2D-3D-Convertible, pH-Responsive Lipid Nanosheets.

2D nanosheets self-assembled with amphiphilic molecules are promising tools for biomedical applications; yet, there are challenges to form and stabilize these nanosheets under complex physiological conditions. Here, the development of lipid nanosheets with high structural stability that can be reversibly converted to cell-sized vesicles by changes in pH within the physiological range robustly, are described. The system is controlled by the membrane disruptive peptide E5 and a cationic copolymer anchored on lipid membranes. It is envisioned that nanosheets formed using the dual anchoring peptide/cationic copolymer system can be employed in dynamic lipidic nanodevices, such as the vesosomes described here, drug delivery systems, and artificial cells.

A Cationic Copolymer Enhances Responsiveness and Robustness of DNA Circuits.

Toehold-mediated DNA circuits are extensively employed to construct diverse DNA nanodevices and signal amplifiers. However, operations of these circuits are slow and highly susceptive to molecular noise such as the interference from bystander DNA strands. Herein, this work investigates the effects of a series of cationic copolymers on DNA catalytic hairpin assembly, a representative toehold-mediated DNA circuit. One copolymer, poly(L -lysine)-graft-dextran, significantly enhances the reaction rate by 30-fold due to its electrostatic interaction with DNA. Moreover, the copolymer considerably alleviates the circuit's dependency on the length and GC content of toehold, thereby enhancing the robustness of circuit operation against molecular noise. The general effectiveness of poly(L -lysine)-graft-dextran is demonstrated through kinetic characterization of a DNA AND logic circuit. Therefore, use of a cationic copolymer is a versatile and efficient approach to enhance the operation rate and robustness of toehold-mediated DNA circuits, paving the way for more flexible design and broader application.

Smart Protein Refolding System Based on UCST-Type Ureido Polymers.

We have reported that ureido polymers exhibit upper critical solution temperature (UCST)-type phase behavior in solution, which is the opposite of lower critical solution temperature (LCST)-type behavior. Furthermore, UCST-type ureido polymers undergo liquid-liquid phase separation (LLPS) upon cooling rather than the liquid-solid phase transition of the typical LCST-type polymers. In this study, ureido polymers with hydrophobic groups were prepared to evaluate the effects of cooling-induced LLPS of UCST-type polymers on refolding of proteins. When protein was heated with a ureido polymer functionalized with undecyl groups, aggregation of the protein was prevented. Subsequent cooling incubation resulted in the spontaneous release of the protein from the polymer. The released protein had enzymatic activity, suggesting that the protein refolded properly. Interestingly, efficient refolding was observed when the solution of the UCST-type ureido polymer and protein was incubated at around the phase separation temperature of the polymer, implying that cooling-induced LLPS of the polymer enhanced the release of the protein. Additionally, by centrifugation at 4 °C, the refolded protein was readily separated from the ureido polymers, which precipitated upon cooling.

Highly Ordered Polypeptide with UCST Phase Separation Behavior.

Manipulating phase separation structures of thermoresponsive polymers will enhance the usefulness of structure-controllable materials in fields such as drug delivery and tissue engineering. However, behaviors of upper critical solution temperature (UCST) have been less investigated so far, despite the importance of UCST. Here, we examined two citrulline-based polypeptides, poly(d-ornithine- co-d-citrulline) (PdOC) and poly(dl-ornithine- co-dl-citrulline) (PdlOC), to investigate how stereoregularity of the polypeptides influences UCST behavior, in addition to poly(l-ornithine- co-l-citrulline) (PlOC) previously studied. Homochiral PlOC and PdOC showed phase separation temperatures ( Tps) higher than that of racemic PdlOC. Moreover, PdlOC underwent liquid to coacervate phase separation at Tp, whereas PlOC and PdOC underwent liquid to solid-like aggregation transitions. From a structural point of view, circular dichroism and small-angle X-ray scattering measurements revealed that homochiral PlOC and PdOC polypeptides formed α-helical structures and assembled into a regular hexagonal lattice upon phase separation. Interactions between the pendent ureido groups of homochiral POCs appear to play pivotal roles in helical folding and assembly into the hexagonal structure. In addition, Tp change in response to biodegradation was confirmed for both PlOC and PdlOC. The biodegradability was considerably influenced by phase-separated structures. These findings of UCST-type POCs in this study would provide important insights into structure-controllable and thermoresponsive biomaterials.

