Banana DNA derivatives as homeotropic alignment layers in optical devices

In this study, deoxyribonucleic acid (DNA) from bananas was extracted and functionalized and used for the first time as a homeotropic alignment layer for liquid crystals (LCs). Our research was aimed at extracting and investigating DNA from bananas via the synthesis and study of DNA complexes with various surfactants to examine the usefulness of such a complex as an alignment layer in electro-optical transducers. We proposed a simple and eco-friendly synthesis of the DNA complexes isolated from bananas with surfactants, so we transformed the DNA isolated from bananas into a functionalized alignment layer. A biopolymer alignment layer like deoxyribonucleic acid (DNA) from a banana complexed with a cationic surfactant is an excellent alternative to a commonly used but toxic polyimide alignment layer. DNA-based materials are promising for photonic applications and biosensors because of their excellent optical and physical properties, biodegradability, and low production cost. The novelty of the research lies in the potential use of these materials as biodegradable biopolymer alignment layers for optical devices instead of conventional polymers, which are usually harmful for the environment.

Plasmid DNA Complexes in Powder Form Studied by Spectroscopic and Diffraction Methods

Currently, new functional materials are being created with a strong emphasis on their ecological aspect. Materials and devices based on DNA biopolymers, being environmentally friendly, are therefore very interesting from the point of view of applications. In this paper, we present the results of research on complexes in the powder form based on plasmid DNA (pDNA) and three surfactants with aliphatic chains containing 16 carbon atoms (cetyltrimethylammonium chloride, benzyldimethylhexadecylammonium chloride and hexadecylpyridinium chloride). The X-ray diffraction results indicate a local hexagonal packing of DNA helices in plasmid DNA complexes, resembling the packing for corresponding complexes based on linear DNA. Based on the Fourier-transform infrared spectroscopy results, the DNA conformation in all three complexes was determined as predominantly of A-type. The two relaxation processes revealed by dielectric spectroscopy for all the studied complexes are connected with two different contributions to total conductivity (crystallite part and grain boundaries). The crystallite part (grain interior) was interpreted as an oscillation of the polar surfactant head groups and is dependent on the conformation of the surfactant chain. The influence of the DNA type on the properties of the complexes is discussed, taking into account our previous results for complexes based on linear DNA. We showed that the type of DNA has an impact on the properties of the complexes, which has not been demonstrated so far. It was also found that the layer of pDNA-surfactant complexes can be used as a layer with variable specific electric conductivity by selecting the frequency, which is interesting from an application point of view.

Recent Progress and Challenges of Implantable Biodegradable Biosensors

Implantable biosensors have evolved to the cutting-edge technology of personalized health care and provide promise for future directions in precision medicine. This is the reason why these devices stand to revolutionize our approach to health and disease management and offer insights into our bodily functions in ways that have never been possible before. This review article tries to delve into the important developments, new materials, and multifarious applications of these biosensors, along with a frank discussion on the challenges that the devices will face in their clinical deployment. In addition, techniques that have been employed for the improvement of the sensitivity and specificity of the biosensors alike are focused on in this article, like new biomarkers and advanced computational and data communicational models. A significant challenge of miniaturized in situ implants is that they need to be removed after serving their purpose. Surgical expulsion provokes discomfort to patients, potentially leading to post-operative complications. Therefore, the biodegradability of implants is an alternative method for removal through natural biological processes. This includes biocompatible materials to develop sensors that remain in the body over longer periods with a much-reduced immune response and better device longevity. However, the biodegradability of implantable sensors is still in its infancy compared to conventional non-biodegradable ones. Sensor design, morphology, fabrication, power, electronics, and data transmission all play a pivotal role in developing medically approved implantable biodegradable biosensors. Advanced material science and nanotechnology extended the capacity of different research groups to implement novel courses of action to design implantable and biodegradable sensor components. But the actualization of such potential for the transformative nature of the health sector, in the first place, will have to surmount the challenges related to biofouling, managing power, guaranteeing data security, and meeting today's rules and regulations. Solving these problems will, therefore, not only enhance the performance and reliability of implantable biodegradable biosensors but also facilitate the translation of laboratory development into clinics, serving patients worldwide in their better disease management and personalized therapeutic interventions.

Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories

We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.

Sterically Enhanced Control of Enzyme-Assisted DNA Assembly

Traditional methods for the assembly of functionalised DNA structures, involving enzyme restriction and modification, present difficulties when working with small DNA fragments (<100 bp), in part due to a lack of control over enzymatic action during the DNA modification process. This limits the design flexibility and range of accessible DNA structures. Here, we show that these limitations can be overcome by introducing chemical modifications into the DNA that spatially restrict enzymatic activity. This approach, sterically controlled nuclease enhanced (SCoNE) DNA assembly, thereby circumvents the size limitations of conventional Gibson assembly (GA) and allows the preparation of well-defined, functionalised DNA structures with multiple probes for specific analytes, such as IL-6, procalcitonin (PCT), and a biotin reporter group. Notably, when using the same starting materials, conventional GA under typical conditions fails. We demonstrate successful analyte capture based on standard and modified sandwich ELISA and also show how the inclusion of biotin probes provides additional functionality for product isolation.

