Lycium Barbarum Polysaccharides and Wolfberry Juice Prevent DEHP-Induced Hepatotoxicity via PXR-Regulated Detoxification Pathway

Environmental di(2-Ethylhexyl) phthalate (DEHP) is widely used in various industries as a plasticizer, and has been reported to induce reproductive and developmental toxicities in organisms. The purpose of this study was to evaluate the detoxification capacity of Lycium barbarum polysaccharides (LBP) and wolfberry juice (WJ) against DEHP-induced hepatotoxicity. Two groups of rats were purchased to study two different intervention method experiments: LBP (50, 100, 200 mg/kg·bw) intervention before DEHP (2000 mg/kg·bw) exposure, and LBP (200 mg/kg·bw) or WJ (8 mL/kg·bw) intervention after DEHP (3000 mg/kg·bw) exposure. The rats were exposed to DEHP once, while the intervention lasted for seven days. At the end of the intervention, enzyme-linked immunosorbent assay (ELISA) was used to measure the related index. The LBP intervention before DEHP exposure experiment (the first experimental method) found that LBP group rats showed a strong capacity toward DEHP detoxification, evidenced by the significant upregulation of activities and concentrations of the partner retinoid, X receptor alpha (RXRα), and downstream regulators Cytochrome P4502E1 (CYP2E1), Cytochrome P4503A1 (CYP3A1), Glutathione S-Transferase Pi (GSTpi), and UDP-glucuronosyltransferase 1 (UGT1) in a dose-dependent manner. The LBP and WJ intervention after DEHP exposure experiment (the second intervention experiment) found that WJ could downregulate pregnane X receptor (PXR), and upregulate downstream regulators, CYP2E1, CYP3A1, and Glutathione S-Transferase (GST) with the extension of intervention time, to alleviate the toxicity of DEHP. However, the intervention effect of WJ was more obvious than that of LBP. These results suggested that LBP and WJ might be effective detoxification agents against DEHP-induced toxic effects, by activating PXR and PXR-related detoxifying enzymes.     

Chemically Synthesized,Self-Assembling Small Interfering RNA-Prohead RNA Molecules Trigger Dicer-Independent Gene Silencing

RNA interference (RNAi) mediated by small interfering RNA (siRNA) duplexes is a powerful therapeutic modality, but the translation of siRNAs from the bench into clinical application has been hampered by inefficient delivery in vivo. An innovative delivery strategy involves fusing siRNAs to a three-way junction (3WJ) motif derived from the phi29 bacteriophage prohead RNA (pRNA). Chimeric siRNA-3WJ molecules are presumed to enter the RNAi pathway through Dicer cleavage. Here, we fused siRNAs to the phi29 3WJ and two phylogenetically related 3WJs. We confirmed that the siRNA-3WJs are substrates for Dicer in vitro. However, our results reveal that siRNA-3WJs transfected into Dicer-deficient cell lines trigger potent gene silencing. Interestingly, siRNA-3WJs transfected into an Argonaute 2-deficient cell line also retain some gene silencing activity. siRNA-3WJs are most efficient when the antisense strand of the siRNA duplex is positioned 5′ of the 3WJ (5′-siRNA-3WJ) relative to 3′ of the 3WJ (3′-siRNA-3WJ). This work sheds light on the functional properties of siRNA-3WJs and offers a design rule for maximizing their potency in the human RNAi pathway.     

A Multi-component All-DNA Biosensing System Controlled by a DNAzyme

We report on a programmable all-DNA biosensing system that centers on the use of a 4-way junction (4WJ) to transduce a DNAzyme reaction into an amplified signal output. A target acts as a primary input to activate an RNA-cleaving DNAzyme, which then cleaves an RNA-containing DNA substrate that is designed to be a component of a 4WJ. The formation of the 4WJ controls the release of a DNA output that becomes an input to initiate catalytic hairpin assembly (CHA), which produces a second DNA output that controls assembly of a split G-quadruplex as a fluorescence signal generator. The 4WJ can be configured to produce either a turn-off or turn-on switch to control the degree of CHA, allowing target concentration to be determined in a quantitative manner. We demonstrate this approach by creating a sensor for E. coli that could detect as low as 50 E. coli cells mL⁻¹ within 85 min and offers an amplified bacterial detection method that does not require a protein enzyme.     

