Inhibitor-GCPII Interaction: Selective and Robust System for Targeting Cancer Cells with Structurally Diverse Nanoparticles

Topical siRNA therapy of diabetic-like wound healing

Non-healing wounds are a serious complication in diabetic patients. One of the detrimental factors contributing to limited wound healing is the accumulation of metalloproteinase-9 (MMP-9) in the wound. Selective inhibition of MMP-9 is one of the established therapeutic targets for diabetic wound healing. Here, a functional and biocompatible wound dressing is developed to enable a controlled release of a traceable vector loaded with the antisense siRNA against MMP-9 in the wound. The dressing consists of degradable polymer nanofibers embedded with a vector nanosystem - polymer-coated fluorescent nanodiamonds optimized for the binding of siRNA and colloidal stability of nanodiamond-siRNA complexes in a physiological environment. The developed dressing is tested on murine fibroblasts and also applied to wounds in a diabetic murine model to evaluate its suitability in terms of in vivo toxicity, biological efficacy, and handling. The treatment results in significant local inhibition of MMP-9 and a shortening of the wound healing time. The scar formation in treated diabetic-like mice becomes comparable with that in non-treated diabetes-free mice. Our results suggest that the application of our biocompatible dressing loaded with a non-toxic vector nanosystem is an effective and promising approach to gene therapy of non-healing wounds.

Iridium-based Polymeric Multifunctional Imaging Tools for Biochemistry

Herein, we report the development of a macromolecular multifunctional imaging tool for biological investigations, which is comprised of an N-(2-hydroxypropyl)methacrylamide backbone, iridium-based luminescent probe, glutamate carboxypeptidase II (GCPII) targeting ligand, and biotin affinity tag. The iridium luminophore is a tris-cyclometalated complex based on [Ir(ppy)3] with one of its 2-phenylpyridine ligands functionalized to allow conjugation. Synthesized macromolecular probes differed in the structure of the polymer and content of the iridium complex. The applicability of the developed imaging tools has been tested in flow cytometry (FACS) based assay, laser confocal microscopy, and fluorescence lifetime imaging microscopy (FLIM). The FACS analysis has shown that the targeted iBodies containing the iridium luminophore exhibit selective labelling of GCPII expressing cells. This observation was also confirmed in the imaging experiments with laser confocal microscopy. The FLIM experiment has shown that the iBodies with the iridium label exhibit a lifetime greater than 100 ns, which distinguishes them from typically used systems labelled with organic fluorophores exhibiting short fluorescence lifetimes. The results of this investigation indicate that the system exhibits interesting properties, which supports the development of additional biological tools utilizing the key components (iridium complexes, iBody concept), primarily focusing on the longer lifetime of the iridium emitter.

Cellular uptake and fate of cationic polymer-coated nanodiamonds delivering siRNA: a mechanistic study

Gene silencing using small interfering RNAs (siRNAs) is a selective and promising approach for treatment of numerous diseases. However, broad applications of siRNAs are compromised by their low stability in a biological environment and limited ability to penetrate cells. Nanodiamonds (NDs) coated with cationic polymers can enable cellular delivery of siRNAs. Recently, we developed a new type of ND coating based on a random copolymer consisting of (2-dimethylaminoethyl) methacrylate (DMAEMA) and N-(2-hydroxypropyl) methacrylamide (HPMA) monomers. These hybrid ND-polymer particles (Cop+-FND) provide near-infrared fluorescence, form stable complexes with siRNA in serum, show low toxicity, and effectively deliver siRNA into cells in vitro and in vivo. Here, we present data on the mechanism of cellular uptake and cell trafficking of Cop+-FND : siRNA complexes and their ability to selectively suppress mRNA levels, as well as their cytotoxicity, viability and colloidal stability. We identified clathrin-mediated endocytosis as the predominant entry mechanism for Cop+-FND : siRNA into U-2 OS human bone osteosarcoma cells, with a substantial fraction of Cop+-FND : siRNA following the lysosome pathway. Cop+-FND : siRNA potently inhibited the target GAPDH gene with negligible toxicity and sufficient colloidal stability. Based on our results, we suggest that Cop+-FND : siRNA can serve as a suitable in vivo delivery system for siRNA.

Production, surface modification, physicochemical properties, biocompatibility, and bioimaging applications of nanodiamonds

Nanodiamonds (ND) are chemically inert and stable owing to their sp3 covalent bonding structure, but their surface sp2 graphitic carbons can be easily homogenized with diverse functional groups via oxidation, reduction, hydrogenation, amination, and halogenation. Further surface conjugation of NDs with hydrophilic ligands can boost their colloidal stability and functionality. In addition, NDs are non-toxic as they are made of carbons. They exhibit stable fluorescence without photobleaching. They also possess paramagnetic and ferromagnetic properties, making them suitable for use as a new type of fluorescence imaging (FI) and magnetic resonance imaging (MRI) probe. In this review, we focused on recently developed ND production methods, surface homogenization and functionalization methods, biocompatibilities, and biomedical imaging applications as FI and MRI probes. Finally, we discussed future perspectives.

