Multiphoton characterization and live cell imaging using fluorescent adenine analogue 2CNqA

Fluorescent nucleobase analogues (FBAs) are established tools for studying oligonucleotide structure, dynamics and interactions, and have recently also emerged as an attractive option for labeling RNA-based therapeutics. A recognized drawback of FBAs, however, is that they typically require excitation in the UV region, which for imaging in biological samples may have disadvantages related to phototoxicity, tissue penetration, and out-of-focus photobleaching. Multiphoton excitation has the potential to alleviate these issues and therefore, in this work, we characterize the multiphoton absorption properties and detectability of the highly fluorescent quadracyclic adenine analogue 2CNqA as a ribonucleotide monomer as well as incorporated, at one or two positions, into a 16mer antisense oligonucleotide (ASO). We found that 2CNqA has a two-photon absorption cross section that, among FBAs, is exceptionally high, with values of σ_2PA(700 nm) = 5.8 GM, 6.8 GM, and 13 GM for the monomer, single-, and double-labelled oligonucleotide, respectively. Using fluorescence correlation spectroscopy, we show that the 2CNqA has a high 2P brightness as the monomer and when incorporated into the ASO, comparing favorably to other FBAs. We furthermore demonstrate the usefulness of the 2P imaging mode for improving detectability of 2CNqA-labelled ASOs in live cells.

Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

To expand the antisense oligonucleotide (ASO) fluorescence labeling toolbox beyond covalent conjugation of external dyes (e.g. ATTO-, Alexa Fluor-, or cyanine dyes), we herein explore fluorescent base analogues (FBAs) as a novel approach to endow fluorescent properties to ASOs. Both cytosine and adenine analogues (tC, tC^O, 2CNqA, and pA) were incorporated into a 16mer ASO sequence with a 3-10-3 cEt-DNA-cEt (cEt = constrained ethyl) gapmer design. In addition to a comprehensive photophysical characterization, we assess the label-induced effects on the gapmers' RNA affinities, RNA-hybridized secondary structures, and knockdown efficiencies. Importantly, we find practically no perturbing effects for gapmers with single FBA incorporations in the biologically critical gap region and, except for pA, the FBAs do not affect the knockdown efficiencies. Incorporating two cytosine FBAs in the gap is equally well tolerated, while two adenine analogues give rise to slightly reduced knockdown efficiencies and what could be perturbed secondary structures. We furthermore show that the FBAs can be used to visualize gapmers inside live cells using fluorescence microscopy and flow cytometry, enabling comparative assessment of their uptake. This altogether shows that FBAs are functional ASO probes that provide a minimally perturbing in-sequence labeling option for this highly relevant drug modality.

Interbase-FRET binding assay for pre-microRNAs

The aberrant expression of microRNAs (miRs) has been linked to several human diseases. A promising approach for targeting these anomalies is the use of small-molecule inhibitors of miR biogenesis. These inhibitors have the potential to (i) dissect miR mechanisms of action, (ii) discover new drug targets, and (iii) function as new therapeutic agents. Here, we designed Förster resonance energy transfer (FRET)-labeled oligoribonucleotides of the precursor of the oncogenic miR-21 (pre-miR-21) and used them together with a set of aminoglycosides to develop an interbase-FRET assay to detect ligand binding to pre-miRs. Our interbase-FRET assay accurately reports structural changes of the RNA oligonucleotide induced by ligand binding. We demonstrate its application in a rapid, qualitative drug candidate screen by assessing the relative binding affinity between 12 aminoglycoside antibiotics and pre-miR-21. Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) were used to validate our new FRET method, and the accuracy of our FRET assay was shown to be similar to the established techniques. With its advantages over SPR and ITC owing to its high sensitivity, small sample size, straightforward technique and the possibility for high-throughput expansion, we envision that our solution-based method can be applied in pre-miRNA–target binding studies.

Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery

Methods for tracking RNA inside living cells without perturbing their natural interactions and functions are critical within biology and, in particular, to facilitate studies of therapeutic RNA delivery. We present a stealth labeling approach that can efficiently, and with high fidelity, generate RNA transcripts, through enzymatic incorporation of the triphosphate of tC^O, a fluorescent tricyclic cytosine analogue. We demonstrate this by incorporation of tC^O in up to 100% of the natural cytosine positions of a 1.2 kb mRNA encoding for the histone H2B fused to GFP (H2B:GFP). Spectroscopic characterization of this mRNA shows that the incorporation rate of tC^O is similar to cytosine, which allows for efficient labeling and controlled tuning of labeling ratios for different applications. Using live cell confocal microscopy and flow cytometry, we show that the tC^O-labeled mRNA is efficiently translated into H2B:GFP inside human cells. Hence, we not only develop the use of fluorescent base analogue labeling of nucleic acids in live-cell microscopy but also, importantly, show that the resulting transcript is translated into the correct protein. Moreover, the spectral properties of our transcripts and their translation product allow for their straightforward, simultaneous visualization in live cells. Finally, we find that chemically transfected tC^O-labeled RNA, unlike a state-of-the-art fluorescently labeled RNA, gives rise to expression of a similar amount of protein as its natural counterpart, hence representing a methodology for studying natural, unperturbed processing of mRNA used in RNA therapeutics and in vaccines, like the ones developed against SARS-CoV-2.

Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor

With the central role of nucleic acids there is a need for development of fluorophores that facilitate the visualization of processes involving nucleic acids without perturbing their natural properties and behaviour. Here, we incorporate a new analogue of adenine, 2CNqA, into both DNA and RNA, and evaluate its nucleobase-mimicking and internal fluorophore capacities. We find that 2CNqA displays excellent photophysical properties in both nucleic acids, is highly specific for thymine/uracil, and maintains and slightly stabilises the canonical conformations of DNA and RNA duplexes. Moreover, the 2CNqA fluorophore has a quantum yield in single-stranded and duplex DNA ranging from 10% to 44% and 22% to 32%, respectively, and a slightly lower one (average 12%) inside duplex RNA. In combination with a comparatively strong molar absorptivity for this class of compounds, the resulting brightness of 2CNqA inside double-stranded DNA is the highest reported for a fluorescent base analogue. The high, relatively sequence-independent quantum yield in duplexes makes 2CNqA promising as a nucleic acid label and as an interbase Förster resonance energy transfer (FRET) donor. Finally, we report its excellent spectral overlap with the interbase FRET acceptors qAnitro and tCnitro, and demonstrate that these FRET pairs enable conformation studies of DNA and RNA.

Interbase FRET in RNA: from A to Z

Interbase FRET can reveal highly detailed information about distance, orientation and dynamics in nucleic acids, complementing the existing structure and dynamics techniques. We here report the first RNA base analogue FRET pair, consisting of the donor tC^O and the non-emissive acceptor tC_nitro. The acceptor ribonucleoside is here synthesised and incorporated into RNA for the first time. This FRET pair accurately reports the average structure of A-form RNA, and its utility for probing RNA structural changes is demonstrated by monitoring the transition from A- to Z-form RNA. Finally, the measured FRET data were compared with theoretical FRET patterns obtained from two previously reported Z-RNA PDB structures, to shed new light on this elusive RNA conformation.

A Caged Ret Kinase Inhibitor and its Effect on Motoneuron Development in Zebrafish Embryos

Proto-oncogene tyrosine-protein kinase receptor RET is implicated in the development and maintenance of neurons of the central and peripheral nervous systems. Attaching activity-compromising photocleavable groups (caging) to inhibitors could allow for external spatiotemporally controlled inhibition using light, potentially providing novel information on how these kinase receptors are involved in cellular processes. Here, caged RET inhibitors were obtained from 3-substituted pyrazolopyrimidine-based compounds by attaching photolabile groups to the exocyclic amino function. The most promising compound displayed excellent inhibitory effect in cell-free, as well as live-cell assays upon decaging. Furthermore, inhibition could be efficiently activated with light in vivo in zebrafish embryos and was shown to effect motoneuron development.