MVF Sensor Enables Analysis of Nucleic Acids with Stable Secondary Structures

One major challenge in nucleic acids analysis by hybridization probes is a compromise between the probe's tight binding and sequence‐selective recognition of nucleic acid targets folded into stable secondary structures. We have been developing a four‐way junction (4WJ)‐based sensor that consists of a universal stem‐loop (USL) probe immobilized on an electrode surface and two adaptor strands (M and F). The sensor was shown to be highly selective towards single base mismatches at room temperature, able to detect multiple targets using the same USL probe, and have improved ability to detect folded nucleic acids. However, some nucleic acid targets, including natural RNA, are folded into very stable secondary and tertiary structures, which may represent a challenge even for the 4WJ sensors. This work describes a new sensor, named MVF since it uses three probe stands M, V and F, which further improves the performance of 4WJ sensors with folded targets. The MVF sensor interrogating a 16S rRNA NASBA amplicon with calculated folding energy of ?32.82 kcal/mol has demonstrated 2.5‐fold improvement in a signal‐to‐background ratio in comparison with a 4WJ sensor lacking strand V. The proposed design can be used as a general strategy in the analysis of folded nucleic acids including natural RNA.     

A Multi‐component All‐DNA Biosensing System Controlled by a DNAzyme

We report on a programmable all‐DNA biosensing system that centers on the use of a 4‐way junction (4WJ) to transduce a DNAzyme reaction into an amplified signal output. A target acts as a primary input to activate an RNA‐cleaving DNAzyme, which then cleaves an RNA‐containing DNA substrate that is designed to be a component of a 4WJ. The formation of the 4WJ controls the release of a DNA output that becomes an input to initiate catalytic hairpin assembly (CHA), which produces a second DNA output that controls assembly of a split G‐quadruplex as a fluorescence signal generator. The 4WJ can be configured to produce either a turn‐off or turn‐on switch to control the degree of CHA, allowing target concentration to be determined in a quantitative manner. We demonstrate this approach by creating a sensor for E. coli that could detect as low as 50 E. coli cells mL^?1 within 85 min and offers an amplified bacterial detection method that does not require a protein enzyme.     

Catalytic Hairpin Assembly‐Programmed DNA Three‐Way Junction for Enzyme‐Free and Amplified Electrochemical Detection of Target DNA

DNA three‐way junctions (DNA 3WJ) have been widely used as important building blocks for the construction of DNA architectures and dynamic assemblies. Herein, we describe for the first time a catalytic hairpin assembly‐programmed DNA three‐way junction (CHA‐3WJ) strategy for the enzyme‐free and amplified electrochemical detection of target DNA. It takes full advantage of the target‐catalyzed hairpin assembly‐induced proximity effect of toehold and branch‐migration domains for the ingenious execution of the strand displacement reaction to form the DNA 3WJ on the electrode surface. A low detection limit of 0.5 pM with an excellent selectivity was achieved for target DNA detection. The developed CHA‐3WJ strategy also offers distinct advantages of simplicity in probe design and biosensor fabrication, as well as enzyme‐free operation. Thus, it opens a promising avenue for applications in bioanalysis, design of DNA‐responsive devices, and dynamic DNA assemblies.     

