based CuNC with high brightness and outstanding photostability.

Scaling Up DNA Origami Lattice Assembly

The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm2 is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm2 areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm2 , this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.

DNA nanostructures as templates for biomineralization

Nature uses extracellular matrix scaffolds to organize biominerals into hierarchical structures over various length scales. This has inspired the design of biomimetic mineralization scaffolds, with DNA nanostructures being among the most promising. DNA nanotechnology makes use of molecular recognition to controllably give 1D, 2D and 3D nanostructures. The control we have over these structures makes them attractive templates for the synthesis of mineralized tissues, such as bones and teeth. In this Review, we first summarize recent work on the crystallization processes and structural features of biominerals on the nanoscale. We then describe self-assembled DNA nanostructures and come to the intersection of these two themes: recent applications of DNA templates in nanoscale biomineralization, a crucial process to regenerate mineralized tissues.

Single-strand DNA-scaffolded copper nanoclusters for the determination of inorganic pyrophosphatase activity and screening of its inhibitor

A fluorescence method for the determination of inorganic pyrophosphatase (PPase) activity has been established based on copper nanoclusters (CuNCs). The polythymine of 40 mer (T40) acts as a template for the reduction reaction from Cu²⁺ to Cu⁰ by ascorbic acid (AA). This reaction leads to the formation of fluorescent CuNCs with excitation/emission peaks at 340/640 nm. However, the higher binding affinity between inorganic pyrophosphate (PPi) and Cu²⁺ hinders the effective formation of CuNCs. This shows low fluorescence intensity. PPase catalyzes the hydrolysis of PPi into Pi during which free Cu²⁺ ions are produced. This facilitates the formation of fluorescent CuNCs. Thus, the fluorescence intensity was restored. The fluorescence enhancement of the system has a linear relationship with PPase activity in the range 0.3 to 20 mU·mL^-1, and the detection limit is0.2 mU·mL^-1. The relative intensity (I/I₀) at 640 nm for the analytical solution versus system is also employed to screen the inhibitor for PPase with high efficiency. Graphical abstract Schematic representation of a fluorescent assay for the determination of inorganic pyrophosphatase activity and screening its inhibitor based on single-strand polythymine-scaffolded copper nanoclusters.

A novel fluorescent nanoprobe that based on poly(thymine) single strand DNA-templated copper nanocluster for the detection of hydrogen peroxide

In this paper, a label-free fluorescence nanoprobe is constructed based on poly(thymine) single strand DNA-templated Copper nanocluster (denote as: T-CuNCs) for the detection of hydrogen peroxide. In the assay, the fluorescent T-CuNCs will generate though the reaction of Cu²⁺, poly(thymine) and sodium ascorbate. However, the hydroxyl radical (^.OH) will generated in the presence of H₂O₂, which is able to induced the oxidative lesions of poly(thymine) single chain DNA and lead to the poly(thymine) being splitted into shorter or single oligonucleotide fragments and lose the ability to template the fluorescent T-CuNCs again. Therefore, H₂O₂ can be detected by monitoring the fluorescence strength change of T-CuNCs. The experimental results show that the fluorescence intensity change of T-CuNCs has fantastic linearity versus H₂O₂ concentration in the range of 1-30 μM (R² = 0.9947) and 30-80 μM (R² = 0.9972) with the limit of detection (LOD) as low as 0.5 μM (S/N = 3). More important, the fluorescent nanoprobe was also successfully utilized on the detection of H₂O₂ in serum samples. Therefore, a label-free, costless and effective fluorescence method has been established for the detection of H₂O₂, the intrinsic properties of the nanoprobe endow its more potential applications in chemical and biological study.

A Label-Free Fluorescent Sensor Based on the Formation of Poly(thymine)-Templated Copper Nanoparticles for the Sensitive and Selective Detection of MicroRNA from Cancer Cells

In this work, a simple and label-free fluorescence “off” to “on” platform was designed for the sensitive and selective detection of microRNA (miRNA) in cancer cells. This method utilized a padlock DNA-based rolling circle amplification (P-RCA) to synthesize fluorescent poly(thymine) (PolyT) which acted as a template for the synthesis of copper nanoparticles (CuNPs) within 10 minutes under mild conditions. While the repeated PolyT sequence was used as the template for CuNP synthesis, other non-PolyT parts (single strand-DNAs without the capacity to act as the template for CuNP formation) served as “smart glues” or rigid linkers to build complex nanostructures. Under the excitation wavelength of 340 nm, the synthesized CuNPs emitted strong red fluorescence effectively at 620 nm. To demonstrate the use of this method as a universal biosensor platform, lethal-7a (let-7a) miRNA was chosen as the standard target. This sensor could achieve highly sensitive and selective detection of miRNA in the presence of other homologous analogues for the combination of P-RCA with the fluorescent copper nanoparticle. Overall, this novel label-free method holds great potential in the sensitive detection of miRNA with high specificity in real samples.