Design, Synthesis and Inhibitory Activity of Photoswitchable RET Kinase Inhibitors

REarranged during Transfection (RET) is a transmembrane receptor tyrosine kinase required for normal development and maintenance of neurons of the central and peripheral nervous systems. Deregulation of RET and hyperactivity of the RET kinase is intimately connected to several types of human cancers, most notably thyroid cancers, making it an attractive therapeutic target for small-molecule kinase inhibitors. Novel approaches, allowing external control of the activity of RET, would be key additions to the signal transduction toolbox. In this work, photoswitchable RET kinase inhibitors based on azo-functionalized pyrazolopyrimidines were developed, enabling photonic control of RET activity. The most promising compound displays excellent switching properties and stability with good inhibitory effect towards RET in cell-free as well as live-cell assays and a significant difference in inhibitory activity between its two photoisomeric forms. As the first reported photoswitchable small-molecule kinase inhibitor, we consider the herein presented effector to be a significant step forward in the development of tools for kinase signal transduction studies with spatiotemporal control over inhibitor concentration in situ.

8-Triazolylpurines: Towards Fluorescent Inhibitors of the MDM2/p53 Interaction

Small molecule nonpeptidic mimics of α-helices are widely recognised as protein-protein interaction (PPIs) inhibitors. Protein-protein interactions mediate virtually all important regulatory pathways in a cell, and the ability to control and modulate PPIs is therefore of great significance to basic biology, where controlled disruption of protein networks is key to understanding network connectivity and function. We have designed and synthesised two series of 2,6,9-substituted 8-triazolylpurines as α-helix mimetics. The first series was designed based on low energy conformations but did not display any biological activity in a biochemical fluorescence polarisation assay targeting MDM2/p53. Although solution NMR conformation studies demonstrated that such molecules could mimic the topography of an α-helix, docking studies indicated that the same compounds were not optimal as inhibitors for the MDM2/p53 interaction. A new series of 8-triazolylpurines was designed based on a combination of docking studies and analysis of recently published inhibitors. The best compound displayed low micromolar inhibitory activity towards MDM2/p53 in a biochemical fluorescence polarisation assay. In order to evaluate the applicability of these compounds as biologically active and intrinsically fluorescent probes, their absorption/emission properties were measured. The compounds display fluorescent properties with quantum yields up to 50%.

A photoswitchable supramolecular complex with release-and-report capabilities

A supramolecular platform with an inherent report function has been designed for photoreversible control of guest concentration in solution.

An all-photonic molecule-based parity generator/checker for error detection in data transmission

The function of a parity generator/checker, which is an essential operation for detecting errors in data transmission, has been realized with multiphotochromic switches by taking advantage of a neuron-like fluorescence response and reversible light-induced transformations between the implicated isomers.

Light-induced cytotoxicity of a photochromic spiropyran

In this work we present a novel water soluble spiropyran photoswitch that can be photonically activated inside live cells from a form that has no significant effect on the cellular survival to a form that induces a dramatic toxic response.

Vanadate affects nuclear division and induces aberrantly-shaped cells during subsequent cytokinesis in Tetrahymena

Sodium orthovanadate at 0.1-5.0 mM affected cell proliferation of Tetrahymena in a dose-dependent manner. At 1 h the cell increment was 76-12% of the control (100%), but after lag periods in 1-5 mM the growth rate remained at 76% of control in 0.1 mM vanadate and at 64-61% of control in 0.2-5.0 mM vanadate. Endocytosis was affected in both a time- and dose-dependent manner; an increasing number of cells did not form vacuoles. Cell motility increased initially in 0.1 mM vanadate but decreased later as it did in 0.5-2.0 mM vanadate where the proportion of immobile cells increased with time. Cell divisions occurred at all concentrations but macronuclear elongation was disturbed and subsequent cytokinesis resulted in daughter cells containing the entire G2 macronucleus, a large or small portion of it, or no nucleus at all. Moreover, odd cell shapes appeared with time. The size of the cell and nucleus increased but there was great variation with disturbed cytoplasm/nucleus ratios. Treated cells had dilated rough endoplasmic reticulum that included dense material, presumed to be vanadate, which was not seen in control cells. Scant amounts of dense material were found in dense granules, small vacuoles, and abundantly in contractile vacuoles. It is argued that interference with proper microtubular function is the main effect of vanadate.

pH-dependent effects of 2,4-dinitrophenol (DNP) on proliferation, endocytosis, fine structure and DNP resistance in Tetrahymena

