Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications.

This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.

Polydopamine-Induced Modification on the Highly Charged Surface of Asymmetric Nanofluidics: A Strategy for Adjustable Ion Current Rectification Properties.

Surface charge effects in nanoconfines is one of the fundamentals in the ion current rectification (ICR) of nanofluidics, which provides entropic driving force by asymmetric surface charges and causes ion enrichment/depletion by the electrostatic interaction of fixed surface charges. However, the surface charge effect causes a significant electrostatic repulsion in nanoconfines, restricting additional like charge or elaborate chemistry on the highly charged confined surface, which limits ICR manipulation. Here, we use polydopamine (PDA), a nearly universal adhesive, that adheres to the highly positive-charged poly(ethyleneimine) (PEI) gel network in a nanochannel array. PDA enhances the ICR effect from a low rectification ratio of 9.5 to 92.6 by increasing the surface charge and hydrophobicity of the PEI gel network and, meanwhile, shrinking its gap spacing. Theoretical and experimental results demonstrate the determinants of the fixed surface charge in the enrichment/depletion region on ICR properties, which is adjustable by PDA-induced change in a nanoconfined environment. Chemically active PDA brings Au nanoparticles by chloroauric reduction for further hydrophobization and the modification of negative-charged DNA complexes in nanochannels, whereby ICR effects can be manipulated in versatile means. The results describe an adjustable and versatile strategy for adjusting the ICR behaviors of nanofluidics by manipulating local surface charge effects using PDA.

Revealing Ionic Signal Enhancement with Probe Grafting Density on the Outer Surface of Nanochannels.

Probe-modified nanopores/nanochannels are one of the most advanced sensors because the probes interact strongly with ions and targets in nanoconfinement and create a sensitive and selective ionic signal. Recently, ionic signals have been demonstrated to be sensitive to the probe-target interaction on the outer surface of nanopores/nanochannels, which can offer more open space for target recognition and signal conversion than nanoconfined cavities. To enhance the ionic signal, we investigated the effect of grafting density, a critical parameter of the sensing interface, of the probe on the outer surface of nanochannels on the change rate of the ionic signal before and after target recognition (ß). Electroneutral peptide nucleic acids and negatively charged DNA are selected as probes and targets, respectively. The experimental results showed that when adding the same number of targets, the ß value increased with the probe grafting density on the outer surface. A theoretical model with clearly defined physical properties of each probe and target has been established. Numerical simulations suggest that the decrease of the background current and the aggregation of targets at the mouth of nanochannels with increasing probe grafting density contribute to this enhancement. This work reveals the signal mechanism of probe-target recognition on the outer surface of nanochannels and suggests a general approach to the nanochannel/nanopore design leading to sensitivity improvement on the basis of relatively good selectivity.

Nanometer-Scale Force Profiles of Short Single- and Double-Stranded DNA Molecules on a Gold Surface Measured Using a Surface Forces Apparatus.

Using a surface forces apparatus (SFA), we have studied the nanomechanical behavior of short single-stranded and partially and fully double-stranded DNA molecules attached via one end to a self-assembled monolayer on a gold surface. Our results confirm the previously proposed "mushroom-like" polymer structure for surface-attached, single-stranded DNA at low packing density and a "brush-like" structure for the same construct at higher density. At low density we observe a transition to "rigid rod" behavior upon addition of DNA complementary to the surface-attached single strand as the fraction of molecules that are double-stranded increases, with a concomitant increase in the SFA-observed thickness of the monolayer and the characteristic length of the observed repulsive forces. At higher densities, in contrast, this transition is effectively eliminated, presumably because the single-stranded state is already extended in its "brush" state. Taken together, these studies offer insights into the structure and physics of surface-attached short DNAs, providing new guidance for the rational design of DNA-modified functional surfaces.

Estimation of the reproduction number and identification of periodicity for HFMD infections in northwest China.

