Synthesis of stable peptide nucleic acid-modified gold nanoparticles and their assembly onto gold surfaces

Nanoligomers Targeting Human miRNA for the Treatment of Severe COVID-19 Are Safe and Nontoxic in Mice

The devastating effects of the coronavirus disease 2019 (COVID-19) pandemic have made clear a global necessity for antiviral strategies. Most fatalities associated with infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) result at least partially from uncontrolled host immune response. Here, we use an antisense compound targeting a previously identified microRNA (miRNA) linked to severe cases of COVID-19. The compound binds specifically to the miRNA in question, miR-2392, which is produced by human cells in several disease states. The safety and biodistribution of this compound were tested in a mouse model via intranasal, intraperitoneal, and intravenous administration. The compound did not cause any toxic responses in mice based on measured parameters, including body weight, serum biomarkers for inflammation, and organ histopathology. No immunogenicity from the compound was observed with any administration route. Intranasal administration resulted in excellent and rapid biodistribution to the lungs, the main site of infection for SARS-CoV-2. Pharmacokinetic and biodistribution studies reveal delivery to different organs, including lungs, liver, kidneys, and spleen. The compound was largely cleared through the kidneys and excreted via the urine, with no accumulation observed in first-pass organs. The compound is concluded to be a safe potential antiviral treatment for COVID-19.

Cyclopentane peptide nucleic acid: Gold nanoparticle conjugates for the detection of nucleic acids in a microfluidic format

Routine patient testing for viral infections is critical to identify infected individuals for treatment and to prevent spreading of infections to others. Developing robust and reliable diagnostic tools to detect nucleic acids of viruses at the point-of-care could greatly assist the clinical management of viral infections. The remarkable stability and high binding affinity of peptide nucleic acids (PNAs) to target nucleic acids could make PNA-based biosensors an excellent starting point to develop new nucleic acid detection technologies. We report the application of cyclopentane-modified PNAs to capture target nucleic acids in a microfluidic channel, and the use of bioorthogonal PNAs conjugated to gold nanoparticles as probes to semi-quantitatively signal the presence of a target nucleic acid derived from HIV-1. The basic results presented could be used to develop more advanced devices to detect nucleic acids from viruses such as HIV, SARS-CoV-2, and a wide range of other human diseases.

Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly

The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.

PNA-Based MicroRNA Detection Methodologies

MicroRNAs (miRNAs or miRs) are small noncoding RNAs involved in the fine regulation of post-transcriptional processes in the cell. The physiological levels of these short (20-22-mer) oligonucleotides are important for the homeostasis of the organism, and therefore dysregulation can lead to the onset of cancer and other pathologies. Their importance as biomarkers is constantly growing and, in this context, detection methods based on the hybridization to peptide nucleic acids (PNAs) are gaining their place in the spotlight. After a brief overview of their biogenesis, this review will discuss the significance of targeting miR, providing a wide range of PNA-based approaches to detect them at biologically significant concentrations, based on electrochemical, fluorescence and colorimetric assays.

Exploiting Double Exchange Diels-Alder Cycloadditions for Immobilization of Peptide Nucleic Acids on Gold Nanoparticles

The generation of PNA-decorated gold nanoparticles (AuNPs) has revealed to be more difficult as compared to the generation of DNA-functionalized ones. The less polar nature of this artificial nucleic acid system and the associated tendency of the neutral poly-amidic backbone to aspecifically adsorb onto the gold surface rather than forming a covalent bond through gold-thiol interaction, combined with the low solubility of PNAs itself, form the main limiting factors in the functionalization of AuNP. Here, we provide a convenient methodology that allows to easily conjugate PNAs to AuNP. Positively charged PNAs containing a masked furan moiety were immobilized via a double exchange Diels-Alder cycloaddition onto masked maleimide-functionalized AuNPs in a one-pot fashion. Conjugated PNA strands retain their ability to selectively hybridize with target DNA strands. Moreover, the duplexes resulting from hybridization can be detached through a retro-Diels-Alder reaction, thus allowing straightforward catch-and-release of specific nucleic acid targets.