In view of the importance of external pH on cytotoxic effects of ionizable agents, the pH-dependent effects of 2,4-dinitrophenol (DNP) were investigated. As uncoupler of oxidative phosphorylation, DNP interferes with the proton gradient across the inner mitochondrial membrane. DNP was added to proliferating Tetrahymena pyriformis in media of different initial pH. Effects studied were rates of cell proliferation and endocytosis, and fine structure. Findings correlated with the calculated concentration of undissociated DNP, taking into account that pH changes with time and cell density in Tetrahymena cultures. A linear relationship thus emerged between initial concentrations of undissociated DNP and lengths of the lag preceding cell proliferation. Once resumed, the rate of proliferation corresponded to that of control cells, even in different concentrations of undissociated DNP, presumably indicating an adaptation mechanism. Endocytosis was elevated throughout a wide range of undissociated DNP concentrations with a sharp transition towards inhibition at high DNP concentrations causing lethality with time. Changes in fine structure of DNP-treated cells (mitochondria, peroxisomes, nucleoli) also depended on the concentration of undissociated DNP.

Does chloroquine, an antimalarial drug, affect autophagy in Tetrahymena pyriformis?

The effect of chloroquine (CQ) on autophagy was studied in starved Tetrahymena pyriformis. When a proliferating Tetrahymena culture is transferred to a starvation medium, autophagy commences although cells most advanced in the cell cycle will divide. The drug was added to 1-h starved cells at different pH values because CQ affects pH dependently. The CQ concentration blocking all cell divisions was determined as the lowest toxic, but sublethal, concentration. Hence, the highest tolerated concentrations at pH 6.8, 7.1, and 7.7 were 1.0, 0.3, and 0.03 mM CQ, respectively. Lower CQ concentrations had a dose-dependent effect on cell increment and higher concentrations induced cell mortality. Rates of cell motility and decreases in cell volume were affected by the drug, while the capacity for endocytosis was unaffected in low concentrations but affected dose dependently in high concentrations. Light microscopically, all drug-treated cells contained small refractive bodies, but in toxic concentrations they also contained conspicuously large vacuoles. After 1 h and 4 h in CQ, fine structure analysis showed autophagosomes with electron-dense material in cells in tolerated concentrations and of enlarged size, but decreased number, in toxic concentrations. The contents of autophagosomes revealed cell organelles in different stages of disintegration. The conclusion is that the drug enhances autophagy in Tetrahymena in a pH-, dose-, and time-dependent manner.

Variation in the growth medium during the culture cycle of Tetrahymena: with special reference to ammonia (NH3), ammonium (NH4+), and pH1

The ciliate Tetrahymena pyriformis was grown in a peptone medium without added glucose. The interrelationship between increasing cell density and pH of the growth medium was studied from mid-log to the stationary phase, i.e. from 50,000 to 1,000,000 cells/ml, by continuous registration of the pH of the growth medium. The present findings correlate with the known physiological, biochemical, and structural changes occurring in Tetrahymena as it passes through the culture cycle. The ammonia production of the cells and the buffer capacity of the growth medium were determined throughout the growth cycle. The results revealed that the ammonia excreted by the cells can explain the increase in pH of the medium from 6.8 to about 8.3 normally seen during the culture cycle. Moreover, neither the increased pH nor the raised level of ammonia were found to be the responsible factor for cessation of cell proliferation in the stationary growth phase although these factors may affect cell proliferation in concentrations well beyond the range found in normal cultures.

Cytotoxic effects of cisplatin, cis-dichlorodiammineplatinum(II), on Tetrahymena

A study was made of the effects of cisplatin, cis-dichlorodiammineplatinum(II) (5–250 mg l-1), on the physiology and fine structure of Tetrahymena. The physiological effects observed were dose-dependent. Endocytosis was inhibited reversibly in all, but late in the high, concentrations. After an initial dose-related increase, due to division of cells most advanced in the cell cycle, proliferation ceased for at least two normal cell generations (6 h) in 50 and 100 mg drug l-1, but for 24 h in 250 mg l-1, after which multiplication was resumed in a dose-dependent manner. Exposure to cisplatin resulted in the appearance of small, refractive granules and platinum (i.e. electron-dense material) accumulated in these granules. Fine structural observations of cells exposed to 250 mg drug l-1 showed nucleolar fusion and appearance initially of lipid droplets, dense granules and autophagosomes. A time-dependent redistribution of cell organelles was revealed by morphometry; in particular, the mitochondria increased in number, but decreased in size. Moreover, after prolonged treatment (24 h) and without cell division, the inner mitochondrial membrane had diminished and the ratio of the inner to the outer mitochondrial membrane was only half of the value for control mitochondria. Concomitantly with this decrease, the cell content of ATP was reduced to a similar extent. The findings indicate a specific action of cisplatin on mitochondria, resembling that induced in Tetrahymena by chloramphenicol and methotrexate.