Liposome-Surface-Initiated ARGET ATRP: Surface Softness Generated by "Grafting from" Polymerization.

Liposomes are self-assembled vesicles of amphiphilic lipid molecules, which have been investigated as models of cells, or tools for drug delivery systems. In these systems, the surface property of the liposomes plays an important role. In this study, we demonstrated a novel polymer modification of liposome surfaces using a controlled radical polymerization, "activators regenerated by electron transfer for atom transfer radical polymerization", in aqueous media without a deoxygenation step. Dynamic light scattering and 1H NMR measurement indicated the successful modification of the polymer on the liposome surface. The molecular weight of the grafted polymer chain was systematically controlled by changing the monomer concentrations in the "grafting from" polymerization. Moreover, the modification resulted in a notable increase in surface softness as indicated by electrophoretic behavior, which was comparable to the surface of cells. The preparation method and the characterization presented in this study would be a helpful guideline in designing the polymer/liposome hybrid having target surface properties.

Synthesis and Properties of Upper Critical Solution Temperature Responsive Nanogels.

A random copolymer ((U/A10)165) bearing pendent ureido groups and a small amount (10 mol %) of primary amino groups exhibits an upper critical solution temperature (UCST). We prepared a diblock copolymer (PMPC20P(U/A10)165) composed of water-soluble poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) and (U/A10)165 blocks via reversible addition-fragmentation chain-transfer radical polymerization with postmodification reaction. The subnumbers are the degrees of polymerization of each block. Although in water PMPC20P(U/A10)165 dissolves as a unimer above the UCST phase transition temperature ( Tp), it forms polymer micelles composed of dehydrated (U/A10)165 cores and hydrophilic PMPC shells. A nanogel was prepared by cross-linking the pendent primary amines in the micelle core using (hydroxymethyl)phosphonium chloride below Tp. NMR and light-scattering data indicated that the nanogel core shrinks upon dehydration below Tp and swells upon hydration above Tp. The nanogel can encapsulate guest molecules such as hydrophobic fluorescence probes and bovine serum albumin (BSA) below Tp mainly owing to hydrophobic interactions in the core. Encapsulated BSA can be held in the nanogel core below Tp and subsequently released above Tp.

Fluorescence Redox Blinking Adaptable to Structural Analysis of Nucleic Acids.

The phenomenon of blinking is unique to single-molecule fluorescence measurements. By designing a fluorophore with an appropriate dark-state lifetime τoff , a kinetic analysis based on the control of fluorescence blinking (KACB) was devised to investigate the dynamics of biomolecules. By controlling the redox-reaction-based blinking (rKACB), conformational dynamics of RNA at the single-molecule level was previously investigated. However, there is little knowledge about suitable fluorescent molecules for rKACB, and the application of rKACB has been limited to the analysis of hairpins and duplex structures of nucleic acids. In this work, various fluorescent molecules, including Alexa 488, R6G, TAMRA, ATTO 647N and ATTO 655, were evaluated for rKACB. Moreover, rKACB was adapted to the discrimination of DNA/DNA and DNA/RNA nucleic acid duplexes and investigation of antigen-antibody interactions. By changing the size of the oxidant, it was possible to determine the solvent accessibility of the target domain of the analyzed biomolecules.

A Thermoresponsive Cationic Comb-Type Copolymer Enhances Membrane Disruption Activity of an Amphiphilic Peptide.

Membrane active peptides (MAPs) have potential applications in drug delivery systems and as antimicrobials. We previously showed that a cationic comb-type copolymer, poly(allylamine)- graft-dextran (PAA- g-Dex), forms a soluble inter-polyelectrolyte complex with an anionic MAP, the E5 peptide, resulting in significant enhancement of the membrane disruption activity of E5. In this study, we designed a novel comb-type cationic copolymer composed of a PAA main chain and thermoresponsive poly( N-isopropylacrylamide) graft chains (PAA- g-PNIPAAm). We hypothesized that the thermoresponsive hydrophilic/hydrophobic transition of the grafted polymer would regulate the membrane disruption activity of E5 peptide. Both the binding affinity of the complex and the membrane disruption activity of E5/PAA- g-PNIPAAm were found to be enhanced above the phase transition temperature of the grafted chain. Our analysis suggests that the hydrophilic/hydrophobic environment around the cationic polymer chain plays important roles in the enhancement of the activity of the anionic peptide.