DNA Nanoribbon-Templated Self-Assembly of Ultrasmall Fluorescent Copper Nanoclusters with Enhanced Luminescence

Fluorescent copper nanoclusters (CuNCs) have been widely used in chemical sensors, biological imaging, and light-emitting devices. However, individual fluorescent CuNCs have limitations in their capabilities arising from poor photostability and weak emission intensities. As one kind of aggregation-induced emission luminogen (AIEgen), the formation of aggregates with high compactness and good order can efficiently improve the emission intensity, stability, and tunability of CuNCs. Here, DNA nanoribbons, containing multiple specific binding sites, serve as a template for in situ synthesis and assembly of ultrasmall CuNCs (0.6 nm). These CuNC self-assemblies exhibit enhanced luminescence and excellent fluorescence stability because of tight and ordered arrangement through DNA nanoribbons templating. Furthermore, the stable and bright CuNC assemblies are demonstrated in the high-sensitivity detection and intracellular fluorescence imaging of biothiols.

From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies

DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.

Progress in biosensor based on DNA-templated copper nanoparticles

During the last decades, by virtue of their unique physicochemical properties and potential application in microelectronics, biosensing and biomedicine, metal nanomaterials (MNs) have attracted great research interest and been highly developed. Deoxyribonucleic acid (DNA) is a particularly interesting ligand for templating bottom-up nanopreparation, by virtue of its excellent properties including nanosized geometry structure, programmable and artificial synthesis, DNA-metal ion interaction and powerful molecular recognition. DNA-templated copper nanoparticles (DNA-CuNPs) has been developed in recent years. Because of its advantages including simple and rapid preparation, high efficiency, MegaStokes shifting and low biological toxicity, DNA-CuNPs has been highly exploited for biochemical sensing from 2010, especially as a label-free detection manner, holding advantages in multiple analytical technologies including fluorescence, electrochemistry, surface plasmon resonance, inductively coupled plasma mass spectrometry and surface enhanced Raman spectroscopy. This review comprehensively tracks the preparation of DNA-CuNPs and its application in biosensing, and highlights the potential development and challenges regarding this field, aiming to promote the advance of this fertile research area.

Fabrication of Metal Nanostructures on DNA Templates

Metal nanoarchitectures fabrication based on DNA assembly has attracted a good deal of attention. DNA nanotechnology enables precise organization of nanoscale objects with extraordinary structural programmability. The spatial addressability of DNA nanostructures and sequence-dependent recognition allow functional elements to be precisely positioned; thus, novel functional materials that are difficult to produce using conventional methods could be fabricated. This review focuses on the recent development of the fabrication strategies toward manipulating the shape and morphology of metal nanoparticles and nanoassemblies based on the rational design of DNA structures. DNA-mediated metallization, including DNA-templated conductive nanowire fabrication and sequence-selective metal deposition, etc., is briefly introduced. The modifications of metal nanoparticles (NPs) with DNA and subsequent construction of heterogeneous metal nanoarchitectures are highlighted. Importantly, DNA-assembled dynamic metal nanostructures that are responsive to different stimuli are also discussed as they allow the design of smart and dynamic materials. Meanwhile, the prospects and challenges of these shape-and morphology-controlled strategies are summarized.

Electrochemical DNA Sensors with Layered Polyaniline-DNA Coating for Detection of Specific DNA Interactions

A DNA sensor has been proposed on the platform of glassy carbon electrode modified with native DNA implemented between two electropolymerized layers of polyaniline. The surface layer was assembled by consecutive stages of potentiodynamic electrolysis, DNA drop casting, and second electrolysis, which was required for capsulation of the DNA molecules and prevented their leaching into the solution. Surface layer assembling was controlled by cyclic voltammetry, electrochemical impedance spectroscopy, atomic force, and scanning electron microscopy. For doxorubicin measurement, the DNA sensor was first incubated in the Methylene blue solution that amplified signal due to DNA intercalation and competition with the doxorubicin molecules for the DNA binding sites. The charge transfer resistance of the inner layer interface decreased with the doxorubicin concentration in the range from 1.0 pM to 0.1 μM (LOD 0.6 pM). The DNA sensor was tested for the analysis of spiked artificial urine samples and showed satisfactory recovery in concentration range of 0.05⁻10 μM. The DNA sensor developed can find application in testing of antitumor drugs and some other DNA damaging factors.

