Chaperone‐Polymer‐Assisted,Photodriven DNA Strand Displacement

Photodriven DNA strand displacement by using a 2′,6′‐dimethylazobenzene‐tethered strand and poly(l ‐lysine)‐graft‐dextran (PLL‐g‐Dex) as a chaperone is reported. Rapid strand displacement was reversibly induced by UV and visible‐light irradiation without any toehold portion. To further improve the method, the concentration of PLL‐g‐Dex and the number of equivalents of the photoresponsive strand were optimised. Optimally, 64 % strand displacement was reversibly induced by alternating UV and visible‐light irradiation.     

Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo-crosslinking

DNA strand displacement is an essential reaction in genetic recombination, biological processes, and DNA nanotechnology. In particular, various DNA nanodevices enable complicated calculations. However, it takes time before the output is obtained, so acceleration of DNA strand displacement is required for a rapid-response DNA nanodevice. Herein, DNA strand displacement by using DNA photo-crosslinking to accelerate this displacement is evaluated. The DNA photo-crosslinking of 3-cyanovinylcarbazole (^CNVK) was accelerated at least 20 times, showing a faster DNA strand displacement. The rate of photo-crosslinking is a key factor and the rate of DNA strand displacement is accelerated through ultrafast photo-crosslinking. The rate of DNA strand displacement was regulated by photoirradiation energy.     

Integrating Ligands into Nucleic Acid Systems

Signal transduction from non-nucleic acid ligands (small molecules and proteins) to structural changes of nucleic acids plays a crucial role in both biomedical analysis and cellular regulations. However, how to bridge between these two types of molecules without compromising the expandable complexity and programmability of the nucleic acid nanomachines is a critical challenge. Compared with the previously most widely applied transduction strategies, we review the latest advances of a kinetically controlled approach for ligand-oligonucleotide transduction in this Concept article. This new design works through an intrinsic conformational alteration of the nucleic acid aptamer upon the ligand binding as a governing factor for nucleic acid strand displacement reactions. The functionalities and applications of this transduction system as a ligand converter on biosensing and DNA computation are described and discussed. Furthermore, we propose some potential scenarios for utilization of this ligand transduction design to regulate gene expression through synthetic RNA switches in the cellular contexts. Finally, future perspectives regarding this ligand-oligonucleotide transduction platform are also discussed.     

Crosslinking structures of gelatin hydrogels crosslinked with genipin or a water‐soluble carbodiimide

It was suggested in our previous studies that carbodiimide‐ and genipin‐crosslinked gelatin hydrogels could be used as bioadhesives to overcome the cytotoxicity problem associated with formaldehyde‐crosslinked gelatin hydrogels. In this study, we investigated the crosslinking structures of carbodiimide‐ and genipin‐crosslinked gelatin hydrogels. We found that crosslinking gelatin hydrogels with carbodiimide or genipin could produce distinct crosslinking structures because of the differences in their crosslinking types. Carbodiimide could form intramolecular crosslinks within a gelatin molecule or short‐range intermolecular crosslinks between two adjacent gelatin molecules. On the basis of gel permeation chromatography, we found that the polymerization of genipin molecules could occur under the conditions used in crosslinking gelatin hydrogels via a possible aldol condensation. Therefore, besides intramolecular and short‐range intermolecular crosslinks, additional long‐range intermolecular crosslinks could be introduced into genipin‐crosslinked gelatin hydrogels. Crosslinking a gelatin hydrogel with carbodiimide was more rapid than crosslinking with genipin. Therefore, the gelation time for the carbodiimide‐crosslinked gelatin hydrogels was significantly shorter than that of the genipin‐crosslinked gelatin hydrogels. However, the cohesive (interconnected) structure of the carbodiimide‐crosslinked gelatin hydrogels was readily broken because, unlike the genipin‐crosslinked gelatin hydrogels, there were simply intramolecular and short‐range intermolecular crosslinks present in the carbodiimide‐crosslinked hydrogel. In the cytotoxicity study, the carbodiimide‐crosslinked gelatin hydrogels were dissolved into small fragments in the cultural medium within 10 min. In contrast, the genipin‐crosslinked gelatin hydrogels remained intact in the medium throughout the entire course of the study. Again, this may be attributed to the differences in their crosslinking structures. The genipin‐crosslinked gelatin hydrogels were less cytotoxic than the carbodiimide‐crosslinked gelatin hydrogels. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 91: 4017–4026, 2004     

Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

The complex physical and chemical reactions between the large number of low-energy (0–30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.     