Rational Design of UCST-type Ureido Copolymers Based on a Hydrophobic Parameter.

Thermoresponsive polymers exhibiting upper critical solution temperature (UCST)-type behavior under physiologically relevant conditions have potential as biomaterials. The phase separation temperature ( Tp) of the UCST-type polymers can be increased by copolymerization with hydrophobic comonomers. Quantitative index parameters that could be used to rationally tune the Tp are lacking, however. We have reported that ureido copolymers such as poly(allylamine- co-allylurea) (AM-PU) and poly(l-ornithine- co-citrulline) exhibit UCST-type solution behavior under physiologically relevant conditions. In this study, AM-PU was hydrophobized by acylation. Tp of AM-PU can be regulated in a wide temperature range from about 20 to 80 °C or even higher by 20 mol % acylation with acetyl, propionyl, isobutanoyl, or pivaloyl groups, implying considerable impacts of hydrophobic groups on UCST phase separation. We observed a liner relationship between Tp and the hydrophobic parameter, log P, of the acyl groups. Furthermore, the acylation significantly reduced the influence of serum components on Tp by eliminating interactions of copolymers with serum components such as proteins and lipids. Acylation also abolished pH dependence of Tp which had been observed for unmodified AM-PU. Owing to the simple relationship between log P and Tp and the inertness of the acylated copolymer to serum components and pH changes, it is possible to rationally design copolymers exhibiting UCST-type behavior at a desired temperature under biological conditions.

Allosteric Control of Peroxidase-Mimicking DNAzyme Activity with Cationic Copolymers.

Control of protein conformation and function, induced by the binding of an effector, plays significant roles in modulating biochemical reaction. Although the DNAzymes catalytic activity is similar to protein-based enzymes, reports of allosterically controlled DNAzymes are still limited except for aptamer-DNAzymes hybrrids. Here, we report allosteric control of peroxidase-mimicking DNAzyme activity using cationic copolymers. The DNAzyme requires a structured G-quadruplex core and hemin for activity, and the DNAzyme with a parallel G-quadruplex core has higher DNAzyme activity than DNAzymes based on other types of structure. We previously reported that a cationic copolymer composed of a cationic backbone and hydrophilic dextran side chains selectively stabilizes parallel G-quadruplex structures. In this study, we investigated effects of the cationic copolymer on peroxidase-mimicking DNAzyme activity. The cationic copolymer enhanced the DNAzyme activity by more than 30-fold by stabilizing the parallel G-quadruplex structure. Furthermore, reversible allosteric control of DNAzyme activity was achieved by adding cationic and anionic polymers.

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.

Single-Molecule Monitoring of the Structural Switching Dynamics of Nucleic Acids through Controlling Fluorescence Blinking.

Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful tool to investigate the dynamics of biomolecular events in real time. However, it requires two fluorophores and can be applied only to dynamics that accompany large changes in distance between the molecules. Herein, we introduce a method for kinetic analysis based on control of fluorescence blinking (KACB), a general approach to investigate the dynamics of biomolecules by using a single fluorophore. By controlling the kinetics of the redox reaction the blinking kinetics or pattern can be controlled to be affected by microenvironmental changes around a fluorophore (rKACB), thereby enabling real-time single-molecule measurement of the structure-changing dynamics of nucleic acids.

Design of a Tunable Self-Oscillating Polymer with Ureido and Ru(bpy)3 Moieties.

An upper critical solution temperature (UCST)-type self-oscillating polymer was designed that exhibited rhythmic soluble-insoluble changes induced by the Belousov-Zhabotinsky (BZ) reaction. The target polymers were prepared by conjugating Ru(bpy)3 , a catalyst for the BZ reaction, to ureido-containing poly(allylamine-co-allylurea) (PAU) copolymers. The Ru(bpy)3 -conjugated PAUs exhibited a UCST-type phase-transition behavior, and the solubility of the polymer changed in response to the alternation in the valency of Ru(bpy)3 . The ureido content influences the temperature range of self-oscillation, and the oscillation occurred at higher temperatures than conventional LCST-type self-oscillating polymers. Furthermore, the self-oscillating behavior of the Ru-PAU could be regulated by addition of urea, which is a unique tuning strategy. We envision that novel self-oscillating polymers with widely tunable soluble-insoluble behaviors can be rationally designed based these UCST-type polymers.