Repeated outbreaks of Hand, foot and mouth disease (HFMD) infections have been observed in recent decades and dominated by various enteroviral serotypes. In particular, enterovirus 71 (EV-A71), coxsackievirus A16 (CV-A16) and coxsackievirus A6 (CV-A6) dominated the prevalence of HFMD infections alternatively in recent years with various outbreak sizes in Baoji, a city of Shaanxi Province in Northwest China. Estimating the reproduction number for various enteroviruses serotypes in northwest China (north temperate zone) and identification of cyclicity of HFMD infections are therefore an issue of great importance for future epidemics prediction and control. The basic/effective reproduction numbers for EV-A71, CV-A16 and CV-A6 were estimated based on daily new cases in 2010, 2011 and 2018, respectively, in which the corresponding pathogen dominated the epidemic. Two different methods based on serial interval were adopted and the basic reproduction number were estimated to be in the range of (1.33, 1.46) for CV-A16, (1.20, 1.29) for EV-A71, and (1.38, 1.59) for CV-A6, respectively. The estimated daily effective reproduction numbers significantly fluctuated before June or after July but varied mildly in (0.5,2) in around June to July for three serotypes. The weekly effective reproduction number for HFMD was estimated based on weekly new cases from year 2010 to 2018, and in most years it peaked in the range of (1.6,2.0) in February to March as well as in the range of (1.0,1.2) in September to October. The wavelet analysis based on the time series of HFMD cases from 2008 to 2018 showed obvious annual and semi-annual cyclicity, while the inter-annual cycles are infeasible. In this study we found that CV-A6 shows the greatest transmission ability among these three pathogens while EV-A71 exhibits the weakest ability of transmission, and moreover, the estimated values of basic reproduction number in northwest China are lower than those in Singapore, Hongkong and Guangdong, which may be due to different climatic circumstances.

Two-Photon Lithographic Patterning of DNA-Coated Single-Microparticle Surfaces.

The spatially defined functionalization of microparticles with asymmetric shape-controlled nucleic acid patterns is a major challenge in materials science. The asymmetric patterning of microparticles is important to allow the controlled fabrication of crystalline lattices or controlled aggregates of microparticles. We present the combination of two-photon lithography and photocleavable o-nitrobenzylphosphate ester nucleic acid coating-modified microparticles as a versatile means to asymmetrically pattern single microparticle surfaces. The two-photon patterning of microparticles with predesigned nucleic acid structures of different sizes (700 nm to 2.8 µm) and shapes (circles, rings, triangles, and squares) are demonstrated. In addition, complex patterned domains consisting of two different asymmetric nucleic acid domains are fabricated by the controlled Z-positioning of the microparticles in respect to the two-photon irradiation sources. In addition, the two-photon lithographic patterning of the photocleavable DNA coating allows the generation of functional nucleic acid domains for the photostimulated activation of the catalytic hybridization assembly (CHA) of branched nucleic acid structures on single microparticles.

Recent Advances in Cyclodextrin-Based Light-Responsive Supramolecular Systems.

Cyclodextrins (CDs), one of the host molecules in supramolecular chemistry, can host guest molecules to form inclusion complexes via non-covalent and reversible host-guest interactions. CD-based light-responsive supramolecular systems are typically constructed using CDs and guest molecules with light-responsive moieties, including azobenzene, arylazopyrazole, o-nitrobenzyl ester, pyrenylmethyl ester, coumarin, and anthracene. To date, numerous efforts have been reported on the topic of CD-based light-responsive supramolecular systems, but these have not yet been highlighted in a separated review. This review summarizes the efforts reported over the past ten years. The main text of this review is divided into five sections (vesicles, micelles, gels, capturers, and nanovalves) according to the formation of self-assemblies. This feature article aims to afford a comprehensive understanding of the light-responsive moieties used in the construction of CD-based light-responsive supramolecular systems and to provide a helpful guide for the further design of CD-based light-responsive supramolecular systems.

Unsaturation of very-long-chain ceramides protects plant from hypoxia-induced damages by modulating ethylene signaling in Arabidopsis.

Lipid remodeling is crucial for hypoxic tolerance in animals, whilst little is known about the hypoxia-induced lipid dynamics in plants. Here we performed a mass spectrometry-based analysis to survey the lipid profiles of Arabidopsis rosettes under various hypoxic conditions. We observed that hypoxia caused a significant increase in total amounts of phosphatidylserine, phosphatidic acid and oxidized lipids, but a decrease in phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Particularly, significant gains in the polyunsaturated species of PC, PE and phosphatidylinositol, and losses in their saturated and mono-unsaturated species were evident during hypoxia. Moreover, hypoxia led to a remarkable elevation of ceramides and hydroxyceramides. Disruption of ceramide synthases LOH1, LOH2 and LOH3 enhanced plant sensitivity to dark submergence, but displayed more resistance to submergence under light than wild type. Consistently, levels of unsaturated very-long-chain (VLC) ceramide species (22:1, 24:1 and 26:1) predominantly declined in the loh1, loh2 and loh3 mutants under dark submergence. In contrast, significant reduction of VLC ceramides in the loh1-1 loh3-1 knockdown double mutant and lacking of VLC unsaturated ceramides in the ads2 mutants impaired plant tolerance to both dark and light submergences. Evidence that C24:1-ceramide interacted with recombinant CTR1 protein and inhibited its kinase activity in vitro, enhanced ER-to-nucleus translocation of EIN2-GFP and stabilization of EIN3-GFP in vivo, suggests a role of ceramides in modulating CTR1-mediated ethylene signaling. The dark submergence-sensitive phenotypes of loh mutants were rescued by a ctr1-1 mutation. Thus, our findings demonstrate that unsaturation of VLC ceramides is a protective strategy for hypoxic tolerance in Arabidopsis.