Gold nanoparticles and angiogenesis: molecular mechanisms and biomedical applications

Angiogenesis is the formation of new blood vessels from pre-existing vessels. It is a highly regulated process as determined by the interplay between pro-angiogenic and anti-angiogenic factors. Under certain conditions the balance between angiogenesis stimulators and inhibitors is altered, which results in a shift from physiological to pathological angiogenesis. Therefore, the goal of therapeutic targeting of angiogenic process is to normalize vasculature in target tissues by enhancing angiogenesis in disease conditions of reduced vascularity and blood flow, such as tissue ischemia, or alternatively to inhibit excessive and abnormal angiogenesis in disorders like cancer. Gold nanoparticles (AuNPs) are special particles that are generated by nanotechnology and composed of an inorganic core containing gold which is encircled by an organic monolayer. The ability of AuNPs to alter vasculature has captured recent attention in medical literature as potential therapeutic agents for the management of pathologic angiogenesis. This review provides an overview of the effects of AuNPs on angiogenesis and the molecular mechanisms and biomedical applications associated with their effects. In addition, the main synthesis methods, physical properties, uptake mechanisms, and toxicity of AuNPs are briefly summarized.

Quantum Dot-PNA Conjugates for Target-Catalyzed RNA Detection

Detection of pathogenic nucleic acids remains one of the most reliable approaches for the diagnosis of a broad range of diseases. Current PCR-based methods require experienced personnel and cannot be easily used for point-of-care diagnostics, making alternative strategies for the sensitive, reliable, and cost-efficient detection of pathogenic nucleic acids highly desirable. Here, we report an enzyme-free method for the fluorometric detection of RNA that relies on a target-induced fluorophore transfer onto a semiconductor quantum dot (QD), uses PNA probes as selective recognition elements and can be read out with simple and inexpensive equipment. For QD-PNA conjugates with optimized PNA content, limits of detection of dengue RNA in the range of 10 pM to 100 nM can be realized within 5 h in the presence of a high excess of noncomplementary RNA.

Peptide-templated noble metal catalysts: syntheses and applications

Noble metal catalysts have been widely used in many applications because of their high activity and selectivity. However, a controllable preparation of noble metal catalysts still remains as a significant challenge. To overcome this challenge, peptide templates can play a critical role in the controllable syntheses of catalysts owing to their flexible binding with specific metallic surfaces and self-assembly characteristics. By employing peptide templates, the size, shape, facet, structure, and composition of obtained catalysts can all be specifically controlled under the mild synthesis conditions. In addition, catalysts with spherical, nanofiber, and nanofilm structures can all be produced by associating with the self-assembly characteristics of peptide templates. Furthermore, the peptide-templated noble metal catalysts also reveal significantly enhanced catalytic behaviours compared with conventional catalysts because the electron conductivity, metal dispersion, and reactive site exposure can all be improved. In this review, we summarize the research progresses in the syntheses of peptide-templated noble metal catalysts. The applications of the peptide-templated catalysts in organic reactions, photocatalysis, and electrocatalysis are discussed, and the relationship between structure and activity of these catalysts are addressed. Future opportunities, including new catalytic materials designed by using biological principles, are indicated to achieve selective, eco-friendly, and energy neutral synthesis approaches.

A Bifunctional Monomer for On-Resin Synthesis of Polyfunctional PNAs and Tailored Induced-Fit Switching Probes

A synthetic strategy for the production of polyfunctional PNAs bearing substituent groups both on the nucleobase and on the backbone C5 carbon of the same monomer is described; this is based on the use of a tris-orthogonally protected monomer and subsequent solid-phase selective functionalization. This strategy can be used for synthesizing PNAs that are not readily accessible by use of preformed modified monomers. As an example, a PNA-based probe that undergoes a switch in its fluorescence emission upon hybridization with a target oligonucleotide, induced by tailor-made movement of two pyrene substituent groups, was synthesized.

Insertion of organometallic moieties into peptides and peptide nucleic acids using alternative “click” strategies

Application of alternative “click” strategies (metal-free photoclick and one-pot click) to cymantrene and ferrocene derivatives yielded novel metal-containing conjugates.

In vivo demonstration of an active tumor pretargeting approach with peptide nucleic acid bioconjugates as complementary system

A novel, promising strategy for cancer diagnosis and therapy is the use of a pretargeting approach. For this purpose, the non-natural DNA/RNA analogues Peptide Nucleic Acids (PNAs) are ideal candidates as in vivo recognition units due to their high metabolic stability and lack of unspecific accumulation. In the pretargeting approach, an unlabeled, highly specific antibody-PNA conjugate has sufficient time to target a tumor before administration of a small fast-clearing radiolabeled complementary PNA that hybridizes with the antibody-PNA conjugate at the tumor site. Herein, we report the first successful application of this multistep process using a PNA-modified epidermal growth factor receptor (EGFR) specific antibody (cetuximab) and a complementary 99mTc-labeled PNA. In vivo studies on tumor bearing mice demonstrated a rapid and efficient in vivo hybridization of the radiolabeled PNA with the antibody-PNA conjugate. Decisively, a high specific tumor accumulation was observed with a tumor-to-muscle ratio of >8, resulting in a clear visualization of the tumor by single photon emission computed tomography (SPECT).