Mutational analysis of hepatitis B virus pre-S1 (9-24) fusogenic peptide.

A hollow nanoparticle known as a bio-nanocapsule (BNC) consisting of hepatitis B virus (HBV) envelope L protein and liposome (LP) can encapsulate drugs and genes and thereby deliver them in vitro and in vivo to human hepatic tissues, specifically by utilizing the HBV-derived infection machinery. Recently, we identified a low pH-dependent fusogenic domain at the N-terminal part of the pre-S1 region of the HBV L protein (amino acid residues 9 to 24; NPLGFFPDHQLDPAFG), which shows membrane destabilizing activity (i.e., membrane fusion, membrane disruption, and payload release) upon interaction with target LPs. In this study, instead of BNC and HBV, we generated LPs displaying a mutated form of the pre-S1 (9-24) peptide, and performed a membrane disruption assay using target LPs containing pyranine (fluorophore) and p-xylene-bis (N-pyridinium bromide) (DPX) as a quencher. The membrane disruption activity was found to correlate with the hydrophobicity of the whole structure, while the peptide retained a random-coil structure even under low pH condition. One large hydrophobic cluster (I) and one small hydrophobic cluster (II) residing in the peptide would be connected by the protonation of residues D16 and D20, and thereby exhibit strong membrane disruption activity in a low pH-dependent manner. Furthermore, the introduction of a positively charged residue enhanced the activity significantly, suggesting that a sole positively charged residue (H17) may be important for the interaction with target LPs by electrostatic interaction. Collectively, these results suggest that the pre-S1 (9-24) peptide may be involved in the endosomal escape of the BNC's payloads, as well as in the HBV uncoating process.

Cooperative enhancement of deoxyribozyme activity by chemical modification and added cationic copolymer.

Deoxyribozymes (DNAzymes) having RNA-cleaving activity have widely been explored as tools for therapeutic and diagnostic purposes. Both the chemical cleaving step and the turnover step should be improved for enhancing overall activity of DNAzymes. We have shown that cationic copolymer enhanced DNAzyme activity by increasing turnover efficacy. In this paper, effectｓ of the copolymer on DNAzymes modified with locked nucleic acids (LNA) or 2'-O-methylated (2'-OMe) nucleic acids were studied. The copolymer increased activity of these chemically modified DNAzymes. More than 30-fold enhancement in multiple-turnover catalytic activity was observed with 2'-OMe-modified DNAzyme in the presence of the copolymer. DNAzyme catalytic activity was successfully enhanced by cooperation of the added copolymer and chemical modification of DNAzyme.

Preparation of upper critical solution temperature (UCST) responsive diblock copolymers bearing pendant ureido groups and their micelle formation behavior in water.

Poly(2-ureidoethyl methacrylate) (PUEM) was prepared via reversible addition-fragmentation chain transfer (RAFT) controlled radical polymerization and a post-modification reaction. PUEM shows upper critical solution temperature (UCST) behavior in aqueous solution. Although PUEM can dissolve in water above the UCST, it cannot dissolve in water below the UCST. Diblock copolymers (MmUn) composed of a biocompatible hydrophilic poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) block and a PUEM block with different compositions were prepared via RAFT radical polymerization and a post-modification reaction. "M" and "U" represent PMPC and PUEM blocks, respectively, and the subscripts represent the degree of polymerization of each block. M95U149 and M20U163 formed polymer micelles comprising a PUEM core and a PMPC shell below the critical aggregation temperature (Tc) in aqueous solution. Polymer micelles were formed from M20U163 below 32 °C, which can incorporate guest molecules into the core.

Spontaneous Liquid Droplet-to-Gel Transition of Citrulline Polypeptide Complexed with Nucleic Acids.