In vitro evolution reveals non-cationic protein-RNA interaction mediated by metal ions

RNA–peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA–protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 10¹⁰ library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K⁺/Mg²⁺) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein–RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.

Virus-Based Supramolecular Structure and Materials: Concept and Prospects

Rodlike and spherelike viruses are various monodisperse nanoparticles that can display small molecules or polymers with unique distribution following chemical modifications. Because of the monodisperse property, aggregates in synthetic protein-polymer nanoparticles could be eliminated, thus improving the probability for application in protein-polymer drug. In addition, the monodisperse virus could direct the growth of metal materials or inorganic materials, finding applications in hydrogel, drug delivery, and optoelectronic and catalysis materials. Benefiting from the advantages, the virus or viruslike particles have been widely explored in the field of supramolecular chemistry. In this review, we describe the modification and application of virus and viruslike particles in surpramolecular structures and biomedical research.

Toward Quantitative Bio-sensing with Nitrogen-Vacancy Center in Diamond

The long-dreamed-of capability of monitoring the molecular machinery in living systems has not been realized yet, mainly due to the technical limitations of current sensing technologies. However, recently emerging quantum sensors are showing great promise for molecular detection and imaging. One of such sensing qubits is the nitrogen-vacancy (NV) center, a photoluminescent impurity in a diamond lattice with unique room-temperature optical and spin properties. This atomic-sized quantum emitter has the ability to quantitatively measure nanoscale electromagnetic fields via optical means at ambient conditions. Moreover, the unlimited photostability of NV centers, combined with the excellent diamond biocompatibility and the possibility of diamond nanoparticles internalization into the living cells, makes NV-based sensors one of the most promising and versatile platforms for various life-science applications. In this review, we will summarize the latest developments of NV-based quantum sensing with a focus on biomedical applications, including measurements of magnetic biomaterials, intracellular temperature, localized physiological species, action potentials, and electronic and nuclear spins. We will also outline the main unresolved challenges and provide future perspectives of many promising aspects of NV-based bio-sensing.

The role of the biotin linker in polymer antibody mimetics, iBodies, in biochemical assays

We investigated the effect of a linker between the polymer backbone and biotin, and the influence of the number of biotins per polymer chain as well as the biotin position on the polymer chain on the efficacy of the ELISA or pull-down assays.

Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer

Prostate-specific membrane antigen (PSMA) is a well-characterized tumor marker associated with prostate cancer and neovasculature of most solid tumors. PSMA-specific ligands are thus being developed to deliver imaging or therapeutic agents to cancer cells. Here, we report on a crystal structure of human PSMA in complex with A9g, a 43-bp PSMA-specific RNA aptamer, that was determined to the 2.2 Å resolution limit. The analysis of the PSMA/aptamer interface allows for identification of key interactions critical for nanomolar binding affinity and high selectivity of A9g for human PSMA. Combined with in silico modeling, site-directed mutagenesis, inhibition experiments and cell-based assays, the structure also provides an insight into structural changes of the aptamer and PSMA upon complex formation, mechanistic explanation for inhibition of the PSMA enzymatic activity by A9g as well as its ligand-selective competition with small molecules targeting the internal pocket of the enzyme. Additionally, comparison with published protein-RNA aptamer structures pointed toward more general features governing protein-aptamer interactions. Finally, our findings can be exploited for the structure-assisted design of future A9g-based derivatives with improved binding and stability characteristics.

Nanoscale Dynamic Readout of a Chemical Redox Process Using Radicals Coupled with Nitrogen-Vacancy Centers in Nanodiamonds

Biocompatible nanoscale probes for sensitive detection of paramagnetic species and molecules associated with their (bio)chemical transformations would provide a desirable tool for a better understanding of cellular redox processes. Here, we describe an analytical tool based on quantum sensing techniques. We magnetically coupled negatively charged nitrogen-vacancy (NV) centers in nanodiamonds (NDs) with nitroxide radicals present in a bioinert polymer coating of the NDs. We demonstrated that the T₁ spin relaxation time of the NV centers is very sensitive to the number of nitroxide radicals, with a resolution down to ∼10 spins per ND (detection of approximately 10^-23 mol in a localized volume). The detection is based on T₁ shortening upon the radical attachment, and we propose a theoretical model describing this phenomenon. We further show that this colloidally stable, water-soluble system can be used dynamically for spatiotemporal readout of a redox chemical process (oxidation of ascorbic acid) occurring near the ND surface in an aqueous environment under ambient conditions.