External Electric Field Effects on AFM-like Magnetism in Nitroxide-Functionalized C+:C Base Pair

In this work, we computationally designed a set of nitroxide diradical base pairs (rC⁺:rC) to propose promising magnetic building blocks for spintronic or magnetic molecular materials. C⁺:C12 is found to possess a considerably large antiferromagnetic-like (AFM-like) spin-coupling magnitude (J = -3286.681 cm^-1) and sensitive magnetic responses to the external electric field. Especially, the presence of the Y direction field that is oriented perpendicular to intermolecular hydrogen bonds has the greatest influence on the magnetic exchange interaction (J being from -2549.578 to -4231.286 cm^-1, ΔJ_Y = 1681.708 cm^-1), which could be understood by two simultaneously occurring effects. On the one hand, the external electric field in the -Y direction can regulate the charge polarization of negative and positive electrostatic potentials on C12 moiety and further facilitate the spin transport property. On the other hand, with increasing electric field strength on the -Y axis, the spin density on diradical sources diminishes and that on the coupler increases, which can lead to a homogenous spin-density distribution. The achieved understanding provides a new strategy for designing self-assembly magnetic nanomaterials or nanodevices and enhancing the AFM coupling through the assistance of external electric field.

Structure-Dependent Electrical Conductance of DNA Origami Nanowires

Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si₃ N₄ ) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si₃ N₄ substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼10¹³ ohms) than on native Si₃ N₄ substrates without HMDS (∼10¹⁴ ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si₃ N₄ substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.

DNA foams constructed by freeze drying and their optoelectronic characteristics

The distinctive properties of DNA make it a promising biomaterial to use in nanoscience and nanotechnology. In the present study, DNA foam was fabricated into multi-dimensional shapes using a freeze drying process with liquid nitrogen and 3D printed molds. The physicochemical and optoelectronic properties of the fabricated DNA foams were investigated using Fourier transform infrared (FTIR) spectrum, X-ray photoelectron spectrum (XPS), thermogravimetric analysis (TGA), ultraviolet-visible (UV-Vis) absorption spectrum, and current-voltage (I-V) characteristics to understand the changes formed in the DNA structure and their effect on properties during the fabrication of DNA foam. The FTIR and XPS analyses confirmed that nitrogen was diffusing into the DNA structure during the DNA foam fabrication. The diffused nitrogen caused a decrease in bond lengths, strong chemical bonds, compaction of DNA structure, existence of additional carbon-nitrogen bonds, and variation in the electron density of the base elements in DNA. These changes in the DNA structure of the DNA foam were reflected in their chemical, optical, and electrical properties. Furthermore, the proper utilization of DNA foams as a template for functional materials by embedding carbon nanotubes (CNTs) and thermocolor was demonstrated.

Preparation of bioplastic consisting of salmon milt DNA

The microplastic that pollutes the ocean is a serious problem around the world. The bioplastic consisting of biopolymers which is degraded in nature, is one of the strategies to solve this problem. Although the bioplastics consisting of protein, polysaccharide, polylactic acid, etc., have been reported, which consist of DNA, one of the most important materials in the genetic process, have not been reported to the best of our knowledge. In addition, a large amount of DNA-containing materials, such as salmon milts, is discarded as industrial waste around the world. Therefore, we demonstrated the preparation of a bioplastic consisting of salmon milt DNA. The DNA plastic was prepared by the immersion of a DNA pellet in a formaldehyde (HCHO) solution and heating. As a result, the water-stable DNA plastics were obtained at the HCHO concentration of 20% or more. Particularly, the DNA plastic with a 25% HCHO treatment showed water-insoluble, thermally stable, and highly mechanical properties. These are due to the formation of a three-dimensional network via the crosslinking reaction between the DNA chains. In addition, since DNA in plastic possesses the double-stranded structure, these plastics effectively accumulated the DNA intercalator, such as ethidium bromide. Furthermore, the DNA plastics indicated a biodegradable property in a nuclease-containing aqueous solution and the biodegradable stability was able to be controlled by the HCHO concentration. Therefore, salmon milt DNA has shown the potential to be a biodegradable plastic.

N/OB dative bond supplemented by N-HN/HC Hydrogen Bonds make BN-cages an attractive candidate for DNA-nucleobase adsorption – An MP2 prediction

The response of B12N12-nanocage towards DNA-nucleobases (adenine, guanine, cytosine, and thymine) is investigated using MP2 and DFT (M06-2X) levels of theory with 6-311+G** basis set. Multiple BN-cage-nucleobase structures for each...