DNA-Templated In Situ Synthesis of Highly Dispersed AuNPs on Nitrogen-Doped Graphene for Real-Time Electrochemical Monitoring of Nitric Oxide Released from Live Cancer Cells

Dispersion promotion of nanomaterials can significantly enhance their catalytic activities. With a new DNA-templated in situ synthesis approach, we report the preparation of highly dispersed AuNPs on nitrogen-doped graphene sheets (NGS) with significantly improved electrocatalytic ability for the monitoring of nitric oxide (NO) released from live cancer cells. The template DNA is adsorbed on NGS via π-π stacking, and the Au precursor chelates along the DNA lattice through dative bonding. Subsequent introduction of the reducing agent leads to in situ nucleation and growth of AuNPs, eventually resulting in highly dispersed AuNPs on NGS. Because of the synergistic enhancement of the catalytic activities of AuNPs and NGS, as well as the high dispersion of AuNPs, such a nanocomposite shows significant electro-oxidation capability toward NO, leading to a highly sensitive subnanomolar detection limit for NO in vitro. More importantly, the laminin glycoproteins can be readily adsorbed on the surface of the nanomaterials to render excellent biocompatibility for the adhesion and proliferation of live cells, enabling the biointerface for electrochemical detection of NO released from live cancer cells.

Salt-Induced Assembly Transformation of DNA-AuNP Conjugates Based on RCA Origami: From Linear Arrays to Nanorings

We developed a simple method to adjust the structural transformation of DNA-gold nanoparticles assemblies from linear arrays to nanorings by increasing salt concentrations. A DNA nanoladder constructing from RCA origami acted as templates to assemble periodic AuNPs arrays by a terminal thiol located on staple oligonucleotides. The linear AuNPs arrays could be transformed into nanorings only by changing the concentration of NaCl aqueous solution during the assembly process. It was proven that the electrostatic repulsion, being asymmetrically diminished by the high concentration of NaCl, caused the formation of nanoring architectures.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

Hairpin loop-enhanced fluorescent copper nanoclusters and application in S1 nuclease detection

A novel hairpin DNA template with an AT24 double strand stem and a six-base loop was demonstrated for the first time to prepare CuNCs with dramatically enhanced fluorescence and applied for the sensitive detection of S1 nuclease.

In situ formed copper nanoparticles templated by TdT-mediated DNA for enhanced SPR sensor-based DNA assay

For the efficient surface plasmon resonance (SPR)-based DNA assay researching, signal amplification tactics were absolutely necessary. In this work, a sensitive SPR-DNA sensor was developed by employing in situ synthesis of copper nanoparticles (CuNPs) templated by poly-T sequences DNA from terminal deoxynucleotidyl transferase (TdT)-mediated extension, and synergistically with nano-effect deposition as the mass relay. The objective of this strategy was manifold: firstly, tDNA hybridized with the optimal designed probes to active the TdT-mediated DNA extension onto the surface of SPR chip, resulted a long poly-T sequences ssDNA chain in dsDNA terminal onto surface of gold chip and characterized by SPR signal amplitudes. Secondly, copper ion (Cu²⁺) adsorbed into the skeleton of poly-T sequences DNA, with the aid of ascorbic acid (VC) to achieve the Cu²⁺ reduction, copper nanostructures (CuNPs) was synchronously generated onto the single nucleotide chain anchoring in dsDNA derivatives and the formation was featured by transmission electron micrographs (TEM) and electrochemistry. Lastly, dsDNA-complexed CuNPs (CuNPs@dsDNA) triggered the final signal amplification via real-time conversion of the additive catechol violet (CV) into oligomer or chelation precipitation by CuNPs-tagged reporters. With the proposed setups, a precise and replicable DNA sensing platform for specific target oligo was obtained with a detection limit down to 3.21 femtomolar, demonstrating a beneficial overlapping exploitation of nanomaterials and biochemical reaction as unique SPR infrastructure. Such triple-amplification strategic setups, the possibility of various methods abutment and biocompatibility weight reactor was amassed and adapted to more biological detection field.