Mg2+‐Dependent High Mechanical Anisotropy of Three‐Way‐Junction pRNA as Revealed by Single‐Molecule Force Spectroscopy

Mechanical anisotropy is ubiquitous in biological tissues but is hard to reproduce in synthetic biomaterials. Developing molecular building blocks with anisotropic mechanical response is the key towards engineering anisotropic biomaterials. The three‐way‐junction (3WJ) pRNA, derived from ϕ 29 DNA packaging motor, shows strong mechanical anisotropy upon Mg²⁺ binding. In the absence of Mg²⁺, 3WJ‐pRNA is mechanically weak without noticeable mechanical anisotropy. In the presence of Mg²⁺, the unfolding forces can differ by more than 4‐fold along different pulling directions, ranging from about 47 pN to about 219 pN. Mechanical anisotropy of 3WJ‐pRNA stems from pulling direction dependent cooperativity for the rupture of two Mg²⁺ binding sites, which is a novel mechanism for the mechanical anisotropy of biomacromolecules. It is anticipated that 3WJ‐pRNA can be used as a key element for the construction of biomaterials with controllable mechanical anisotropy.     

Induction of a Four‐Way Junction Structure in the DNA Palindromic Hexanucleotide 5′‐d(CGTACG)‐3′ by a Mononuclear Platinum Complex

Four‐way junctions (4WJs) are supramolecular DNA assemblies comprising four interacting DNA strands that in biology are involved in DNA‐damage repair. In this study, a new mononuclear platinum(II) complex 1 was prepared that is capable of driving the crystallization of the DNA oligomer 5′‐d(CGTACG)‐3′ specifically into a 4WJ‐like motif. In the crystal structure of the 1 –CGTACG adduct, the distorted‐square‐planar platinum complex binds to the core of the 4WJ‐like motif through π–π stacking and hydrogen bonding, without forming any platinum–nitrogen coordination bonds. Our observations suggest that the specific molecular properties of the metal complex are crucially responsible for triggering the selective assembly of this peculiar DNA superstructure.     

Use of Wheeler–Jonas equation to explain xenon dynamic adsorption breakthrough curve on granular activated carbon

The Wheeler–Jonas equation (WJ equation) is widely used to predict breakthrough of volatile organic compounds on granular activated carbon (GAC) and the most important criteria is to calculate the overall adsorption rate constant (k _v ) and amount adsorbed based on breakthrough curve. The operational factors, including temperatures, concentrations and flow rates, for packed bed, can affect the values of k _v more or less and to what degree has not yet been systematically investigated. What’s more, the relation between the dynamic adsorption coefficient (k _d) or Henry constant, which is used for the design of packed bed, and WJ equation is not clear. In order to solve these problems, we performed xenon dynamic adsorption on GAC adsorber experiments under different values of xenon concentrations, flow rates and temperatures, obtained the breakthrough curves for elution times versus xenon concentrations, and then employed WJ equation to explain breakthrough curves. The experimental results indicate that the WJ equation can fit the breakthrough curve very well and k _d be integrated into the WJ equation. The values of k _v are proportional to the values of flow rates and k _d, but independent of that of temperatures and xenon concentrations.     

Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting

DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, U_bpy- 3 , in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand Ni^II(bpy)₃ complex at the junction core (ΔT_m=+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside U_bpy- 2 , the degree of the Ni^II-mediated stabilization observed with U_bpy- 3 was comparable to that of U_bpy- 2 . Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of Ni^II ions. Furthermore, Ni^II-mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of Ni^II(bpy)₃ complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.     

DNA three-way junction with a dinuclear iron(II) supramolecular helicate at the center: a NMR structural study