Linear and nonlinear optical properties of transfer ribonucleic acid (tRNA) thin solid films

We successfully obtained transfer ribonucleic acid (tRNA) thin solid films (TSFs) using an aqueous solution precursor in an optimized deposition process. By varying the concentration of RNA and deposition process parameters, uniform solid layers of solid RNA with a thickness of 30 to 46 nm were fabricated consistently. Linear absorptions of RNA TSFs on quartz substrates were experimentally investigated in a wide spectral range covering UV–VIS–NIR to find high transparency for λ > 350 nm. We analyzed the linear refractive indices, n(λ) of tRNA TSFs on silicon substrates by using an ellipsometer in the 400 to 900 nm spectral range to find a linear correlation with the tRNA concentration in the aqueous solution. The thermo-optic coefficient (dn/dT) of the films was also measured to be in a range −4.21 × 10⁻⁴ to −5.81 × 10⁻⁴ °C⁻¹ at 40 to 90 °C. We furthermore characterized nonlinear refractive index and nonlinear absorption of tRNA TSFs on quartz using a Z-scan method with a femtosecond laser at λ = 795 nm, which showed high potential as an efficient nonlinear optical material in the IR spectral range.

Optical measurements of one of the vital biological molecules (RNA) in the human body.

Sustainability in wood materials science: an opinion about current material development techniques and the end of lifetime perspectives

Wood is considered the most important renewable resource for a future sustainable bioeconomy. It is traditionally used in the building sector, where it has gained importance in recent years as a sustainable alternative to steel and concrete. Additionally, it is the basis for the development of novel bio-based functional materials. However, wood's sustainability as a green resource is often diminished by unsustainable processing and modification techniques. They mostly rely on fossil-based precursors and yield inseparable hybrids and composites that cannot be reused or recycled. In this article, we discuss the state of the art of environmental sustainability in wood science and technology. We give an overview of established and upcoming approaches for the sustainable production of wood-based materials. This comprises wood protection and adhesion for the building sector, as well as the production of sustainable wood-based functional materials. Moreover, we elaborate on the end of lifetime perspective of wood products. The concept of wood cascading is presented as a possibility for a more efficient use of the resource to increase its beneficial impact on climate change mitigation. We advocate for a holistic approach in wood science and technology that not only focuses on the material's development and production but also considers recycling and end of lifetime perspectives of the products. This article is part of the theme issue 'Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)'.

Metal Ions Sensing by Biodots Prepared from DNA, RNA, and Nucleotides

Nucleic acids that exhibit a high affinity toward noble and transition metal ions have attracted growing attention in the fields of metal ion sensing, toxic metal ion removal, and the construction of functional metal nanostructures. In this study, fluorescent nanoparticles (biodots) were synthesized from DNA, RNA, and RNA nucleotides (AMP, GMP, UMP, and CMP) using a hydrothermal (HT) method, in order to study their metal ion sensing characteristics. The fluorescent properties of biodots differ markedly between those prepared from purine and pyrimidine nucleobases. All biodots demonstrate a high sensitivity to the presence of mercury cations (Hg2+), while biodots prepared from DNA, RNA, and guanosine monophosphate (GMP) are also sensitive to Ag+ and Cu2+ ions, but to a lesser extent. The obtained results show that biodots inherit the metal ion recognition properties of nucleobases, while the nucleobase composition of biodot precursors affects metal ion sensitivity and selectivity. A linear response of biodot fluorescence to Hg2+ concentration in solution was observed for AMP and GMP biodots in the range 0-250 μM, which can be used for the analytic detection of mercury ion concentration. A facile paper strip test was also developed that allows visual detection of mercury ions in solutions.

Adsorptive Removal of Heavy Metal Ions, Organic Dyes, and Pharmaceuticals by DNA-Chitosan Hydrogels

DNA-chitosan (DNA-CS) hydrogel was prepared by in situ complexation between oppositely charged DNA and chitosan polyelectrolytes via electrostatic cross-linking to study its adsorption characteristics. The DNA-chitosan hydrogel matrix contains (i) cationic (NH3+) and anionic (PO4-) sites for electrostatic binding with ionic species, (ii) -OH and -NH2 groups and heteroaromatic DNA nucleobases for chelation of heavy metal ions, and (iii) DNA double-helix for recognition and binding to small organic molecules of various structures and polarities. DNA-CS hydrogels efficiently bind with Hg2+, Pb2+, Cd2+, and Cu2+ metal cations of significant environmental concern. Adsorption capacities of DNA-CS hydrogels for studied metal ions depend on hydrogel composition and pH of solution and reach ca. 50 mg/g at neutral pHs. Hydrogels with higher DNA contents show better adsorption characteristics and notably higher adsorption capacity to Hg2+ ions. Because of the co-existence of cationic and anionic macromolecules in the DNA-CS hydrogel, it demonstrates an affinity to both anionic (Congo Red) and cationic (Methylene Blue) dyes with moderate adsorption capacities of 12.6 mg/g and 29.0 mg/g, respectively. DNA-CS hydrogel can also be used for adsorptive removal of pharmaceuticals on conditions that their molecules are sufficiently hydrophobic and have ionogenic group(s). Facile preparation and multitarget adsorption characteristics of DNA-CS hydrogel coupled with sustainable and environmentally friendly characteristics render this system promising for environmental cleaning applications.

