Comparing Agent-Based Delivery of DNA and PNA Forced Intercalation (FIT) Probes for Multicolor mRNA Imaging

ASOBIOTICS 2024: an interdisciplinary symposium on antisense-based programmable RNA antibiotics

The international symposium ASOBIOTICS 2024 brought together scientists across disciplines to discuss the challenges of advancing antibacterial antisense oligomers (ASOs) from basic research to clinical application. Hosted by the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, Germany, on September 12-13, 2024, the event featured presentations covering major milestones and current challenges of this antimicrobial technology and its applications against pathogens, commensals, and bacterial viruses. General design principles and modification of ASOs based on peptide nucleic acid (PNA) or phosphorodiamidate-morpholino-oligomer (PMO) chemistry, promising cellular RNA targets, new delivery technologies, as well as putative resistance mechanisms, were discussed. A panel discussion noted the challenge of nomenclature: antibacterial ASOs lack a single, universally used name. To address this, the term "asobiotics" was proposed to unite a community of like-minded scientists that are committed to advancing ASOs as antimicrobials. A consistent name will simplify literature searches and help scientists and funders appreciate the potential of programmable RNA antibiotics to combat antimicrobial resistance and enable precise microbiome editing.

Implantable Fluorogenic DNA Biosensor for Stress Detection

Implantable sensors that can monitor analytes related to cognitive and physiological status have gained significant focus in recent years. We have developed an implantable biosensor to detect dehydroepiandrosterone sulfate (DHEA-S), a biomarker related to stress. The biosensor strategy was based on the principle of forced intercalation (FIT) aptamers designed to detect subtle intramolecular changes during aptamer-target binding events. By incorporating a steroid-specific fluorogenic aptamer into a hydrogel, the sensitivity and biostability of the FIT biosensor fiber were improved, which were essential for designing implantable sensors to monitor biomarker levels in the living body. The polyethylenimine-based hydrogel chosen for this study produced an optically transparent cross-linked network with optimal microstructure, physicochemical, and mechanical properties, making it suitable for optical biosensors. The in vitro studies showed that the biosensor fiber was successfully activated in human serum and skin analogue, providing a linear response to physiological concentrations of the steroid. We believe that this type of implantable platform can be effective in monitoring more complex biomarkers associated with physiological or psychological health.

Light harvesting FIT DNA hybridization probes for brightness-enhanced RNA detection

Fluorogenic hybridization probes are essential tools in modern molecular biology techniques. They allow detection of specific nucleic acid molecules without the need to separate target-bound from unbound probes. To enable detection of targets at low concentration, fluorogenic probes should have high brightness. Here, we report the development of RNA hybridization probes (RNA FIT probes) that use smart quenching and a light harvesting principle to enhance the brightness of fluorescence signaling. The signaling mechanism is based on FRET between brightly emitting donor dyes and a fluorescent base surrogate, such as quinoline blue (QB) or thiazole orange (TO). In the single-stranded state, QB/TO nucleotides fluoresce weakly and quench the fluorescence of the donor dyes. Upon target recognition, QB/TO stack with adjacent base pairs, resulting in enhanced fluorescence quantum yields. The donor dyes are blue-shifted by only 5-20 nm relative to the QB/TO nucleotides, allowing simultaneous excitation of both dye groups with efficient energy transfer. The combined photon absorption results in exceptionally bright FIT probes. This feature facilitated the detection of RNA target in undiluted cell lysates. The present study examines the utilization of probes to detect mRNA targets in live T cells using flow cytometry.

Recent advances in living cell nucleic acid probes based on nanomaterials for early cancer diagnosis

The early diagnosis of cancer is vital for effective treatment and improved prognosis. Tumor biomarkers, which can be used for the early diagnosis, treatment, and prognostic evaluation of cancer, have emerged as a topic of intense research interest in recent years. Nucleic acid, as a type of tumor biomarker, contains vital genetic information, which is of great significance for the occurrence and development of cancer. Currently, living cell nucleic acid probes, which enable the in situ imaging and dynamic monitoring of nucleic acids, have become a rapidly developing field. This review focuses on living cell nucleic acid probes that can be used for the early diagnosis of tumors. We describe the fundamental design of the probe in terms of three units and focus on the roles of different nanomaterials in probe delivery.