A tetracationic supramolecular helicate, [Fe2L3]4+ (L = C25H20N4), with a triple-helical architecture is found to induce the formation of a three-way junction (3WJ) of deoxyribonucleotides with the helicate located in the center of the junction. NMR spectroscopic studies of the interaction between the M enantiomer of the helicate and two different oligonucleotides, [5'-d(TATGGTACCATA)]2 and [5'-d(CGTACG)]2, show that, in each case, the 2-fold symmetry of the helicate is lifted, while the 3-fold symmetry around the helicate axis is retained. The 1:3 helicate/DNA stoichiometry estimated from 1D NMR spectra supports a molecular model of a three-way junction composed of three strands. Three separate double-helical arms of the three-way junction are chemically identical giving rise to one set of proton resonances. The NOE contacts between the helicate and DNA unambiguously show that the helicate is fitted into the center of the three-way junction experiencing a hydrophobic 3-fold symmetric environment. Close stacking interactions between the ligand phenyl groups and the nucleotide bases are demonstrated through unusually large downfield shifts (1-2 ppm) of the phenyl protons. The unprecedented 3WJ arrangement observed in solution has also been found to exist in the crystal structure of the helicate adduct of [d(CGTACG)2] (Angew. Chem., Int. Ed. 2006, 45, 1227).     

Triptycene-based small molecules modulate (CAG)·(CTG) repeat junctions

Nucleic acid three-way junctions (3WJs) play key roles in biological processes such as nucleic acid replication in addition to being implicated as dynamic transient intermediates in trinucleotide repeat sequences. Structural modulation of specific nucleic acid junctions could allow for control of biological processes and disease states at the nucleic acid level. Trinucleotide repeat expansions are associated with several neurodegenerative diseases where dynamic slippage is thought to occur during replication, forming transient 3WJ intermediates with the complementary strand. Here, we report triptycene-based molecules that bind to a d(CAG)·(CTG) repeat using a gel shift assay, fluorescence-quenching and circular dichroism.     

The diverse behaviour of the P–Cl bonds in the spiro–cis–ansa spermidine derivative cyclotriphosphazene towards mono-functional nucleophilic reagents

A number of new spiro–ansa spermidine derivative cyclotriphosphazenes (2–10) is synthesized in order to provide insight into the reaction mechanism for nucleophilic substitution. The structures of the compounds were determined by elemental analysis, mass (MS), ¹H, ¹⁹F (for 9) and ³¹P NMR spectroscopies. Compounds (2–8) and 9, 10 can be formed by a proton abstraction–chloride elimination and both the and reaction mechanisms, respectively.     

Branchpoint expansion in a fully complementary three-way DNA junction

Branched nucleic acid molecules serve as key intermediates in DNA replication, recombination, and repair; architectural elements in RNA; and building blocks and functional components for nanoscience applications. Using a combination of high-resolution single-molecule FRET, time-resolved spectroscopy, and molecular modeling, we have probed the local and global structure of a DNA three-way junction (3WJ) in solution. We found that it adopts a Y-shaped, pyramidal structure, in which the bases adjacent to the branchpoint are unpaired, despite the full Watson-Crick complementarity of the molecule. The unpairing allows a nanoscale cavity to form at the junction center. Our structure accounts for earlier observations made of the structure, flexibility, and reactivity of 3WJs. We anticipate that these results will guide the development of new DNA-based supramolecular receptors and nanosystems.     

Linear dependency in the refinement of force constants with the Jacobian method

The Jacobian method in the refinement of force constants is studied. Theoretical and experimental frequencies and other observables, ν_s, are matched by minimizing Σ_sW_s(ν – ν)², where s = 1, 2, 3,…, proceeds over all normal modes and isotopes, and W_s are weighting factors. Modification of the theoretical frequencies is accomplished with the Jacobian matrix, J , with elements J_si = ?ν_s/?k_i involving each force constant or associated parameter, k_i, i = 1, 2, 3,…, by Δν = J Δ k . The parameters are adjusted directly with Δ k = ( J ^T WJ )^?1( JW ) Δν, where W is a diagonal matrix which weights the frequencies. The linear dependence problem must be addressed prior to inversion of J ^T WJ . The approach entails diagonalization of J ^T WJ , analysis of the components of the eigenvectors associated with zero and small eigenvalues, identification of the linearly dependent parameters, successive elimination of selective parameters, and a repeat of this procedure until linear dependency is removed. The Jacobian matrices are obtained by differencing the frequencies when the parameters are varied and by numerical and analytical evaluation of the derivative of the potential. The unitary transformation, U , used to calculate J = U ^T (? F /? k ) U or J = U ^T (Δ F /Δ k ) U , is obtained from the diagonalization of the Hessian, F_mn = ?²ν/?p_m?q_n, where p, q = x, y, z are the Cartesian coordinates for atoms m, n = 1, 2, 3,…, at the initial value of k_i, i = 1, 2, 3, ? The accuracy of and the ability to evaluate the Jacobian matrix by these methods are discussed. Applications to CH₄, H₂CO, C₂H₄, and C₂H₆ are presented. Linearly dependent and ill-conditioned parameters are identified and removed. The procedure is general for any observable quantity. © 1994 by John Wiley & Sons, Inc.     