Nanoparticles selectively immobilized onto large arrays of gold micro and nanostructures through surface chemical functionalizations

Latex nanoparticles (100nm and 200nm diameter) were precisely located onto the gold regions of micro and nanopatterned gold/silica substrates through surface chemical functionalizations. The gold patterns were selectively functionalized with alkylthiols bearing biotin or amine headgroups. This selective functionalization allowed the trapping of streptavidin- or carboxy-functionalized latex nanoparticles onto the gold structures with very little non-specific adsorption onto the surrounding silica. Quantitative data of nanoparticle capture on gold and silica, obtained through SEM image analysis, showed a one to two order of magnitude increase on gold with a similar low coverage on silica (non-specific adsorption) thanks to chemical functionalizations. Single nanoparticles were captured at the gap of dimer gold nanostructures.

Strategy for Internal Labeling of Large RNAs with Minimal Perturbation by Using Fluorescent PNA

Fluorescence techniques for the investigation of biomolecules and their folding pathways require an efficient labeling strategy. A common method to internally label large RNAs involves the introduction of long loops for hybridization of fluorophore-carrying DNA strands. Such loops often disturb the structure, and thus the functionality, of the RNA. Here we show, in a proof of concept study with a >600 nucleotide group II intron ribozyme, that the usage of the nucleic acid analogue peptide nucleic acid (PNA) is more efficient in several aspects, minimizing the required structural modifications of the RNA. We demonstrate by various methods, including smFRET, that much smaller concentrations and shorter PNAs can be applied, compared to DNA, for rapid and specific internal RNA labeling. The folding pathway and catalytic activity of this large ribozyme is only minimally affected by the PNA, but the background signal is significantly reduced.

Biocompatible gold nanorods: one-step surface functionalization, highly colloidal stability, and low cytotoxicity

The conjugation of gold nanorods (AuNRs) with polyethylene glycol (PEG) is one of the most effective ways to reduce their cytotoxicity arising from the cetyltrimethylammonium bromide (CTAB) and silver ions used in their synthesis. However, typical PEGylation occurs only at the tips of the AuNRs, producing partially modified AuNRs. To address this issue, we have developed a novel, facile, one-step surface functionalization method that involves the use of Tween 20 to stabilize AuNRs, bis(p-sulfonatophenyl)phenylphosphine (BSPP) to activate the AuNR surface for the subsequent PEGylation, and NaCl to etch silver from the AuNRs. This method allows for the complete removal of the surface-bound CTAB and the most active surface silver from the AuNRs. The produced AuNRs showed far lower toxicity than other methods to PEGylate AuNRs, with no apparent toxicity when their concentration is lower than 5 μg/mL. Even at a high concentration of 80 μg/mL, their cell viability is still four times higher than that of the tip-modified AuNRs.

Synthesis, optical properties, and electronic structures of nucleobase-containing π-conjugated oligomers

The molecular recognition properties of the nucleobases instruct the formation of complex three-dimensional architectures in natural and synthetic systems; relatively unexplored is their use as building blocks for π-conjugated materials where they might mutually tune electronic and supramolecular structures. Toward this goal, an introductory set (1a-d and 2a-d) of six purine-terminated and two pyrimidine-terminated π-conjugated oligomers has been synthesized and used to develop experimental electronic and photophysical structure-property trends. Unlike 2,2':5',2″-terthiophene (TTT) derivatives 2a-d, intramolecular charge transfer dominates oligomers 1a-d bearing a 4,7-bisthienylbenzothiadiazole (TBT) spacer due to the strong electron-accepting ability of its benzothiadiazole (BTD) ring. The resulting donor-acceptor-donor systems feature lower HOMO-LUMO gaps than the terthiophene-linked nucleobases (ΔE(g) ∼ 1.8 eV vs 2.4 eV based on electrochemical measurements), and the lowest so far for π-conjugated molecules that include nucleobases within the π-framework. Experiments reveal a dependence of photophysical and electronic structure on the nature of the nucleobase and are in good agreement with theoretical calculations performed at the B3LYP/6-31+G** level. Overall, the results show how nucleobase heterocycles can be installed within π-systems to tune optical and electronic properties. Future work will evaluate the consequences of these information-rich components on supramolecular π-conjugated structure.