Adsorption of DNA binding proteins to functionalized carbon nanotube surfaces with and without DNA wrapping

We examined the adsorption of DNA binding proteins on functionalized, single-walled carbon nanotubes (SWNTs). When SWNTs were functionalized with polyethylene glycol (PEG-SWNT), moderate adsorption of protein molecules was observed. In contrast, nanotubes functionalized with CONH₂ groups (CONH₂-SWNT) exhibited very strong interactions between the CONH₂-SWNT and DNA binding proteins. Instead, when these SWNT surfaces were wrapped with DNA molecules (thymine 30-mers), protein binding was a little decreased. Our results revealed that DNA wrapped PEG-SWNT was one of the most promising candidates to realize DNA nanodevices involving protein reactions on DNA-SWNT surfaces. In addition, the DNA binding protein RecA was more adhesive than single-stranded DNA binding proteins to the functionalized SWNT surfaces.

Direct Nanofabrication Using DNA Nanostructure

Recent advances in DNA nanotechnology make it possible to fabricate arbitrarily shaped 1D, 2D, and 3D DNA nanostructures through controlled folding and/or hierarchical assembly of up to several thousands of unique sequenced DNA strands. Both individual DNA nanostructures and their assembly can be made with almost arbitrarily shaped patterns at a theoretical resolution down to 2 nm. Furthermore, the deposition of DNA nanostructures on a substrate can be made with precise control of their location and orientation, making them ideal templates for bottom-up nanofabrication. However, many fabrication processes require harsh conditions, such as corrosive chemicals and high temperatures. It still remains a challenge to overcome the limited stability of DNA nanostructures during the fabrication process.This chapter focuses on the proof-of-principle study to directly convert the structural information of DNA nanostructure to various kinds of materials by nanofabrication.

A novel label-free fluorescent molecular beacon for the detection of 3′–5′ exonuclease enzymatic activity using DNA-templated copper nanoclusters

A label-free biosensor was developed for highly sensitive and selective determination of Exo III based on poly(T) molecular beacon-templated CuNPs.

Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions

In this review, we describe the recent advances in supramolecular helical assemblies formed from chiral and achiral small molecules, oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been observed in or achieved by biological systems. In addition, a brief historical overview of the helical assemblies of small molecules and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.

Biomolecular templating of functional hybrid nanostructures using repeat protein scaffolds

The precise synthesis of materials and devices with tailored complex structures and properties is a requisite for the development of the next generation of products based on nanotechnology. Nowadays, the technology for the generation of this type of devices lacks the precision to determine their properties and is accomplished mostly by 'trial and error' experimental approaches. The use of bottom-up approaches that rely on highly specific biomolecular interactions of small and simple components is an attractive approach for the templating of nanoscale elements. In nature, protein assemblies define complex structures and functions. Engineering novel bio-inspired assemblies by exploiting the same rules and interactions that encode the natural diversity is an emerging field that opens the door to create nanostructures with numerous potential applications in synthetic biology and nanotechnology. Self-assembly of biological molecules into defined functional structures has a tremendous potential in nano-patterning and the design of novel materials and functional devices. Molecular self-assembly is a process by which complex 3D structures with specified functions are constructed from simple molecular building blocks. Here we discuss the basis of biomolecular templating, the great potential of repeat proteins as building blocks for biomolecular templating and nano-patterning. In particular, we focus on the designed consensus tetratricopeptide repeats (CTPRs), the control on the assembly of these proteins into higher order structures and their potential as building blocks in order to generate functional nanostructures and materials.