Towards a templated reaction that translates RNA in cells into a proaptotic peptide-PNA conjugate

Nucleic acid-templated chemistry opens the intriguing prospect of triggering the synthesis of drugs only in diseased cells. Herein, we explore the feasibility of using RNA-templated chemical reactions for the activation of a known Smac peptidomimetic compound (SMC), which has proapoptotic activity. Two peptide nucleic acid (PNA) conjugates were used to enable conditional activation of a masked SMC by reduction of an azide either by Staudinger reduction or catalytic photoreduction using a ruthenium complex. The latter provided ~135 nM SMC-PNA on as little as 10 nM (0.01 eq.) template. For the evaluation of the templated azido-SMC reduction system in cellulo, a stable HEK 293 cell line was generated, which overexpressed a truncated, non-functional form of the XIAP mRNA target. We furthermore describe the development of electroporation protocols that enable a robust delivery of PNA conjugates into HEK 293 cells. The action of the reactive PNA conjugates was evaluated by viability and flow cytometric apoptosis assays. In addition, electroporated probes were re-isolated and analyzed by ultra-high performance liquid chromatography (UPLC). Unfortunately, the ruthenium-PNA conjugate proved phototoxic, and treatment of cells with PNA-linked reducing agent and the azido-masked SMC conjugate did not result in a greater viability loss than treatment with scrambled sequence controls. Intracellular product formation was not detectable. A control experiment in total cellular RNA isolate indicated that the templated reaction can in principle proceed in a complex system. The results of this first-of-its-kind study reveal the numerous hurdles that must be overcome if RNA molecules are to trigger the synthesis of pro-apoptotic drugs inside cells.

Fluorescent Platforms for RNA Chemical Biology Research

Efficient detection and observation of dynamic RNA changes remain a tremendous challenge. However, the continuous development of fluorescence applications in recent years enhances the efficacy of RNA imaging. Here we summarize some of these developments from different aspects. For example, single-molecule fluorescence in situ hybridization (smFISH) can detect low abundance RNA at the subcellular level. A relatively new aptamer, Mango, is widely applied to label and track RNA activities in living cells. Molecular beacons (MBs) are valid for quantifying both endogenous and exogenous mRNA and microRNA (miRNA). Covalent binding enzyme labeling fluorescent group with RNA of interest (ROI) partially overcomes the RNA length limitation associated with oligonucleotide synthesis. Forced intercalation (FIT) probes are resistant to nuclease degradation upon binding to target RNA and are used to visualize mRNA and messenger ribonucleoprotein (mRNP) activities. We also summarize the importance of some fluorescence spectroscopic techniques in exploring the function and movement of RNA. Single-molecule fluorescence resonance energy transfer (smFRET) has been employed to investigate the dynamic changes of biomolecules by covalently linking biotin to RNA, and a focus on dye selection increases FRET efficiency. Furthermore, the applications of fluorescence assays in drug discovery and drug delivery have been discussed. Fluorescence imaging can also combine with RNA nanotechnology to target tumors. The invention of novel antibacterial drugs targeting non-coding RNAs (ncRNAs) is also possible with steady-state fluorescence-monitored ligand-binding assay and the T-box riboswitch fluorescence anisotropy assay. More recently, COVID-19 tests using fluorescent clustered regularly interspaced short palindromic repeat (CRISPR) technology have been demonstrated to be efficient and clinically useful. In summary, fluorescence assays have significant applications in both fundamental and clinical research and will facilitate the process of RNA-targeted new drug discovery, therefore deserving further development and updating.

Emerging landscape of cell-penetrating peptide-mediated nucleic acid delivery and their utility in imaging, gene-editing, and RNA-sequencing

The safety issues like immunogenicity and unacceptable cancer risk of viral vectors for DNA/mRNA vaccine delivery necessitate the development of non-viral vectors with no toxicity. Among the non-viral strategies, cell-penetrating peptides (CPPs) have been a topic of interest recently because of their ability to cross plasma membranes and facilitate nucleic acids delivery both in vivo and in vitro. In addition to the application in the field of gene vaccine and gene therapy, CPPs based nucleic acids delivery have been proved by its potential application like gene editing, RNA-sequencing, and imaging. Here, we focus on summarizing the recent applications and progress of CPPs-mediated nucleic acids delivery and discuss the current problems and solutions in this field.