Slowing and controlling the translocation of DNA in a solid-state nanopore

DNA sequencing methods based on nanopores could potentially represent a low-cost and high-throughput pathway to practical genomics, by replacing current sequencing methods based on synthesis that are limited in speed and cost. The success of nanopore sequencing techniques requires the solution to two fundamental problems: (1) sensing each nucleotide of a DNA strand, in sequence, as it passes through a nanopore; (2) delivering each nucleotide in a DNA strand, in turn, to a sensing site within the nanopore in a controlled manner. It has been demonstrated that a DNA nucleotide can be sensed using electric signals, such as ionic current changes caused by nucleotide blockage at a constriction region in a protein pore or a tunneling current through the nucleotide-bridged gap of two nanoelectrodes built near a solid-state nanopore. However, it is not yet clear how each nucleotide in a DNA strand can be delivered in turn to a sensing site and held there for a sufficient time to ensure high fidelity sensing. This latter problem has been addressed by modifying macroscopic properties, such as a solvent viscosity, ion concentration or temperature. Also, the DNA transistor, a solid state nanopore dressed with a series of metal-dielectric layers has been proposed as a solution. Molecular dynamics simulations provide the means to study and to understand DNA transport in nanopores microscopically. In this article, we review computational studies on how to slow down and control the DNA translocation through a solid-state nanopore.     

Sequence‐Specific DNA Photosplitting of Crosslinked DNAs Containing the 3‐Cyanovinylcarbazole Nucleoside by Using DNA Strand Displacement

An oligodeoxynucleotide (ODN) containing the ultrafast reversible 3‐cyanovinylcarbazole (^CNVK) photo‐crosslinker was photo‐crosslinked to a complementary strand upon exposure to 366 nm irradiation and photosplit by use of 312 nm irradiation. In this paper we report that the photoreaction of ^CNVK on irradiation at 366 nm involves a photostationary state and that its reaction can be controlled by temperature. Guided by this new insight, we proposed and have now demonstrated previously unknown photosplitting of ^CNVK aided by DNA strand displacement as an alternative to heating. The photo‐crosslinked double‐stranded DNA (dsDNA) underwent >80 % photosplitting aided by DNA strand displacement on irradiation at 366 nm without heating. In this photosplitting based on DNA strand displacement, the relative thermal stability of the invader strand with respect to the template strands plays an important role, and an invader strand/template strand system that is more stable than the passenger strand/template strand system induces photosplitting without heating. This new strand‐displacement‐aided photosplitting occurred in a sequence‐specific manner through irradiation at 366 nm in the presence of an invader strand.     

A novel pH‐sensitive gelatin–DNA semi‐interpenetrating polymer network hydrogel

Gelatin and DNA were mixed together in various ratios followed by the addition of glutaraldehyde as a cross‐linker. FT‐IR spectroscopy confirmed the formation of a semi‐interpenetrating polymer network (semi‐IPN) between the gelatin and DNA. The gelatin–DNA semi‐IPN hydrogel underwent, reversibly, remarkable changes in swelling degree in response to the variation of pH. In the low‐pH range, the hydrogel showed a lower swelling degree; with an increment in pH, the hydrogel was highly swollen, which is considered to originate from the complexation and de‐complexation between gelatin and DNA, as was verified by turbidity measurements. Higher contents of DNA result in an increase in the swelling degree, which is presumably due to the easy outward expansion of free DNA moieties. The permeability coefficient, P, for a model molecule, cimetidine, through the semi‐IPN hydrogel membranes was determined in pH 1.0 and pH 12.0 buffer solutions. The results show that the permeation of cimetidine is responsive to pH change, and an evident variation in the P values occurs in response to the pH of the media. Copyright © 2004 Society of Chemical Industry     