Aliidongia dinghuensis gen. nov., sp. nov., a poly-ß-hydroxybutyrate-producing bacterium isolated from Pinus massoniana forest soil.

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated 7M-Z19T, was isolated from a soil sample collected from a Pinus massoniana forest of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain 7M-Z19T grew at pH 4.5-7.5 (optimum pH 6.0-6.5), 10 to 37 °C (optimum 28 °C) and NaCl concentration up to 2.0 % (optimum 0 %, w/v). iso-C17 : 0, C18 : 1ω7c and C19 : 0ω8c cyclo were the major fatty acids (>10 %) while ubiquinone-10 was the only respiratory quinone detected in 7M-Z19T. The polar lipids of the strain consisted of phosphatidylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, six unidentified aminophospholipids, three unidentified phospholipids, six unidentified lipids and a glycolipid. The DNA G+C content was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate formed a distinct lineage with Dongia mobilis and Dongia rigui within the family Rhodospirillaceae, but with a low sequence similarity of 92.7 and 92.0 %, respectively. On the basis of phylogenetic, phenotypic, physiological and chemotaxonomic distinctiveness, strain 7M-Z19T should be placed in the family Rhodospirillaceae as a representative of a novel genus and species, for which the name Aliidongia dinghuensis gen. nov., sp. nov., is proposed. The type strain of the type species is 7M-Z19T (=NBRC 112240T=KCTC 52134T=CGMCC 1.15725T).

Click Chemistry in Functional Aliphatic Polycarbonates.

Click chemistry, one of the most important methods in conjugation, plays an extremely significant role in the synthesis of functional aliphatic polycarbonates, which are a group of biodegradable polymers containing carbonate bonds in their main chains. To date, more than 75 articles have been reported on the topic of click chemistry in functional aliphatic polycarbonates. However, these efforts have not yet been highlighted. Six categories of click reactions (alkyne-azide reaction, thiol-ene reaction, Michael addition, epoxy-amine/thiol reaction, Diels-Alder reaction, and imine formation) that have been afforded for further post-polymerization modification of polycarbonates are reviewed. Through this review, a comprehensive understanding of functional aliphatic polycarbonates aims to afford insight on the design of polycarbonates for further post-polymerization modification via click chemistry and the expectation of the practical application.

Aiming low: A resident male's rank predicts takeover success by challenging males in Yunnan snub-nosed monkeys.

In many primate species that form one-male breeding units (OMUs), the threat of a takeover by a bachelor male represents a major challenge to group stability and individual reproductive success. In the case of snub-nosed monkeys, which live in large multilevel or modular societies (MLS) comprising several OMUs that travel, feed and rest together and as well as one or more all male units (AMUs), the process by which rival males challenge resident OMU males for access to females is poorly understood. From September 2012 to October 2013, we recorded 48 cases in which rival males visited an OMU in a MLS of Yunnan snub-nosed monkeys (Rhinopithecus bieti) inhabiting the Baimaxueshan National Nature Reserve, Yunnan Province, China. In 40 cases, rival males engaged in mild agonistic interactions (approaching, staring, teeth-baring and chasing) but failed to take over the group; we counted these visits as failed takeovers, recognizing that they may nevertheless allow rival males to assess the competitive ability of residents. During eight successful takeovers, however, there was severe physical aggression between challenging and resident males, with serious injuries to participants. We found that neither the number of adult and subadult females in an OMU, the number of non-pregnant, non-lactating adult females in an OMU, nor the rank of a resident male relative to other resident males in the MLS predicted which OMU a challenging male targeted for takeover. However, a resident male's rank significantly predicted whether takeover attempts were successful. Specifically, challenging males were more successful in displacing a lower-ranking resident male than a higher-ranking male. Given that a Yunnan snub-nosed monkey MLS may contain as many as 40 resident and 36 bachelor males, continued research is required to determine the set of factors that enable resident males to maintain high social rank and successfully defend their harems. Am. J. Primatol. 78:974-982, 2016. © 2016 Wiley Periodicals, Inc.