A Nonconventional Approach to Patterned Nanoarrays of DNA Strands for Template-Assisted Assembly of Polyfluorene Nanowires

DNA molecules have been widely recognized as promising building blocks for constructing functional nanostructures with two main features, that is, self-assembly and rich chemical functionality. The intrinsic feature size of DNA makes it attractive for creating versatile nanostructures. Moreover, the ease of access to tune the surface of DNA by chemical functionalization offers numerous opportunities for many applications. Herein, a simple yet robust strategy is developed to yield the self-assembly of DNA by exploiting controlled evaporative assembly of DNA solution in a unique confined geometry. Intriguingly, depending on the concentration of DNA solution, highly aligned nanostructured fibrillar-like arrays and well-positioned concentric ring-like superstructures composed of DNAs are formed. Subsequently, the ring-like negatively charged DNA superstructures are employed as template to produce conductive organic nanowires on a silicon substrate by complexing with a positively charged conjugated polyelectrolyte poly[9,9-bis(6'-N,N,N-trimethylammoniumhexyl)fluorene dibromide] (PF2) through the strong electrostatic interaction. Finally, a monolithic integration of aligned arrays of DNA-templated PF2 nanowires to yield two DNA/PF2-based devices is demonstrated. It is envisioned that this strategy can be readily extended to pattern other biomolecules and may render a broad range of potential applications from the nucleotide sequence and hybridization as recognition events to transducing elements in chemical sensors.

Genetically Engineered Phage-Templated MnO2 Nanowires: Synthesis and Their Application in Electrochemical Glucose Biosensor Operated at Neutral pH Condition

To conveniently obtain one-dimensional MnO2 nanowires (NWs) with controlled structure and unique properties for electron transfer, the genetically engineered M13 phages were used as templates for precise nucleation and growth of MnO2 crystals in filamentous phage scaffolds, via the spontaneous oxidation of Mn(2+) in alkaline solution. It was found that the morphology of NWs could be tailored by the surface charge of M13 mutants. MnO2 crystals were uniformly distributed on the surface of negatively charged tetraglutamate-fused phage (M13-E4), significantly different from irregular MnO2 agglomeration on the weakly negatively charged wild-type phage and positively charged tetraarginine-fused phage. The as-synthesized M13-E4@MnO2 NWs could catalyze the electro-oxidation of H2O2 at neutral pH. To demonstrate the superiority of the electrocatalytic activity in the solution containing plenty of chloride ions at neutral pH, both glucose oxidase and as-prepared MnO2 NWs were used for fabricating the glucose biosensor. The proposed biosensor showed a wide linear range (5 μM to 2 mM glucose), a low limit of detection of 1.8 μM glucose (S/N = 3), good interassay and intra-assay reproducibility and satisfactory storage stability. Due to the superiorities of synthesis and electrochemical performance, the as-prepared MnO2 NWs are promising for applications in electrocatalysis, electrochemical sensor, and supercapacitor.

Metal nanoclusters: novel probes for diagnostic and therapeutic applications

Metal nanoclusters, composed of several to a few hundred metal atoms, have received worldwide attention due to their extraordinary physical and chemical characteristics. Recently, great efforts have been devoted to the exploration of the potential diagnostic and therapeutic applications of metal nanoclusters. Here we focus on the recent advances and new horizons in this area, and introduce the rising progress on the use of metal nanoclusters for biological analysis, biological imaging, therapeutic applications, DNA assembly and logic gate construction, enzyme mimic catalysis, as well as thermometers and pH meters. Furthermore, the future challenges in the construction of biofunctional metal nanoclusters for diagnostic and therapeutic applications are also discussed. We expect that the rapidly growing interest in metal nanocluster-based theranostic applications will certainly not only fuel the excitement and stimulate research in this highly active field, but also inspire broader concerns across various disciplines.

Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology

Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.

Programmably Shaped Carbon Nanostructure from Shape-Conserving Carbonization of DNA

DNA nanostructures are versatile templates for low cost, high resolution nanofabrication. However, due to the limited chemical stability of pure DNA structures, their applications in nanofabrication have long been limited to low temperature processes or solution phase reactions. Here, we demonstrate the use of DNA nanostructure as a template for high temperature, solid-state chemistries. We show that programmably shaped carbon nanostructures can be obtained by a shape-conserving carbonization of DNA nanostructures. The DNA nanostructures were first coated with a thin film of Al2O3 by atomic layer deposition (ALD), after which the DNA nanostructure was carbonized in low pressure H2 atmosphere at 800-1000 °C. Raman spectroscopy and atomic force microscopy (AFM) data showed that carbon nanostructures were produced and the shape of the DNA nanostructure was preserved. Conductive AFM measurement shows that the carbon nanostructures are electrically conductive.

Additive and enhanced fluorescence effects of hairpin DNA template-based copper nanoparticles and their application for the detection of NAD(.)

