A core–brush 3D DNA nanostructure: the next generation of DNA nanomachine for ultrasensitive sensing and imaging of intracellular microRNA with rapid kinetics

A highly loaded and integrated core–brush three-dimensional (3D) DNA nanostructure is constructed by programmatically assembling a locked DNA walking arm (DA) and hairpin substrate (HS) into a repetitive array along a well-designed DNA track generated by rolling circle amplification (RCA) and is applied as a 3D DNA nanomachine for rapid and sensitive intracellular microRNA (miRNA) imaging and sensing. Impressively, the homogeneous distribution of the DA and HS at a ratio of 1 : 3 on the DNA track provides a specific walking range for the DA to avoid invalid and random self-walking and notably improve the executive ability of the core–brush 3D DNA nanomachine, which easily solves the major technical challenges of traditional Au-based 3D DNA nanomachines: low loading capacity and low executive efficiency. As a proof of concept, the interaction of miRNA with the 3D DNA nanomachine could initiate the autonomous and progressive operation of the DA to cleave the HS for ultrasensitive ECL detection of target miRNA-21 with a detection limit as low as 3.57 aM and rapid imaging in living cells within 15 min. Therefore, the proposed core–brush 3D DNA nanomachine could not only provide convincing evidence for sensitive detection and rapid visual imaging of biomarkers with tiny change, but also assist researchers in investigating the formation mechanism of tumors, improving their recovery rates and reducing correlative complications. This strategy might enrich the method to design a new generation of 3D DNA nanomachine and promote the development of clinical diagnosis, targeted therapy and prognosis monitoring.

This study designed a highly loaded and integrated core–brush 3D DNA nanomachine for miRNA imaging and sensing, which easily solves the major technical challenges of traditional Au-based 3D nanomachines: low loading capacity and low executive efficiency.     

Cooperative stabilisation of 14-3-3σ protein–protein interactions via covalent protein modification

14-3-3 proteins are an important family of hub proteins that play important roles in many cellular processes via a large network of interactions with partner proteins. Many of these protein–protein interactions (PPI) are implicated in human diseases such as cancer and neurodegeneration. The stabilisation of selected 14-3-3 PPIs using drug-like ‘molecular glues’ is a novel therapeutic strategy with high potential. However, the examples reported to date have a number of drawbacks in terms of selectivity and potency. Here, we report that WR-1065, the active species of the approved drug amifostine, covalently modifies 14-3-3σ at an isoform-unique cysteine residue, Cys38. This modification leads to isoform-specific stabilisation of two 14-3-3σ PPIs in a manner that is cooperative with a well characterised molecular glue, fusicoccin A. Our findings reveal a novel stabilisation mechanism for 14-3-3σ, an isoform with particular involvement in cancer pathways. This mechanism can be exploited to harness the enhanced potency conveyed by covalent drug molecules and dual ligand cooperativity. This is demonstrated in two cancer cell lines whereby the cooperative behaviour of fusicoccin A and WR-1065 leads to enhanced efficacy for inducing cell death and attenuating cell growth.

The aminothiol WR-1065 covalently modifies 14-3-3σ to stabilse its interactions with p53 and ERα. It enhances the effect of fusicoccin A via a cooperative mechanism that leads to 14-3-3 partner-protein specific activty against cancer cells.      

Synchrotron X-ray 2D and 3D elemental imaging of CdSe/ZnS quantum dot nanoparticles in Daphnia magna

The potential toxicity of nanoparticles to aquatic organisms is of interest given that increased commercialization will inevitably lead to some instances of inadvertent environmental exposures. Cadmium selenide quantum dots (QDs) capped with zinc sulfide are used in the semiconductor industry and in cellular imaging. Their small size (<10 nm) suggests that they may be readily assimilated by exposed organisms. We exposed Daphnia magna to both red and green QDs and used synchrotron X-ray fluorescence to study the distribution of Zn and Se in the organism over a time period of 36 h. The QDs appeared to be confined to the gut, and there was no evidence of further assimilation into the organism. Zinc and Se fluorescence signals were highly correlated, suggesting that the QDs had not dissolved to any extent. There was no apparent difference between red or green QDs, i.e., there was no effect of QD size. 3D tomography confirmed that the QDs were exclusively in the gut area of the organism. It is possible that the QDs aggregated and were therefore too large to cross the gut wall.     

Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation

Predicting relative protein–ligand binding affinities is a central pillar of lead optimization efforts in structure-based drug design. The site identification by ligand competitive saturation (SILCS) methodology is based on functional group affinity patterns in the form of free energy maps that may be used to compute protein–ligand binding poses and affinities. Presented are results obtained from the SILCS methodology for a set of eight target proteins as reported originally in Wang et al. (J. Am. Chem. Soc., 2015, 137, 2695–2703) using free energy perturbation (FEP) methods in conjunction with enhanced sampling and cycle closure corrections. These eight targets have been subsequently studied by many other authors to compare the efficacy of their method while comparing with the outcomes of Wang et al. In this work, we present results for a total of 407 ligands on the eight targets and include specific analysis on the subset of 199 ligands considered previously. Using the SILCS methodology we can achieve an average accuracy of up to 77% and 74% when considering the eight targets with their 199 and 407 ligands, respectively, for rank-ordering ligand affinities as calculated by the percent correct metric. This accuracy increases to 82% and 80%, respectively, when the SILCS atomic free energy contributions are optimized using a Bayesian Markov-chain Monte Carlo approach. We also report other metrics including Pearson''s correlation coefficient, Pearlman''s predictive index, mean unsigned error, and root mean square error for both sets of ligands. The results obtained for the 199 ligands are compared with the outcomes of Wang et al. and other published works. Overall, the SILCS methodology yields similar or better-quality predictions without a priori need for known ligand orientations in terms of the different metrics when compared to current FEP approaches with significant computational savings while additionally offering quantitative estimates of individual atomic contributions to binding free energies. These results further validate the SILCS methodology as an accurate, computationally efficient tool to support lead optimization and drug discovery.

Predicting relative protein–ligand binding affinities is a central pillar of lead optimization efforts in structure-based drug design.     

Peptide-based inhibitors of protein–protein interactions: biophysical,structural and cellular consequences of introducing a constraint

Protein–protein interactions (PPIs) are implicated in the majority of cellular processes by enabling and regulating the function of individual proteins. Thus, PPIs represent high-value, but challenging targets for therapeutic intervention. The development of constrained peptides represents an emerging strategy to generate peptide-based PPI inhibitors, typically mediated by α-helices. The approach can confer significant benefits including enhanced affinity, stability and cellular penetration and is ingrained in the premise that pre-organization simultaneously pays the entropic cost of binding, prevents a peptide from adopting a protease compliant β-strand conformation and shields the hydrophilic amides from the hydrophobic membrane. This conceptual blueprint for the empirical design of peptide-based PPI inhibitors is an exciting and potentially lucrative way to effect successful PPI inhibitor drug-discovery. However, a plethora of more subtle effects may arise from the introduction of a constraint that include changes to binding dynamics, the mode of recognition and molecular properties. In this review, we summarise the influence of inserting constraints on biophysical, conformational, structural and cellular behaviour across a range of constraining chemistries and targets, to highlight the tremendous success that has been achieved with constrained peptides alongside emerging design opportunities and challenges.

This review summarizes the influence of inserting constraints on biophysical, conformational, structural and cellular behaviour for peptides targeting α-helix mediated protein–protein interactions.     

Design and synthesis of highly sensitive and selective fluorescein-derived magnesium fluorescent probes and application to intracellular 3D Mg2+ imaging

The role of intracellular magnesium ions is of high interest in the fields of pharmacology and cellular biology. To accomplish the dynamic and three-dimensional imaging of intracellular Mg2+, there is a strong desire for the development of optimized Mg2+ fluorescent probes. In this paper we describe the design, synthesis, and cellular application of the three novel Mg2+ fluorescent probes KMG-101, -103, and -104. The compounds of this series feature a charged beta-diketone as a binding site specific for Mg2+ and a fluorescein residue as the fluorophore that can be excited with an Ar+ laser such as is widely used in confocal scanning microscopy. This molecular design leads to an intensive off-on-type fluorescent response toward Mg2+ ions. The two fluorescent probes KMG-103 and -104 showed suitable dissociation constants (Kd,Mg2+ = 2 mM) and nearly a 10-fold fluorescence enhancement over the intracellular magnesium ion concentration range (0.1-6 mM), allowing high-contrast, sensitive, and selective Mg2+ measurements. For intracellular applications, the membrane-permeable probe KMG-104AM was synthesized and successfully incorporated into PC12 cells. Upon application of the mitochondria uncoupler FCCP to the probe-incorporated cells, the resulting increase in the free magnesium ion concentration could be followed over time. By using a confocal microscope, the intracellular 3D magnesium ion concentration distributions were satisfactorily observed.     