Rational designed bipolar, conjugated polymer-DNA composite beacon for the sensitive detection of proteins and ions.

Nature owns remarkable capabilities in sensing target molecules, while the artificial biosensor lags far behind nature. Inspired by nature, we devise a new sensing platform that can specifically bind the molecules and synchronously initiate a specific signal response. We rationally designed a type of bipolar probe that is comprised of a hydrophilic DNA part and a hydrophobic conjugated polymer (CP) unit. In aqueous solution, they can form micelles with a hydrophobic CP core and a hydrophilic DNA shell. The aggregation-caused quenching suppresses the fluorescence of CP. Adding telomerase, the hydropathical profile of the bipolar probes is drastically regulated that results in the collapse of micelles and liberates fluorescence simultaneously. The probe has been used in both mimic systems and real urine samples (38 samples). We achieve sensitive and specific detection of telomerase and obtain clearly classification for normal people and cancer patients. It can also be used in a signal off sensor that is used to detect mercury ions.

Colorimetric detection of DNA, small molecules, proteins, and ions using unmodified gold nanoparticles and conjugated polyelectrolytes.

We have demonstrated a novel sensing strategy employing single-stranded probe DNA, unmodified gold nanoparticles, and a positively charged, water-soluble conjugated polyelectrolyte to detect a broad range of targets including nucleic acid (DNA) sequences, proteins, small molecules, and inorganic ions. This nearly "universal" biosensor approach is based on the observation that, while the conjugated polyelectrolyte specifically inhibits the ability of single-stranded DNA to prevent the aggregation of gold-nanoparticles, no such inhibition is observed with double-stranded or otherwise "folded" DNA structures. Colorimetric assays employing this mechanism for the detection of hybridization are sensitive and convenient--picomolar concentrations of target DNA are readily detected with the naked eye, and the sensor works even when challenged with complex sample matrices such as blood serum. Likewise, by employing the binding-induced folding or association of aptamers we have generalized the approach to the specific and convenient detection of proteins, small molecules, and inorganic ions. Finally, this new biosensor approach is quite straightforward and can be completed in minutes without significant equipment or training overhead.

Dynamic Fusion of Nucleic Acid Functionalized Nano-/Micro-Cell-Like Containments: From Basic Concepts to Applications.

Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by artificial means. The recognition and dynamic reconfiguration properties of nucleic acids provide a versatile means to induce membrane fusion. Here we address recent advances in the functionalization of liposomes or membranes with structurally engineered lipidated nucleic acids guiding the fusion of cell-like containments, and the biophysical and chemical parameters controlling the fusion of the liposomes will be discussed. Intermembrane bridging by duplex or triplex nucleic acids and light-induced activation of membrane-associated nucleic acid constituents provide the means for spatiotemporal fusion of liposomes or nucleic acid modified liposome fusion with native cell membranes. The membrane fusion processes lead to exchange of loads in the fused containments and are a means to integrate functional assemblies. This is exemplified with the operation of biocatalytic cascades and dynamic DNA polymerization/nicking or transcription machineries in fused protocell systems. Membrane fusion processes of protocell assemblies are found to have important drug-delivery, therapeutic, sensing, and biocatalytic applications. The future challenges and perspectives of DNA-guided fused containments and membranes are addressed.

Near-Infrared Conjugated Polymers Containing Thermally Activated Delayed Fluorescence Units Enable Enhanced Photothermal Therapy.

Photothermal therapy (PTT) using near-infrared (NIR) conjugated polymers as photosensitizers has exhibited enormous potential for tumor treatment. However, most NIR conjugated polymers have poor therapeutic efficacy due to their faint absorbance in the NIR region and low photothermal conversion efficiency (PCE). Herein, a valuable strategy for designing NIR polymeric photosensitizer PEKBs with an enhanced PCE accompanied by strong NIR absorbance is proposed by means of inserting TPA-AQ as a thermally activated delayed fluorescence unit into a polymeric backbone. In these PEKBs, PEKB-244 with the appropriate molar content of the TPA-AQ unit displays the strongest NIR absorbance and the highest PCE of 64.5%. Theoretical calculation results demonstrate that the TPA-AQ unit in the polymeric backbone can modulate the intramolecular charge transfer effects and the excited energy decay routes for generating higher heat. The prepared nanoparticles (PEKB-244 NPs) exhibit remarkable photothermal conversion capacities and great biocompatibility in aqueous solutions. Moreover, PEKB-244 NPs also show outstanding photothermal stability, displaying negligible changes in the absorbance within 808 nm irradiation of 1 h (800 mW cm-2). Both in vitro and in vivo experimental results further indicate that PEKB-244 NPs can substantially kill cancer cells under NIR laser irradiation. We anticipate that this novel molecular design strategy can be employed to develop excellent NIR photosensitizers for cancer photothermal therapy.