Nucleobases thin films deposited on nanostructured transparent conductive electrodes for optoelectronic applications

Environmentally-friendly bio-organic materials have become the centre of recent developments in organic electronics, while a suitable interfacial modification is a prerequisite for future applications. In the context of researches on low cost and biodegradable resource for optoelectronics applications, the influence of a 2D nanostructured transparent conductive electrode on the morphological, structural, optical and electrical properties of nucleobases (adenine, guanine, cytosine, thymine and uracil) thin films obtained by thermal evaporation was analysed. The 2D array of nanostructures has been developed in a polymeric layer on glass substrate using a high throughput and low cost technique, UV-Nanoimprint Lithography. The indium tin oxide electrode was grown on both nanostructured and flat substrate and the properties of the heterostructures built on these two types of electrodes were analysed by comparison. We report that the organic-electrode interface modification by nano-patterning affects both the optical (transmission and emission) properties by multiple reflections on the walls of nanostructures and the electrical properties by the effect on the organic/electrode contact area and charge carrier pathway through electrodes. These results encourage the potential application of the nucleobases thin films deposited on nanostructured conductive electrode in green optoelectronic devices.

Dye Stabilization and Wavelength Tunability in Lasing Fibers Based on DNA

Lasers based on biological materials are attracting an increasing interest in view of their use in integrated and transient photonics. Deoxyribonucleic acid (DNA) as optical biopolymer in combination with highly emissive dyes has been reported to have excellent potential in this respect. However, achieving miniaturized lasing systems based on solid-state DNA shaped in different geometries to confine and enhance emission is still a challenge, and the physicochemical mechanisms originating fluorescence enhancement are not fully understood. Herein, a class of wavelength-tunable lasers based on DNA nanofibers is demonstrated, for which optical properties are highly controlled through the system morphology. A synergistic effect is highlighted at the basis of lasing action. Through a quantum chemical investigation, it is shown that the interaction of DNA with the encapsulated dye leads to hindered twisting and suppressed channels for the nonradiative decay. This is combined with effective waveguiding, optical gain, and tailored mode confinement to promote morphologically controlled lasing in DNA-based nanofibers. The results establish design rules for the development of bright and tunable nanolasers and optical networks based on DNA nanostructures.

Facile Fabrication of Natural Polyelectrolyte-Nanoclay Composites: Halloysite Nanotubes, Nucleotides and DNA Study

Complexation of biopolymers with halloysite nanotubes (HNTs) can greatly affect their applicability as materials building blocks. Here we have performed a systematic investigation of fabrication of halloysite nanotubes complexes with nucleotides and genomic DNA. The binding of DNA and various nucleotide species (polyAU, UMP Na₂, ADP Na₃, dATP Na, AMP, uridine, ATP Mg) by halloysite nanotubes was tested using UV-spectroscopy. The study revealed that binding of different nucleotides to the nanoclay varied but was low both in the presence and absence of MgCl₂, while MgCl₂ facilitated significantly the binding of longer molecules such as DNA and polyAU. Modification of the nanotubes with DNA and nucleotide species was further confirmed by measurements of ζ-potentials. DNA-Mg-modified nanotubes were characterized using transmission electron (TEM), atomic force (AFM) and hyperspectral microscopies. Thermogravimetric analysis corroborated the sorption of DNA by the nanotubes, and the presence of DNA on the nanotube surface was indicated by changes in the surface adhesion force measured by AFM. DNA bound by halloysite in the presence of MgCl₂ could be partially released after addition of phosphate buffered saline. DNA binding and release from halloysite nanotubes was tested in the range of MgCl₂ concentrations (10–100 mM). Even low MgCl₂ concentrations significantly increased DNA sorption to halloysite, and the binding was leveled off at about 60 mM. DNA-Mg-modified halloysite nanotubes were used for obtaining a regular pattern on a glass surface by evaporation induced self-assembly process. The obtained spiral-like pattern was highly stable and resisted dissolution after water addition. Our results encompassing modification of non-toxic clay nanotubes with a natural polyanion DNA will find applications for construction of gene delivery vehicles and for halloysite self-assembly on various surfaces (such as skin or hair).

Gold Nanoparticles in Conjunction with Nucleic Acids as a Modern Molecular System for Cellular Delivery

Development of nanotechnology has become prominent in many fields, such as medicine, electronics, production of materials, and modern drugs. Nanomaterials and nanoparticles have gained recognition owing to the unique biochemical and physical properties. Considering cellular application, it is speculated that nanoparticles can transfer through cell membranes following different routes exclusively owing to their size (up to 100 nm) and surface functionalities. Nanoparticles have capacity to enter cells by themselves but also to carry other molecules through the lipid bilayer. This quality has been utilized in cellular delivery of substances like small chemical drugs or nucleic acids. Different nanoparticles including lipids, silica, and metal nanoparticles have been exploited in conjugation with nucleic acids. However, the noble metal nanoparticles create an alternative, out of which gold nanoparticles (AuNP) are the most common. The hybrids of DNA or RNA and metal nanoparticles can be employed for functional assemblies for variety of applications in medicine, diagnostics or nano-electronics by means of biomarkers, specific imaging probes, or gene expression regulatory function. In this review, we focus on the conjugates of gold nanoparticles and nucleic acids in the view of their potential application for cellular delivery and biomedicine. This review covers the current advances in the nanotechnology of DNA and RNA-AuNP conjugates and their potential applications. We emphasize the crucial role of metal nanoparticles in the nanotechnology of nucleic acids and explore the role of such conjugates in the biological systems. Finally, mechanisms guiding the process of cellular intake, essential for delivery of modern therapeutics, will be discussed.