Inside cells, proteins complex with nucleic acids to form liquid droplets resulting from liquid-liquid phase separation. The presence of mutated proteins can change the state of these liquid droplets to solids or gels, triggering neurodegenerative diseases. The mechanism of the liquid to solid or gel transition is still unclear. Solutions of poly(l-ornithine-co-l-citrulline) (PLOC) copolymers, which exhibit upper critical solution temperature-type behavior, change state upon cooling. In this study, we evaluated the effect of nucleic acids complexed with PLOC on phase changes. In the presence of nucleic acids, such as polyC and polyU, PLOC formed liquid droplets at low temperatures. The droplets dissolved at temperatures above the phase separation temperature. The phase separation temperature depended on the chemical structure of the nucleobase, implying that electrostatic and hydrogen bonding interactions between the nucleic acid and PLOC influenced phase separation. Furthermore, the liquid droplets spontaneously changed to gel-like precipitates due to spontaneous release of nucleic acids from the complex. The rate of the liquid droplet-to-gel transition depended on the magnitude of electrostatic and hydrogen bonding interactions between PLOC and nucleic acid. PLOC complexed with mRNA also underwent a liquid droplet-to-gel transition upon the release of mRNA. This work provides insights into the mechanism of pathogenic transitions of the cellular droplets.

Design of UCST polymers for chilling capture of proteins.

Ureido-derivatized polymers, such as poly(allylurea) (PU) and poly(L-citrulline) derivatives, exhibited upper critical solution temperature (UCST) behavior under physiological buffer conditions as we previously reported. The PU derivatives having amino groups (PU-Am) also showed UCST behavior. In this study, we modified the amino groups of the polymer with succinyl anhydride (PU-Su) or acetyl anhydride (PU-Ac) to determine the effects of these ionic groups on the UCST behavior and to control interactions between the PU derivatives and biocomponents such as proteins and cells. Succinylation of PU-Am resulted in a significant decrease in phase separation temperature (Tp), whereas acetylation of PU-Am resulted in an increase in Tp. As expected, the Tp of PU-Am and PU-Su changed when the pH of the solution was changed. The Tp of PU-Am increased at higher pH, whereas that of PU-Su increased at lower pH, indicating that ionic charge decreases Tp of PU derivatives by increasing osmotic pressure and by increasing hydrophilicity of the polymer chains. Interestingly, these groups did not significantly change UCST when these groups were nonionic. We then examined capture and separation of particular proteins from a protein mixture by cooling-induced phase separation. Selective and rapid capture of particular proteins from protein mixture by PU derivatives was shown, indicating that the ureido-derivatized polymers are potential media for bioseparation under biofriendly conditions.

Polycation-assisted DNA detection by reduction triggered fluorescence amplification probe.

We have developed a fluorescence detection system for DNA, assisted by a comb-type cationic polymer (PLL-g-DX), for accelerating the reaction turnover. The combination of fluorogenic DNA probes with a comb-type cationic polymer has been demonstrated to be an effective means of signal amplification during the detection process. The method described herein represents a simple and enzyme-free detection.

Malachite green-derivatized cationic comb-type copolymer acts as a photoresponsive artificial chaperone.

Molecular chaperones play vital roles in various physiological reactions by regulating the folding and assembly of biomacromolecules. We have demonstrated that cationic comb-type copolymers exhibit chaperone activity for anionic biomolecules including DNA and ionic peptide via the formation of soluble interpolyelectrolyte complexes. The development of smart artificial chaperones that can be spatiotemporally controlled by a remotely guided signal would expand the functions of artificial chaperones. Herein, to enable photocontrol of chaperone activity, a cationic comb-type copolymer bearing malachite green as a photoresponsive unit was designed. We first prepared a series of carboxylic acid derivatives of malachite green identified a derivative that could be quickly and quantitatively converted to the cationic form from the nonionic form by photoirradiation. This derivative was conjugated to the cationic comb-type copolymer, poly(allylamine)-graft-poly(ethylene glycol) through a condensation reaction. Upon photoirradiation, the copolymer bearing 9 mol% malachite green enhanced the membrane disruptive activity of acidic peptide E5 and induced morphological changes in liposomes. This demonstration of photoresponsive activation of chaperoning activity of a copolymer suggests that the installation of carboxyl derivatives of malachite green will impart photoresponsiveness to various materials including biopolymers.