Gradient adhesion modification of polyacrylamide/alginate-calcium tough hydrogels.

Strong hydrogel adhesion requires the synergy of adhesion and cohesion. Gradient adhesive-tough hydrogels can balance adhesion and cohesion, however, their construction is still a challenging task. Here, we used ethylenediaminetetraacetic acid (EDTA) on-side coordination-induced diffusion chelating Ca2+ to form an adhesive surface in a polyacrylamide/alginate-calcium (PAAm/Alg-Ca2+) tough hydrogel as a facile method for the construction of gradient adhesive-tough hydrogels. The adhesion energy of a gradient adhesive-tough hydrogel to skin is increased by 128% compared with PAAm/Alg-Ca2+ tough hydrogels and the elongation at break is two times higher than that of PAAm/Alg hydrogels. In addition, gradient adhesive-tough hydrogels also exhibit wide linear sensitivity (the gauge factor (GF) = 0.196 (0% < ε < 400%); GF = 0.260 (400% < ε < 650%)) as a wearable strain sensor to monitor human motions. This work provides a versatile strategy for the design of gradient adhesive-tough hydrogels and also provides a practical model for the development of wearable strain sensors.

Insight into Drug Loading Regulated Micellar Rigidity by Nuclear Magnetic Resonance.

The rigidity of polymeric micelles plays an important role in their biological behaviors. However, how drug loading affects the rigidity of polymeric micelles remains elusive. Herein, the indomethacin (IMC)-loaded Pluronic F127 micelle is used as a model system to illustrate the impact of drug loading on the rigidity and biological behaviors of polymeric micelles. Against expectations, micelles with moderate drug loading show higher cellular uptake and more severe cytotoxicity as compared to both high and low drug loading counterparts. Extensive one- and two-dimensional nuclear magnetic resonance (NMR) measurements are employed to reveal that the higher drug loading induces stronger interaction between IMC and hydrophilic block to boost the micellar rigidity; consequently, the moderate drug loading imparts micelles with appropriate rigidity for satisfactory cellular uptake and cytotoxicity. In summary, NMR spectroscopy is an important tool to gain insight into drug loading regulated micellar rigidity, which is helpful to understand their biological behaviors.

Advances in non-covalent crosslinked polymer micelles for biomedical applications.

As a drug delivery system, crosslinked polymer micelles can reduce the drug release in advance in the blood circulation, improve the stability of polymer micelles, effectively deliver drugs to the treatment site, further improve the bioavailability of drugs and reduce the side effects. Among them, non-covalent crosslinked polymer micelles have the advantages of sensitive response to external stimuli, self-healing after damage, and no need to use chemicals for crosslinking. This review mainly introduces the research progress of polymer micelles crosslinked by hydrogen bonding, dipole interaction, hydrophobic interaction, host-guest interaction, π-π stacking, and metal coordination reported in recent years, and summarizes the applications of these micelles in biomedical fields such as drug delivery, gene transfection, and imaging.

Rationally Designed Multivalent Aptamers Targeting Cell Surface for Biomedical Applications.

Specific interactions between ligands and receptors on cell surface play an important role in the cell biological process. Nucleic acid aptamers as commonly used ligands enable specific recognition and tight binding to membrane protein receptors for modulation of cell fate. Therefore, molecular probes with aptamers can be applied for cancer diagnosis and targeted therapy by targeting overexpression membrane proteins of cancer cells. However, because of their fast degradation and rapid glomerulus clearance in vivo, the applications of aptamers in physiological conditions remain challenged. Inspired by natural multivalent interactions, many approaches have been developed to construct multivalent aptamers to improve the performance of aptamers in complex matrices with higher binding affinity, more stability, and longer circulation time. In this review, we first introduce the aptamer generation from purified protein-based SELEX and whole cell-based SELEX for targeting the cell surface. We then highlight the approaches to fabricate multivalent aptamers and discuss their properties. By integrating different materials (including inorganic nanomaterials, diacyllipid, polymeric nanoparticles, and DNA nanostructures) as scaffolds with an interface modification technique, we have summarized four kinds of multivalent aptamers. After that, representative applications in biosensing and targeted therapy are illustrated to show the elevated performance of multivalent aptamers. In addition, we analyze the challenges and opportunities for the clinical practices of multivalent aptamers.