Unambiguous Intracellular Localization and Quantification of a Potent Iridium Anticancer Compound by Correlative 3D Cryo X‐Ray Imaging

The iridium half‐sandwich complex [Ir(η⁵:κ¹‐C₅Me₄CH₂py)(2‐phenylpyridine)]PF₆ is highly cytotoxic: 15–250× more potent than clinically used cisplatin in several cancer cell lines. We have developed a correlative 3D cryo X‐ray imaging approach to specifically localize and quantify iridium within the whole hydrated cell at nanometer resolution. By means of cryo soft X‐ray tomography (cryo‐SXT), which provides the cellular ultrastructure at 50 nm resolution, and cryo hard X‐ray fluorescence tomography (cryo‐XRF), which provides the elemental sensitivity with a 70 nm step size, we have located the iridium anticancer agent exclusively in the mitochondria. Our methodology provides unique information on the intracellular fate of the metallodrug, without chemical fixation, labeling, or mechanical manipulation of the cells. This cryo‐3D correlative imaging method can be applied to a number of biochemical processes for specific elemental localization within the native cellular landscape.     

Jahn-Teller effect in CH3D+ and CD3H+: conformational isomerism, tunneling-rotation structure, and the location of conical intersections

High-resolution pulsed-field-ionization zero-kinetic-energy photoelectron spectra of CH(3)D and CD(3)H have been recorded at rotational resolution from the adiabatic ionization energy up to 600 cm(-1) of internal energy of the respective cations. The spectra are characterized by the effects of a large-amplitude pseudorotational motion exchanging the equivalent nuclei in each molecule. With increasing internal energy, a transition from the tunneling regime with splittings of the order of 1-10 cm(-1) to the free pseudorotation regime is observed. A theoretical model that treats the simultaneous rotational and pseudorotational motions and incorporates the effects of the geometric phase has been developed. The model provides the appropriate rovibronic symmetries in the C(3v)(M) molecular symmetry group and reaches a near-quantitative agreement with the experimental data. The complete group-theoretical analysis of the rovibronic problem is also given. The analysis of the spectra has revealed the existence of two different isomers for both CH(3)D(+) and CD(3)H(+), which differ in the bond length between the carbon atom and the unique ligand atom. All isomers are subject to a fast pseudorotational motion between three equivalent minima with a period of 3-5 ps in CH(3)D(+) and 18-28 ps in CD(3)H(+). The analysis has also provided the ordering of the tunneling sublevels for each isomer, which enables the location of the twofold conical intersections on the potential energy surface that could not be determined from experiments on CH(4) (+).     

3D nanoscale imaging of the yeast, Schizosaccharomyces pombe, by full-field transmission X-ray microscopy at 5.4 keV

Three-dimensional (3D) nanoscale structures of the fission yeast, Schizosaccharomyces pombe, can be obtained by full-field transmission hard X-ray microscopy with 30 nm resolution using synchrotron radiation sources. Sample preparation is relatively simple and the samples are portable across various imaging environments, allowing for high-throughput sample screening. The yeast cells were fixed and double-stained with Reynold's lead citrate and uranyl acetate. We performed both absorption contrast and Zernike phase contrast imaging on these cells in order to test this method. The membranes, nucleus, and subcellular organelles of the cells were clearly visualized using absorption contrast mode. The X-ray images of the cells could be used to study the spatial distributions of the organelles in the cells. These results show unique structural information, demonstrating that hard X-ray microscopy is a complementary method for imaging and analyzing biological samples.     

A new SIMS paradigm for 2D and 3D molecular imaging of bio-systems

With the implementation of focused primary ion beams, secondary ion mass spectrometry (SIMS) has become a significant technique in the rapidly emerging field of mass spectral imaging in the biological sciences. Liquid metal ion guns (LMIG) offered the prospect of sub-100 nm spatial resolution, however this aspiration has yet to be reached for molecular imaging. This brief review shows that using LMIG the limitations of the static limit and low ionization probability will restrict useful imaging to around 2 μm spatial resolution with high-yield molecules. The only prospect of going beyond this in the absence of factors of 100 increase in ionization probability is to use polyatomic ion beams such as C₆₀⁺, for which bombardment induced damage is low. In these cases sub-micron imaging becomes possible, using voxels together with molecular depth profiling and 3D imaging. The discussion shows that conventional ToF-SIMS instrumentation then becomes a limitation in that the pulsed ion beam has a very low duty cycle which results in inordinately long analysis times, and pulsing the beam means that high-mass resolution and high spatial resolution are mutually incompatible. New instrumental configurations are described that allow the use of a dc ion beam and separate the mass spectrometry for the ion formation process. Early results from these instruments suggest that sub-micron analysis and imaging with high mass resolution and good ion yields are now realizable, although the low ion yield issue still needs to be solved.     