Uracil-doped DNA thin solid films: a new way to control optical dispersion of DNA film using a RNA constituent

Among five nucleobases, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U), uracil is a key distinctive constituent existing only in ribonucleic acid (RNA). RNA shares the common A, G, and C with deoxyribonucleic acid (DNA) made of A-T, G-C hydrogen bonding. We explored a new attempt to combine uracil (U) with DNA, successfully realizing U-doped DNA thin solid films for the first time. Impacts of uracil on optical properties of the films were thoroughly investigated. The method was based on optimal spin-coating of an aqueous solution of DNA and uracil over silicon or silica substrates. Optical absorption of both aqueous solution and U-doped DNA thin solid films was characterized in a wide spectral range covering UV-visible-IR. Immobilization of uracil within DNA thin solid films was experimentally confirmed by FTIR spectroscopy studies. By using an ellipsometer, we measured the refractive indices of the films and discovered that U-doping was a very effective means to control optical dispersion DNA thin solid film. We further investigated thermo-optic behavior to find impacts of U-doping in DNA films. Detailed thin film processes and optical characterizations are discussed.

Synthesis of self-assembled nucleobases and their anhydrous proton conductivity

We synthesized self-assembled nucleobases (SANs), such as 1-dodecylthymine (DOT) or 9-dodecyladenine (DOA), in which the nucleobase is immobilized on a long alkyl chain. The thermal stability of the SAN was increased by mixing with the acidic surfactant mono-dodecyl phosphate (MDP). Additionally, the SAN-MDP composite material showed proton conductivity of 4.62 × 10-4 S cm-1 at 160 °C under anhydrous conditions. Additionally, the activation energy of the proton conduction was approximately 0.2 eV and this value was one order of magnitude higher than that of a typical humidified perfluorinated membrane, in which the proton can be moved by vehicle molecules, such as water molecules. In contrast, when the nucleobase without the immobilization of a long alkyl chain was mixed with MDP, the proton conductivity of these composite materials was two orders of magnitude less than that of the SAN-MDP composite. Therefore, we measured the XRD spectra of the SAN-MDP composite material. As a result, the SAN-MDP composite material showed a self-assembled structure with a two-dimensional proton conducting pathway, such as a lamellar structure, and that the anhydrous proton conduction was related to the interaction between the nucleobase of the SAN and the phosphate group of MDP. Consequently, the self-assembled nucleobase derivatives have the potential for use as novel anhydrous proton conductors with a two-dimensional proton conducting pathway.

Determination of nucleobase-pairing free energies from rotamer equilibria of 2-(methylamino)pyrimidines

A fast straightforward method for the determination of free energies of modified nucleobase pairing is proposed. The method is based on the nuclear magnetic resonance (NMR) spectroscopy monitoring of conformational changes of 2-(methylamino)-pyrimidines upon intermolecular binding.

Rational magnetic modification of N,N-dioxidized pyrazine ring expanded adenine and thymine: a diradical character induced by base pairing and double protonation

Rational modification of biomolecules especially DNA base pairs for the theoretical design of molecular magnets has attracted extensive interest. In this work, we report a modification strategy for adenine/thymine-based magnets through introducing a N,N-dioxidized pyrazine ring to either adenine or thymine to form ring-expanded bases (noA/noT) based on their experimentally synthesized derivatives. Further functionalization is conducted by double protonation and pairing with a normal complementary base (nohA-T/nohT-A), respectively. The diversity of protonation sites in noA generates totally six nohA-Ts, together with nohT-A forming seven two-step modified topic base pairs. DFT calculations are performed to characterize the magnetic properties and the diradical character, which indicate three diamagnetic (DM) nohA-Ts and three antiferromagnetic (AFM) nohA-Ts with extremely large magnetic coupling constants J ranging from -1279.7 to -2807.4 cm-1, while a relatively mild AFM nohT-A with a J of -194.6 cm-1. The electron separation effect induced by attraction of positive charges originating from protonation is proposed to explain the diradicalization, which is different from the traditional radical-coupler-radical coupling mode. In addition, atomic natural charges and spin densities, and H-bond and molecular orbital analyses are further discussed for verification and deep understanding of the observed unique phenomena. It should be noted that our designed seven topic base pairs have excellent characters including a good synthetic basis, a large scope of the |J| values, and the AFM-DM magnetic conversion or AFM strength modulation controlled by protonation/deprotonation, prototropic tautomerization, base pairing/dissociation, single proton transfer, and even the applied electric field. All these indicate the promising applications in the field of magnetic information storage or switch control. This work highlights the magnetic modification schemes and possible modulation methods of double positive charge doped DNA base pairs by utilizing their potential spin coupling modes.