Shape memorizing properties of a hydrogel of poly(vinyl alcohol)

Hydrogel prepared by repetitive freezing and thawing of poly(vinyl alcohol) aqueous solution was chemically crosslinked with glutaraldehyde. The chemically crosslinked hydrogel hardly changed its physical appearance, and showed good elasticity and strength as original gel. However, after treating in boiling water, it swelled a little, depending on the condition of the chemical treatment. The melted gel thus obtained showed shape memorizing property, that is, it could firmly hold nearly 200% of strain, keeping its original high elasticity. The strain could be released very quickly (< 1 s) in boiling water, and the gel was suggested to be applied to a new type of gel actuator. X-ray diffraction study revealed that the melted gel does not necessarily reform the physical crosslinks in exactly the same manner as the original gel in the process of shape restoring, but the distribution of the physical crosslinks can be restored as they were. It was suggested that the chemical crosslinks which remember the distribution of the physical crosslinks plays a critical roll in the shape restoring process.     

Sequence-Independent Logical Regulation of the Assembly and Disassembly of DNA Polyhedra

Controlling the self-assembly of DNA nanostructures using rationally designed logic gates is a major goal of dynamic DNA nanotechnology, which could facilitate the development of biomedicine, molecular computation, et al. In previous works, the regulations mostly relied on either toehold-mediated strand displacement or stimuli-driven conformational switch, requiring elaborately-designed or specific DNA sequences. Herein, we reported a facile, base-sequence-independent strategy for logically controlling DNA self-assembly through external molecules. The INHIBIT and XOR logic controls over the assembly/disassembly of DNA polyhedra were realized through cystamine ( Cyst ) and ethylenediamine ( EN ) respectively, which were further integrated into a half subtractor circuit thanks to the sharing of the same inputs. Our work provides a sequence-independent strategy in logically controlling DNA self-assembly, which may open up new possibilities for dynamic DNA nanotechnology.     

Formation of the first injectable poly(vinyl alcohol) hydrogel by mixing of functional PVA precursors

In this study we describe the development of an injectable, in situ chemical hydrogel forming system. The gelation occurs under neutral pH and at room temperature immediately upon mixing of the two aqueous poly (vinyl alcohol) components specifically derivatized through carbamate linkages with aldehyde (PVA‐AL) and hydrazide (PVA‐HY) functional groups, respectively. Aldehyde and hydrazide pendant groups were incorporated with a low degree of substitution (DS) into the PVA backbone to keep PVA structural homogeneity minimally altered. As a result, the hydrazone crosslinks are formed rapidly between aldehyde and hydrazide pendant groups when the correspondingly modified PVA components are brought in contact as water solutions. To assess in situ hydrazone crosslinks formation for in vitro cytocompatibility, murine neuroblastoma N2a cells were suspended in cell culture medium with the dissolved PVA‐HY prior to addition to the PVA‐AL aqueous solution. Thus, the cells were chemically encapsulated in a polymer network that was formed by mixing of the corresponding aqueous solutions of PVA functional precursors. Biochemical analysis revealed that cells survived chemical crosslinking and remained viable in the hydrogel for 4 days of culture. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007     

Synthesis and characterization of polysaccharide hydrogel based on hydrophobic interactions

Hydrogels based on hydrophobic, or micellar interactions, are physically crosslinked hydrogels which are an attempt to overcome the poor mechanical properties of traditional, chemically crosslinked gels, such as low shear strength. We have prepared a polysaccharide-based hydrogel with physical crosslinks via hydrophobic interactions. In this work, we have synthesized hydrogel by grafting a hydrophobic moiety dioctylamine onto hydrophilic precursor carboxymethyl cellulose (CMC) through an amide bond formation, where ~33% of the carboxyl group in CMC was reacted with dioctylamine. The thermosensitive hydrogel can arrest 100 mL of deionized water per gram of gelator within few seconds. It showed the moderate rheological property. The hydrogel is nontoxic and does not show any adverse to human hemoglobin. It is a CMC based a unique gelator with high biocompatibility represent to be useful materials for biomedical application. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019 , 136, 47665.     