Toward conditional control of Smac mimetic activity by RNA-templated reduction of azidopeptides on PNA or 2'-OMe-RNA

Oligonucleotide templated reactions can be used to control the activity of functional molecules based on the presence of a specific trigger sequence. We report an RNA-controlled reaction system to conditionally restore the N-terminal amino group and thus binding affinity of azide-modified Smac mimetic compounds (SMCs) for their target protein X-linked Inhibitor of Apoptosis Protein (XIAP). Two templated reactions were compared: Staudinger reduction with phosphines and a photocatalytic reaction with Ru(bpy)₂ (mcbpy). The latter proved faster and more efficient, especially for the activation of a bivalent SMC, which requires two consecutive reduction steps. The templated reaction proceeds with turnover when 2'-OMe-RNA probes are used, but is significantly more efficient with PNA, catalyzing a reaction in the presence of low, substoichiometric amounts (1%-3%, 10 nM) of target RNA.

Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions

Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.

Cyclopentane FIT-PNAs: bright RNA sensors

Cyclopentane modified FIT-PNA (cpFIT-PNA) probes are reported as highly emissive RNA sensors with the highest reported brightness for FIT-PNAs. Compared to FIT-PNAs, cpFIT-PNAs have improved mismatch discrimination for several pyrimidine-pyrimidine single nucleotide variants (SNVs).

Monitoring Dicer-Mediated miRNA-21 Maturation and Ago2 Loading by a Dual-Colour FIT PNA Probe Set

The inhibition of micro RNA (miRNA) maturation by Dicer and loading matured miRNAs into the RNA-induced silencing complex (RISC) is envisioned as a modality for treatment of cancer. Existing methods for evaluating maturation either focus on the conversion of modified precursors or detect mature miRNA. Whereas the former is not applicable to native pre-miRNA, the latter approach underestimates maturation when both nonmatured and matured miRNA molecules are subject to cleavage. We present a set of two orthogonally labelled FIT PNA probes that distinguish between cleaved pre-miRNA and the mature miRNA duplex. The probes allow Dicer-mediated miR21 maturation to be monitored and Ago2-mediated unwinding of the miR21 duplex to be assayed. A two-channel fluorescence readout enables measurement in real-time without the need for specialized instrumentation or further enzyme mediated amplification.

Nucleic-Acid Structures as Intracellular Probes for Live Cells

The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.

Bioorthogonal mRNA labeling at the poly(A) tail for imaging localization and dynamics in live zebrafish embryos

Live imaging of mRNA in cells and organisms is important for understanding the dynamic aspects underlying its function.

Live imaging of mRNA in cells and organisms is important for understanding the dynamic aspects underlying its function. Ideally, labeling of mRNA should not alter its structure or function, nor affect the biological system. However, most methods applied in vivo make use of genetically encoded tags and reporters that significantly enhance the size of the mRNA of interest. Alternately, we utilize the 3′ poly(A) tail as a non-coding repetitive hallmark to covalently label mRNAs via bioorthogonal chemistry with different fluorophores from a wide range of spectra without significantly changing the size. We demonstrate that the labeled mRNAs can be visualized in cells and zebrafish embryos, and that they are efficiently translated. Importantly, the labeled mRNAs acquired the proper subcellular localization in developing zebrafish embryos and their dynamics could be tracked in vivo.

Delivery of cell membrane impermeable peptides into living cells by using head-to-tail cyclized mitochondria-penetrating peptides

A series of cyclic Arg-rich mitochondria-penetrating peptides were prepared with variation in the macrocycle size and the chirality of Arg residues. A cyclic heptapeptide was demonstrated to be an efficient mitochondria-specific delivery vector for delivering membrane impermeable peptides.

Comparing Agent-Based Delivery of DNA and PNA Forced Intercalation (FIT) Probes for Multicolor mRNA Imaging

Fluorogenic oligonucleotide probes allow mRNA imaging in living cells. A key challenge is the cellular delivery of probes. Most delivery agents, such as cell‐penetrating peptides (CPPs) and pore‐forming proteins, require interactions with the membrane. Charges play an important role. To explore the influence of charge on fluorogenic properties and delivery efficiency, we compared peptide nucleic acid (PNA)‐ with DNA‐based forced intercalation (FIT) probes. Perhaps counterintuitively, fluorescence signaling by charged DNA FIT probes proved tolerant to CPP conjugation, whereas CPP–FIT PNA conjugates were affected. Live‐cell imaging was performed with a genetically engineered HEK293 cell line to allow the inducible expression of a specific mRNA target. Blob‐like features and high background were recurring nuisances of the tested CPP and lipid conjugates. By contrast, delivery by streptolysin‐O provided high enhancements of the fluorescence of the FIT probe upon target induction. Notably, DNA‐based FIT probes were brighter and more responsive than PNA‐based FIT probes. Optimized conditions enabled live‐cell multicolor imaging of three different mRNA target sequences.