All-optical switching in dye-doped DNA nanofibers

All-optical switches are introduced which are based on deoxyribonucleic acid (DNA) in the form of electrospun fibers, where DNA is semi-intercalated with a push-pull, luminescent nonlinear pyrazoline derivative. Optical birefringence is found in the organic nanofibers, with fully reversible switching controlled through continuous-wave laser irradiation. The photoinduced signal is remarkably large, with birefringence highlighted by optically-driven refractive index anisotropy approaching 0.001. Sub-millisecond characteristic switching times are found. Integrating dye-intercalated DNA complex systems in organic nanofibers, as a convenient and efficient approach to template molecular organization and control it by external stimuli, might open new routes for realizing optical logic gates, reconfigurable photonic networks and sensors through physically-transient biopolymer components.

Recent development in biodegradable nanovehicle delivery system-assisted immunotherapy

A schematic illustration of BNDS biodegradation and release antigen delivery for assisting immunotherapy.

Synthesis of Polylysine/Silica Hybrids through Branched-Polylysine-Mediated Biosilicification

Although many biosilicification methods based on cationic linear α-poly -l- lysine for synthesis of polylysine/silica hybrids have been investigated, these methods tend to rely on the counteranions, added catalysts, and complex synthesis process. To explore a simple and efficient biosilicification method, in this work, branched poly-l-lysine (BPL) is used as both a catalyst to hydrolyze tetraethoxysilane (TEOS) and an in situ template to direct silicic acids forming polylysine/silica hybrids in one-pot mode. The catalysis of BPL to hydrolyze TEOS results from the abundant hydrogen bonding (as the active site) to increase the nucleophilicity of BPL. Meanwhile, the hydrogen bonding is also found to be the key factor determining the self-assembly of BPL. During biosilicification, owing to self-assembly of BPL molecules, BPL would form spherical particles by keeping a random-coil conformation or form lamellar structures by undergoing a conformational transition from a random-coil to β-sheet construction. As a result, polylysine/silica hybrids with tunable topological structures are synthesized using aggregated BPLs as templates after the hydrolysis of TEOS. This finding of applying BPL to fulfill the biosilicification procedure without counteranions and added catalysts would enable a better understanding of the polypeptide-governed biosilicification process and pave a way for fabricating complex inorganic architectures applicable to silica transformational chemistry.

Kinetics of Reversible Protonation of Transient Neutral Guanine Radical in Neutral Aqueous Solution

Time-resolved chemically induced dynamic nuclear polarization (TR-CIDNP) is applied to follow transformation of the short-lived neutral guanine radical into a secondary guanine radical by its protonation, presumably at position N7. In the initial step the photoreaction of guanosine-5'-monophosphate (GMP) with triplet excited 3,3',4,4'-tetracarboxy benzophenone (TCBP) leads to formation of the neutral radical G(-H)^. . The evidence of the radical conversion is based on the inversion of CIDNP sign for TCBP and GMP protons on the microsecond timescale as a result of the change in magnetic resonance parameters in the pairs of TCBP and GMP radicals due to structural changes of the GMP radical. Acceleration of the CIDNP sign change upon addition of phosphate (proton donor) confirms that the radical transformation responsible for the observed CIDNP kinetics is protonation of the neutral guanine radical with formation of the newly characterized cation radical, (G^.+ )'. From the full analysis of the pH-dependent CIDNP kinetics, the protonation and deprotonation behaviour is quantitatively characterized, giving pK_a =8.0±0.2 of the cation radical (G^.+ )'.

Coating ZnO nanoparticle films with DNA nanolayers for enhancing the electron extracting properties and performance of polymer solar cells

Here we present for the first time polymer solar cells that incorporate biological material that show state of the art efficiencies in excess of 8%. The performance of inverted polymer solar cells was improved significantly after deposition of ZnO nanoparticles (ZnO-NPs) together with a thin deoxyribonucleic acid nanolayer and used as an electron extraction layer (EEL). The ZnO-NPs/DNA double layer improved the rectifying ratio, shunt resistance of the cells as well as lowering the work function of the electron-collecting contact. Importantly, the ZnO-NPs/DNA bilayer enhanced the power conversion efficiency of cells considerably compared to cells with EELs made of only DNA (improvement of 56% in relative terms) or only ZnO-NPs (improvement of 19% in relative terms) reaching a best power conversion efficiency of 8.5%. The ZnO-NPs/DNA double layer cells also outperformed ones made with one of the most efficient previous synthetic composite EELs (i.e. ZnO/PEIE(poly(ethyleneimine)-ethoxylated)). Since all fabrication procedures were carried out at low (<150 °C) or room temperature, we have applied the findings to flexible substrates as well as on glass obtaining a high PCE of 7.2%. The solar cells with the biological/metal-oxide composite EELs also delivered an improvement in the stability (∼20% in relative term) compared to that with ZnO-NPs only. All these findings show that natural materials, in this case DNA, the premium biological material, can be incorporated in organic semiconductor devices in tandem with inorganic devices delivering uncompromising levels of performance as well as significant improvements.