Introduction of molecular spacers between the crosslinks of a cellulose‐based superabsorbent hydrogel: Effects on the equilibrium sorption properties

The possibility to modulate cellulose‐based hydrogel sorption properties through the insertion of molecular spacers between the crosslinks was investigated. Starting polymers were the sodium salt of carboxymethyl cellulose, a polyelectrolyte cellulose derivative, and hydroxyethyl cellulose, a nonpolyelectrolyte derivative. Poly(ethylene glycol) with various molecular weights was linked by its free ends at two divinyl sulfone (DVS) crosslinker molecules, to increase the average distance between two crosslinking sites and thus to act as a spacer. Both the effect of the concentration and the molecular weight of the spacer on the hydrogel final sorption properties in water and water solutions were investigated. The presence of the spacer allowed us also to perform hydrogel synthesis with higher concentrations of cellulose in the reactive mixture, and the effect of the polymer concentration in the batch was analyzed. Hydrogels obtained in the presence of spacers displayed significantly higher equilibrium sorption properties than those of the ones obtained without spacers. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 168–174, 2003     

A Dual‐Crosslinked Strategy to Construct Physical Hydrogels with High Strength,Toughness, Good Mechanical Recoverability,and Shape‐Memory Ability

A novel type of physical hydrogel based on dual‐crosslinked strategy is successfully synthesized by micellar copolymerization of stearyl methacrylate, acrylamide, and acrylic acid, and subsequent introduction of Fe³⁺. Strong hydrophobic associations among poly(stearyl methacrylate) blocks form the first crosslinking point and ionic coordination bonds between carboxyl groups and Fe³⁺ serve as the second crosslinking point. The mechanical properties of the hydrogel can be tuned in a wide range by controlling the densities of two crosslinks. The optimal hydrogel shows excellent mechanical properties (tensile strength of ≈6.8 MPa, elastic modulus of ≈8.0 MPa, elongation of ≈1000%, toughness of 53 MJ m^?3) and good self‐recovery property. Furthermore, owing to stimuli responsiveness of physical interaction, this hydrogel also shows a triple shape memory effect. The combination of two different physical interactions in a single network provides a general strategy for designing of high‐strength hydrogels with functionalities.     

Mechanism of Sensitization to UV Radiation by 5-Br-Uracil Substituted DNA

DNA, in which thymine is substituted by 5-bromouracil is sensitized to the effect of ultraviolet light. Various chemical changes produced in the DNA are described. These include single and double strand breaks, base loss, protein DNA crosslinks as well as the influence of the three dimensional structure of DNA on some of these changes.     

Chelidamic acid functionalized stimuli-responsive hydrogel supported-palladium catalyst for copper-free Sonogashira reaction in aqueous media

A thermo and pH-responsive hydrogel (PNIPAM-co-PPAP) was synthesized via free radical polymerization of N-isopropylacrylamide (NIPAM) and potassium 4-(acryloyloxy) pyridine-2, 6-dicarboxylate (PAP) in mixed solvents of water and tetrahydrofuran. SEM micrographs revealed that the hydrogel was macroporous and the pores within the matrixes were interconnected. The chelidamic acid functionalized PNIPAM-co-PPAP hydrogel exhibited excellent capacity to anchor palladium (II) and the resulting material showed well catalytic activity for copper-free Sonogashira reaction of aryl halides with phenylacetylene in aqueous media. The reactions proceeded well with 0.1 mol% of Pd (II) catalyst, due to the good dispersion of Pd²⁺ in the macroporous structure as well as the enrichment of reactants within hydrogel under reaction conditions. Through the reversibly swelling/deswelling, the PNIPAM-co-PPAP hydrogel-immobilized Pd (II) catalyst could be easily recovered by simple method. Furthermore, the PNIPAM-co-PPAP /Pd catalyst exhibited good recyclability and could be recycled six times without remarkable loss in catalytic activity.     