DNA is an excellent molecular scaffold for the preparation of copper nanoparticles (CuNPs). However, screening and designing an efficient template for the formation of fluorescent CuNPs remains a challenge. Herein, we synthesized CuNPs using a novel hairpin DNA template with a poly T loop and a random double strand stem which performs efficient in the formation of fluorescent CuNPs. Besides, the additive and enhanced effects between the loop and stem sequences on the fluorescence of induced CuNPs was first proposed and investigated. On comparing different sequences, we found that both the circular poly T sequence on the loop region and the stem sequence play important roles in this fluorescence enhancement effect. A label-free analytical system for the quantitative detection of NAD(+) was designed, demonstrating excellent sensitivity. Based on our design concept proposed herein, any random double-stranded DNA can be used for the design of efficient templates for the formation of fluorescent CuNPs in biochemical sensing.

Nanoscale patterning of self-assembled monolayers using DNA nanostructure templates

We describe a method to pattern arbitrary-shaped silane self-assembled monolayers (SAMs) with nm scale resolution using DNA nanostructures as templates. The DNA nanostructures assembled on a silicon substrate act as a soft-mask to negatively pattern SAMs. Mixed SAMs can be prepared by back filling the negative tone patterns with a different silane.

In-Plane Switching Mode for Liquid Crystal Displays Using a DNA Alignment Layer

We successfully fabricated the in-plane switching mode (IPS) LC display (LCD) based on a double stranded DNA (dsDNA) alignment layer. As widely known, the DNA has the right-handed double helical structure that has naturally grown grooves with a very regular period, which can be used as an alignment layer to control the orientation of liquid crystal (LC) molecules. The LC molecules on this topographical layer of DNA material align obliquely at a specific angle with respect to the direction of DNA chains, providing an instant and convenient tool for the fabrication of the IPS display compared to the conventional ways such as rubbing and mechanical shearing methods. The electro-optical performance and response time of this device were also investigated. Our result will be of great use in further exploration of the electro-optical properties of the other biomaterials.

DNA-modulated photo-transformation of AgCl to silver nanoparticles: visiting the formation mechanism

Solution-phase synthesis and post-synthetic bio-modification have continued to play a dominant role in preparation of nanostructured biomaterials. Heterogeneous nucleation and growth that occur much more often in nature, however, remain rarely explored in nano-biomaterials research. We have newly developed a DNA-modulated photoconversion approach to uniform silver nanoparticles that afford DNA-directed recognition and multi-mode imaging. The present study was aimed at understanding the rapid heterogeneous nucleation and growth of AgNPs at the solid-liquid interface with the aid of DNA. Dynamic changes in absorbance, size and morphology of silver nanostructures were monitored and analyzed to clarify the growth kinetics, which indicated a synthetic route involving synchronous growth of silver nanostructures and the fragmentation and consumption of AgCl. Various stabilizers, including polymer and amino acids, were assessed and compared with respect to the efficacy in photoconversion of AgCl. DNA was found to offer the best monodispersity and the smallest diameter for the resultant AgNPs, due to its strong interactions to silver species as well as excellent charge dispersion ability. By controlling the physicochemical property of DNA through choice of pH and ionic strength, we have demonstrated tunable structure and composition of the nanoparticles.

Hybrids of Nucleic Acids and Carbon Nanotubes for Nanobiotechnology

Recent progress in the combination of nucleic acids and carbon nanotubes (CNTs) has been briefly reviewed here. Since discovering the hybridization phenomenon of DNA molecules and CNTs in 2003, a large amount of fundamental and applied research has been carried out. Among thousands of papers published since 2003, approximately 240 papers focused on biological applications were selected and categorized based on the types of nucleic acids used, but not the types of CNTs. This survey revealed that the hybridization phenomenon is strongly affected by various factors, such as DNA sequences, and for this reason, fundamental studies on the hybridization phenomenon are important. Additionally, many research groups have proposed numerous practical applications, such as nanobiosensors. The goal of this review is to provide perspective on biological applications using hybrids of nucleic acids and CNTs.

Optimizing gold nanoparticle seeding density on DNA origami

Characterization of various experimental parameters leads to optimized conditions for depositing linear strings of gold nanoparticle seeds on DNA origami.

DNA-templated in situ growth of silver nanoparticles on mesoporous silica nanospheres for smart intracellular GSH-controlled release

AgNPs are prepared in situ by the DNA-templated process as tunable gatekeepers for mesoporous silica nanocontainers for smart intracellular GSH-controlled release.