Benzothiadiazole vs. iso-Benzothiadiazole: Synthesis,Electrochemical and Optical Properties of D–A–D Conjugated Molecules Based on Them

This paper presents an improved synthesis of 4,7-dibromobenzo[d][1,2,3]thiadiazole from commercially available reagents. According to quantum-mechanical calculations, benzo[d][1,2,3]thiadiazole (isoBTD) has higher values of E_LUMO and energy band gap (E_g), which indicates high electron conductivity, occurring due to the high stability of the molecule in the excited state. We studied the cross-coupling reactions of this dibromide and found that the highest yields of π-spacer–acceptor–π-spacer type compounds were obtained by means of the Stille reaction. Therefore, 6 new structures of this type have been synthesized. A detailed study of the optical and electrochemical properties of the obtained π-spacer–acceptor–π-spacer type compounds in comparison with isomeric structures based on benzo[c][1,2,5]thiadiazole (BTD) showed a red shift of absorption maxima with lower absorptive and luminescent capacity. However, the addition of the 2,2′-bithiophene fragment as a π-spacer resulted in an unexpected increase of the extinction coefficient in the UV/vis spectra along with a blue shift of both absorption maxima for the isoBTD-based compound as compared to the BTD-based compound. Thus, a thorough selection of components in the designing of appropriate compounds with benzo[d][1,2,3]thiadiazole as an internal acceptor can lead to promising photovoltaic materials.     

Structural Characterization of Cis– and Trans–Pt(NH3)2Cl2 Conjugations with Chitosan Nanoparticles

The conjugation of chitosan 15 and 100 KD with anticancer drugs cis– and trans–Pt (NH₃)₂Cl₂ (abbreviated cis–Pt and trans–Pt) were studied at pH 5–6. Using multiple spectroscopic methods and thermodynamic analysis to characterize the nature of drug–chitosan interactions and the potential application of chitosan nanoparticles in drug delivery. Analysis showed that both hydrophobic and hydrophilic contacts are involved in drug–polymer interactions, while chitosan size and charge play a major role in the stability of drug–polymer complexes. The overall binding constants are K_{ch–15–cis–Pt} = 1.44 (±0.6) × 10⁵ M⁻¹, K_{ch–100–cis–Pt} = 1.89 (±0.9) × 10⁵ M⁻¹ and K_{ch–15–trans–Pt} = 9.84 (±0.5) × 10⁴ M⁻¹, and K_{ch–100–trans–Pt} = 1.15 (±0.6) × 10⁵ M⁻¹. More stable complexes were formed with cis–Pt than with trans–Pt–chitosan adducts, while stronger binding was observed for chitosan 100 in comparison to chitosan 15 KD. This study indicates that polymer chitosan 100 is a stronger drug carrier than chitosan 15 KD in vitro.     

From 2D framework to quasi-1D nanomaterial: preparation,characterization, and formation mechanism of Cu(3)SnS(4) nanorods

An ion-ion reaction route under solvothermal condition at relatively low temperatures was first put forward to the preparation of tetragonal Cu(3)SnS(4) nanorods, on the basis of the strategy that 2D framework structure of Cu(3)SnS(4) containing layers could provide orientation for the growth of quasi-1D nanomaterials. X-ray diffraction (XRD) pattern, transmission electronic microscope (TEM) images, electronic diffraction (ED) pattern, X-ray photoelectron spectra (XPS), energy-dispersive X-ray analysis (EDXA), M?ssbauer spectrum, Raman spectrum, thermal analysis (DTA and TGA), ultraviolet and visible light (UV-vis) spectrum, and photoluminescence (PL) spectrum were used to characterize the products. On the basis of a series of supplementary experiments and the result of infrared absorption spectrum (IR), a reaction mechanism was proposed: ethanol as solvent and reductant and trace water/CH(3)CSNH(2) as sulfur source and acid-making components could form 2D network through hydrogen bonds, which provided the orientation for the formation of a 2D framework structure; appropriate concentration of CH(3)CSNH(2), warming speed, reaction constant temperatures (T(rc)), and reaction time also played important roles.     