Excitation-dependent fluorescence from atomic/molecular layer deposited sodium-uracil thin films

Atomic/molecular layer deposition (ALD/MLD) offers unique possibilities in the fabrication of inorganic-organic thin films with novel functionalities. Especially, incorporating nucleobases in the thin-film structures could open new avenues in the development of bio-electronic and photonic devices. Here we report an intense blue and widely excitation-dependent fluorescence in the visible region for ALD/MLD fabricated sodium-uracil thin films, where the crystalline network is formed from hydrogen-bonded uracil molecules linked via Na atoms. The excitation-dependent fluorescence is caused by the red-edge excitation shift (REES) effect taking place in the red-edge of the absorption spectrum, where the spectral relaxation occurs in continuous manner as demonstrated by the time-resolved measurements.

Non-ionising UV light increases the optical density of hygroscopic self assembled DNA crystal films

We report on ultraviolet (UV) light induced increases in the UV optical density of thin and optically transparent crystalline DNA films formed through self assembly. The films are comprised of closely packed, multi-faceted and sub micron sized crystals. UV-Vis spectrophotometry reveals that DNA films with surface densities up to 0.031 mg/mm2 can reduce the transmittance of incident UVC and UVB light by up to 90%, and UVA transmittance by up to 20%. Subsequent and independent film irradiation with either UVA or UVB dosages upwards of 80 J/cm2 both reduce UV transmittance, with reductions scaling monotonically with UV dosage. To date the induction of a hyperchromic effect has been demonstrated using heat, pH, high salt mediums, and high energy ionising radiation. Both hyperchromicity and increased light scattering could account for the increased film optical density after UV irradiation. Additional characterisation of the films reveal they are highly absorbent and hygroscopic. When coated on human skin, they are capable of slowing water evaporation and keeping the tissue hydrated for extended periods of time.

Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.

Ultrafast nonlinear optical properties of thin-solid DNA film and their application as a saturable absorber in femtosecond mode-locked fiber laser

A new extraordinary application of deoxyribonucleic acid (DNA) thin-solid-film was experimentally explored in the field of ultrafast nonlinear photonics. Optical transmission was investigated in both linear and nonlinear regimes for two types of DNA thin-solid-films made from DNA in aqueous solution and DNA-cetyltrimethylammonium chloride (CTMA) in an organic solvent. Z-scan measurements revealed a high third-order nonlinearity with n₂ exceeding 10⁻⁹ at a wavelength of 1570 nm, for a nonlinarity about five orders of magnitude larger than that of silica. We also demonstrated ultrafast saturable absorption (SA) with a modulation depth of 0.43%. DNA thin solid films were successfully deposited on a side-polished optical fiber, providing an efficient evanescent wave interaction. We built an organic-inorganic hybrid all-fiber ring laser using DNA film as an ultrafast SA and using Erbium-doped fiber as an efficient optical gain medium. Stable transform-limited femtosecond soliton pulses were generated with full width half maxima of 417 fs for DNA and 323 fs for DNA-CTMA thin-solid-film SAs. The average output power was 4.20 mW for DNA and 5.46 mW for DNA-CTMA. Detailed conditions for DNA solid film preparation, dispersion control in the laser cavity and subsequent characteristics of soliton pulses are discussed, to confirm unique nonlinear optical applications of DNA thin-solid-film.

Diverse gatekeepers for mesoporous silica nanoparticle based drug delivery systems

Progress on the design of diverse gatekeepers for mesoporous silica nanoparticle based drug delivery systems is summarized.

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.

Conformational and phase transitions in DNA--photosensitive surfactant solutions: Experiment and modeling

DNA binding to trans- and cis-isomers of azobenzene containing cationic surfactant in 5 mM NaCl solution was investigated by the methods of dynamic light scattering (DLS), low-gradient viscometry (LGV), atomic force microscopy (AFM), circular dichroism (CD), gel electrophoresis (GE), flow birefringence (FB), UV-Vis spectrophotometry. Light-responsive conformational transitions of DNA in complex with photosensitive surfactant, changes in DNA optical anisotropy and persistent length, phase transition of DNA into nanoparticles induced by high surfactant concentration, as well as transformation of surfactant conformation under its binding to macromolecule were studied. Computer simulations of micelles formation for cis- and trans-isomers of azobenzene containing surfactant, as well as DNA-surfactant interaction, were carried out. Phase diagram for DNA-surfactant solutions was designed. The possibility to reverse the DNA packaging induced by surfactant binding with the dilution and light irradiation was shown.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

DNA bases ring-expanded with a cyclopentadiene free radical: a theoretical investigation of building blocks with diradical character

In this work, we computationally design radical nucleobases which possess improved electronic properties, especially diradical properties through introducing a cyclopentadiene radical. We predict that the detailed electromagnetic features of base assemblies are based on the orientation of the extra five-membered cyclopentadiene ring. Broken symmetry DFT calculations take into account the relevant structures and properties. Our results reveal that both the radicalized DNA bases and the base pairs formed when they combine with their counterparts remain stable and display larger spin delocalization. The mode of embedding the cyclopentadiene free radical in the structures has some influence on the degree of π-conjugation, which results in various diradical characteristics. Single-layered radical base pairs all have an open-shell singlet ground state, but the energy difference between singlet and triplet is not significant. For two-layered radical base pairs, the situation is more complex. All of them have an open-shell state as their ground state, including an open-shell singlet state and an open-shell triplet state. That is, the majority of radical base pairs possess anti-ferromagnetic or ferromagnetic characteristics. We present here a more in-depth discussion and analyses to study the magnetic characteristics of radical bases and base pairs. As an important factor, two-layered radical base pairs also have been carefully analyzed. We hope that all the measurements and results presented here will stimulate further detailed insights into the related mechanisms in modified DNA bases and the design of better ring-expanded DNA magnetic materials.