Stimuli-Responsive and Reversible Nanoassemblies of G-Triplexes

G-triplex (G3) structures formed with three consecutive G-tracts have recently been identified as a new emerging guanine-rich DNA fold. There could likely be a wide range of biological functions for G3s as occurring for G-quadruplex (G4) structures formed with four consecutive G-tracts. However, in comparison to the many reports on G4 nanoassemblies that organize monomers together in a controllable manner, G3-favored nanoassemblies have yet to be explored. In this work, we found that a natural alkaloid of sanguinarine can serve as a dynamic ligand glue to reversibly switch the dimeric nanoassemblies of the thrombin binding aptamer G3 (TBA-G3). The glue planarity was considered to be a crucial factor for realizing this switching. More importantly, external stimuli including pH, sulfite, O₂ and H₂O₂ can be employed as common regulators to easily modulate the glue's adhesivity for constructing and destructing the G3 nanoassemblies as a result of the ligand converting between isoforms. However, this assembly behavior does not occur with the counterpart TBA-G4. Our work demonstrates that higher-order G3 nanoassemblies can be reversibly operated by manipulating ligand adhesivity. This provides an alternative understanding of the unique behavior of guanine-rich sequences and focuses attention on the G3 fold since the nanoassembly event investigated herein might occur in living cells.     

Time dependence of material properties of polyethylene glycol hydrogels chain extended with short hydroxy acid segments

The objective of this work was to investigate the effect of chemical composition and segment number (n) on gelation, stiffness, and degradation of hydroxy acid-chain-extended star polyethylene glycol acrylate (SPEXA) gels. The hydroxy acids included glycolide (G), L-lactide (L), p-dioxanone (D) and ?-caprolactone (C). Chain-extension generated water soluble macromers with faster gelation rates, lower sol fractions, higher compressive moduli, and a wide-ranging degradation times when crosslinked into a hydrogel. SPEGA gels with the highest fraction of inter-molecular crosslinks had the most increase in compressive modulus with n whereas SPELA and SPECA had the lowest increase in modulus. SPEXA gels exhibited a wide range of degradation times from a few days for SPEGA to a few weeks for SPELA, a few months for SPEDA, and many months for SPECA. Marrow stromal cells and endothelial progenitor cells had the highest expression of vasculogenic markers when co-encapsulated in the faster degrading SPELA gel.     

A Review: Tailor-made Hydrogel Structures (Classifications and Synthesis Parameters)

Hydrogels are being prepared for use in a wide variety of applications ranging from medicines, tissue engineering, superabsorbents, controlled release of drugs & fertilizers, and oil absorbers etc. This review highlights hydrogel structure and their different classifications under various heads. It also discusses various routes to obtain tailormade hydrogels by polymerizing a combination of two or more monomers with proper type of crosslinks in order to obtain desired properties in the resulting hydrogel. Novel hydrogel configurations like microgels and nanogels, slide ring gels, double network hydrogels and nanocomposite gels have also been reviewed.     

Hydrophobic interaction-mediated reversible adsorption–desorption of nanoparticles in the honeycomb-patterned thermoresponsive poly(N-isopropylamide) hydrogel surface

Hydrophobic interaction-mediated reversible adsorption–desorption of Ag nanoparticles in water solutions was studied in surface-tailored poly(N-isopropylacrylamide) (PNIPAAm) hydrogel film. Surface-tailoring of PNIPAAm hydrogel was performed by the preparation of the hydrogel as a honeycomb-patterned film using a honeycomb-patterned PS film as a template. The surface morphology and hydrophobic interaction of the patterned hydrogel surface were significantly altered by temperature change of the aqueous solution that came in contact with the gel. The surface of the hydrogel became hydrophobic for adsorption at a higher temperature than the lower critical solution temperature of 32 °C, but became hydrophilic with decreased adsorptivity at lower temperature condition. Adsorptivity was obtained through measuring the concentration of the silver nanoparticles using UV–vis spectroscopy in an aqueous solution. A reversible adsorption–desorption of nanoparticles dependent on the temperature in the hydrogel surface obtained in this study clearly suggested that the hydrophobic interaction was reversibly changed in the patterned temperature-responsive hydrogel surface, similar to various biological systems in nature.