Unambiguous Intracellular Localization and Quantification of a Potent Iridium Anticancer Compound by Correlative 3D Cryo X-Ray Imaging

The iridium half-sandwich complex [Ir(η⁵:κ¹-C₅Me₄CH₂py)(2-phenylpyridine)]PF₆ is highly cytotoxic: 15–250× more potent than clinically used cisplatin in several cancer cell lines. We have developed a correlative 3D cryo X-ray imaging approach to specifically localize and quantify iridium within the whole hydrated cell at nanometer resolution. By means of cryo soft X-ray tomography (cryo-SXT), which provides the cellular ultrastructure at 50 nm resolution, and cryo hard X-ray fluorescence tomography (cryo-XRF), which provides the elemental sensitivity with a 70 nm step size, we have located the iridium anticancer agent exclusively in the mitochondria. Our methodology provides unique information on the intracellular fate of the metallodrug, without chemical fixation, labeling, or mechanical manipulation of the cells. This cryo-3D correlative imaging method can be applied to a number of biochemical processes for specific elemental localization within the native cellular landscape.     

XPS for non-destructive depth profiling and 3D imaging of surface nanostructures

Depth profiling of nanostructures is of high importance both technologically and fundamentally. Therefore, many different methods have been developed for determination of the depth distribution of atoms, for example ion beam (e.g. O₂⁺, Ar⁺) sputtering, low-damage C₆₀ cluster ion sputtering for depth profiling of organic materials, water droplet cluster ion beam depth profiling, ion-probing techniques (Rutherford backscattering spectroscopy (RBS), secondary-ion mass spectroscopy (SIMS) and glow-discharge optical emission spectroscopy (GDOES)), X-ray microanalysis using the electron probe variation technique combined with Monte Carlo calculations, angle-resolved XPS (ARXPS), and X-ray photoelectron spectroscopy (XPS) peak-shape analysis. Each of the depth profiling techniques has its own advantages and disadvantages. However, in many cases, non-destructive techniques are preferred; these include ARXPS and XPS peak-shape analysis. The former together with parallel factor analysis is suitable for giving an overall understanding of chemistry and morphology with depth. It works very well for flat surfaces but it fails for rough or nanostructured surfaces because of the shadowing effect. In the latter method shadowing effects can be avoided because only a single spectrum is used in the analysis and this may be taken at near normal emission angle. It is a rather robust means of determining atom depth distributions on the nanoscale both for large-area XPS analysis and for imaging. We critically discuss some of the techniques mentioned above and show that both ARXPS imaging and, particularly, XPS peak-shape analysis for 3D imaging of nanostructures are very promising techniques and open a gateway for visualizing nanostructures.     

Strong enhancement of two-photon absorption properties in synergic ‘semi-disconnected’ multiporphyrin assemblies designed for combined imaging and photodynamic therapy

The synthesis and photophysical properties of new multiporphyrin assemblies are described. Their design, based on a smooth electronic disconnection between two-photon absorbing (2PA) octupolar or quadrupolar cores and the peripheral porphyrins, leads to a major increase in (non-resonant) 2PA responses in the NIR, while fully retaining the fluorescence and photosensitization properties of isolated porphyrins. This approach, which involves electronic coupling of semi-disconnected moieties in the higher excited states of the synergic systems, is of interest to fully benefit from the advantages of selective 2PA for application in combined two-photon high resolution imaging and photodynamic therapy.     

Preparation and characterization of organic–inorganic hybrids and coating films from 3‐methacryloxypropylpolysilsesquioxane

3‐Methacryloxypropylpolysilsesquioxane (MA‐PS) was prepared by acid‐ or base‐catalyzed hydrolytic polycondensation of 3‐methacryloxypropyltrimethoxysilane (MAS). MA‐PS coating film was prepared by dip‐coating on organic, metal and inorganic substrates, including poly(ethylene terephthalate), aluminum, stainless steel, and glass. The coating films on poly(ethylene terephthalate) and glass showed high adhesive strength. The hardness of coating films increased with increasing heat treatment temperature, whereas they decreased with increasing H₂O/MAS molar ratio. The refractive index of coating films increased with increasing heat treatment temperature. In addition, flat and transparent free‐standing films (0.24–0.27 mm thickness) were prepared from MA‐PS that were crack‐free after heat treatment at 1000 °C. Copyright © 2001 John Wiley & Sons, Ltd.