Sustainable Life Cycles of Natural-Precursor-Derived Nanocarbons

Sustainable societal and economic development relies on novel nanotechnologies that offer maximum efficiency at minimal environmental cost. Yet, it is very challenging to apply green chemistry approaches across the entire life cycle of nanotech products, from design and nanomaterial synthesis to utilization and disposal. Recently, novel, efficient methods based on nonequilibrium reactive plasma chemistries that minimize the process steps and dramatically reduce the use of expensive and hazardous reagents have been applied to low-cost natural and waste sources to produce value-added nanomaterials with a wide range of applications. This review discusses the distinctive effects of nonequilibrium reactive chemistries and how these effects can aid and advance the integration of sustainable chemistry into each stage of nanotech product life. Examples of the use of enabling plasma-based technologies in sustainable production and degradation of nanotech products are discussed-from selection of precursors derived from natural resources and their conversion into functional building units, to methods for green synthesis of useful naturally degradable carbon-based nanomaterials, to device operation and eventual disintegration into naturally degradable yet potentially reusable byproducts.

Exploring the Potential of Nucleic Acid Bases in Organic Light Emitting Diodes

Naturally occurring biomolecules have increasingly found applications in organic electronics as a low cost, performance-enhancing, environmentally safe alternative. Previous devices, which incorporated DNA in organic light emitting diodes (OLEDs), resulted in significant improvements in performance. In this work, nucleobases (NBs), constituents of DNA and RNA polymers, are investigated for integration into OLEDs. NB small molecules form excellent thin films by low-temperature evaporation, enabling seamless integration into vacuum deposited OLED fabrication. Thin film properties of adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) are investigated. Next, their incorporation as electron-blocking (EBL) and hole-blocking layers (HBL) in phosphorescent OLEDs is explored. NBs affect OLED performance through charge transport control, following their electron affinity trend: G < A < C < T < U. G and A have lower electron affinity (1.8-2.2 eV), blocking electrons but allowing hole transport. C, T, and U have higher electron affinities (2.6-3.0 eV), transporting electrons and blocking hole transport. A-EBL-based OLEDs achieve current and external quantum efficiencies of 52 cd A(-1) and 14.3%, a ca. 50% performance increase over the baseline device with conventional EBL. The combination of enhanced performance, wide diversity of material properties, simplicity of use, and reduced cost indicate the promise of nucleobases for future OLED development.

Hierarchical-Multiplex DNA Patterns Mediated by Polymer Brush Nanocone Arrays That Possess Potential Application for Specific DNA Sensing

This paper provides a facile and cost-efficient method to prepare single-strand DNA (ssDNA) nanocone arrays and hierarchical DNA patterns that were mediated by poly(2-hydroxyethyl methacrylate) (PHEMA) brush. The PHEMA brush nanocone arrays with different morphology and period were fabricated via colloidal lithography. The hierarchical structure was prepared through the combination of colloidal lithography and traditional photolithography. The DNA patterns were easily achieved via grafting the amino group modified ssDNA onto the side chain of polymer brush, and the anchored DNA maintained their reactivity. The as-prepared ssDNA nanocone arrays can be applied for target DNA sensing with the detection limit reaching 1.65 nM. Besides, with the help of introducing microfluidic ideology, the hierarchical-multiplex DNA patterns on the same substrate could be easily achieved with each kind of pattern possessing one kind of ssDNA, which are promising surfaces for the preparation of rapid, visible, and multiplex DNA sensors.

Nitroarene reduction: a trusted model reaction to test nanoparticle catalysts

Nitrophenol reduction to aminophenol with a reducing agent is conveniently carried out in aqueous medium mainly with a metal or metal oxide catalyst. This reduction is presently considered as a benchmark reaction to test a catalyst nanoparticle. Thousands of original reports have enriched this field of nanoparticle catalyzed reaction. Synthesis of different metal and metal oxide nanoparticles and their composites along with their role as catalysts for nitrophenol reduction with varying reducing agents have been elucidated here. The progress of the reaction is conveniently monitored by UV-visible spectrophotometry and hence it becomes a universally accepted model reaction. In this review we have discussed the reaction kinetics considering its elegance and importance enlightening the long known Langmuir-Hinshelwood mechanism and Eley-Rideal mechanism at length, along with a few other mechanisms recently reported. A brief description of the synthetic procedures of various nanoparticles and their respective catalytic behaviour towards nitroarene reduction has also been accounted here.