A hexaazatriphenylene-based porous organic polymer for high performance supercapacitor

Porous organic polymers (POPs) with high physiochemical stability and pseudocapacitive activity are crucial for supercapacitors with high specific capacitance and long cycle life. We report herein a hexaazatrinaphthylene-based POP (HPOP-1) for high-performance supercapacitor by introducing redox-active hexaazatrinaphthylene (HATN) moiety through Sonogashira–Hagihara coupling reaction. HATN moiety can undergo a proton-induced electron transfer redox reaction, which endows HPOP-1 with high pseudocapacitive activity. As electrode materials for supercapacitor application, HPOP-1 exhibits high specific capacitance (667 F g⁻¹ at 0.5 A g⁻¹) and long-term cyclic stability (90% capacitance retention after 10,000 cycles at 5 A g⁻¹) in a three-electrode system with 1 M H₂SO₄ as the electrolyte. In addition, HPOP-1 also exhibits a specific capacitance of 376 F g⁻¹ at 0.5 A g⁻¹ in 1 M KOH electrolyte. An asymmetric supercapacitor was further fabricated with HPOP-1 as negative electrode and rGO as positive electrode, respectively. The device delivers a specific capacitance of 63 F g⁻¹ at 0.5 A g⁻¹ and a rate performance of 37 F g⁻¹ at 5 A g⁻¹. Our work provides a facile approach for the design and preparation of pseudocapacitive POPs with high specific capacitance and long cycle life.     

Manganese Oxide/Graphene Aerogel Composites as an Outstanding Supercapacitor Electrode Material

Graphene aerogels (GA), prepared with an organic sol–gel process, possessing a high specific surface area of 793 m² g^?1, a high pore volume of 3 cm³ g^?1, and a large average pore size of 17 nm, were applied as a support for manganese oxide for supercapacitor applications. The manganese oxide was electrochemically deposited into the highly porous GA to form MnO₂/GA composites. The composites, at a high manganese oxide loading of 61 wt. %, exhibited a high specific capacitance of 410 F g^?1 at 2 mV s^?1. More importantly, the high rate specific capacitances measured at 1000 mV s^?1 for these composites were two‐fold higher than those obtained with samples prepared in the absence of the GA support. The specific capacitance retention ratio, based on the specific capacitance obtained at 25 mV s^?1, was maintained high, at 85 %, even at the high scan rate of 1000 mV s^?1, in contrast with the significantly lower value of 67 % for the plain manganese oxide sample. For the cycling stability, the specific capacitance of the composite electrode decayed by only 5 % after 50,000 cycles at 1000 mV s^?1. The success of this MnO₂/GA composite may be attributed to the structural advantages of high specific surface areas, high pore volumes, large pore sizes, and three‐dimensionally well‐connected network of the GA support. These structural advantages made possible the high mass loading of the active material, manganese oxide, large amounts of electroactive surfaces for the superficial redox events, fast mass‐transfer within the porous structure, and well‐connected conductive paths for the involved charge transport.