Coated pits with pinocytosis in Tetrahymena

The possible role in pinocytosis of coated pits at the parasomal sacs of Tetrahymena has been studied using cationized ferritin (CF; pI = 8.5) as a marker of membrane and content. It is shown that CF binds evenly to the surface, including the coated pits, of Tetrahymena in an inorganic salt medium (to avoid formation of food vacuoles) at the normal growth temperature. Moreover, CF is internalized by coated vesicles (shown to be truly free by thin serial-section analysis) and delivered initially (1-5 min of incubation) to cisterna near the cell surface. Later (5-10 min) CF occurs also in autophagic vacuoles, formed as a result of starvation, and eventually (15-90 min) it is present in preformed (old) food vacuoles. These observations indicate that the coated pits at the parasomal sacs of Tetrahymena function in adsorptive pinocytosis in much the same manner as coated pits at the surface of mammalian cells.

Intracellular distribution of lead in Tetrahymena during continuous exposure to the metal

Lead acetate (0.1–0.2%) forms a precipitate with the organic growth medium. The Tetrahymena cells ingest this lead-containing precipitate and cell growth is resumed after a variable lag period. Ingested lead is observed as electron-dense material in food vacuoles. Soon after exposure, cytoplasmic lead (preserved with certain fixation only) is revealed as electron-dense particles in cilia and in a halo around digestive vacuoles. Later the lead particles pervade the entire cell but after the lag period they are confined to membrane-bound spaces. In dilute growth medium, high concentrations of lead inhibit food-vacuole formation and cell growth. Under these conditions lead is deposited in alveoli of the pellicle and is also found in autophagic vacuoles and other membrane-limited structures. The study has revealed that lead enters Tetrahymena through the membrane of digestive vacuoles and through the cell surface. The change in distribution of lead during the lag period indicates that a mechanism is activated for removal of lead into membrane-bound spaces. The final storage of lead seems to be in lysosomes.

The relationship between energy-dependent phagocytosis and the rate of oxygen consumption in Tetrahymena

The induction of high rates of food vacuole formation in Tetrahymena pyriformis increased the rate of respiration in exponentially growing cells by 17% and in starving cells by 47.5%. The increased rate of oxygen uptake was caused by phagocytosis itself, as shown by comparing the rates of respiration of a Tetrahymena mutant exposed to particles at the permissive or restrictive temperatures for food vacuole formation. During cell division, heat-synchronized cells in rich, particle-supplemented medium showed a significant decrease in the rate of respiration. Furthermore, dimethyl sulphoxide, in concentrations sufficient to block food vacuole formation, suppressed the rate of respiration to a level similar to that of starved cells. Cytochalasin B, fowever, did not reduce the rate of oxygen uptake despite the inability of the cells to complete the formation of food vacuoles during treatment; a possible explanation for this finding is discussed. There was a strong correlation between formation of food vacuoles and a high metabolic rate in Tetrahymena.

Fine structure and RNA synthesis of Tetrahymena during cytochalasin B inhibition of phagocytosis

Cytochalasin B inhibits the formation of normal-sized food vacuoles in Tetrahymena but the cells do not starve. Treated cells differ from starved cells in that they retain a high rate of incorporation of tritiated uridine. Large numbers of smaller vacuoles, about 1 micrometer in diameter, are formed, presumably by pinocytic activity of the cytopharyngeal membrane. This effect may perhaps be due to interference with the mechanism by which food vacuoles are sealed off at the cytostome, in which microfilaments may participate. Inhibited organisms may form tubes continuous with the cytopharynx instead of separate food vacuoles. It is not clear, however, why the formation of the small vacuoles is resistant to the drug.

Effects of dimethyl sulfoxide on Tetrahymena pyriformis GL. Fine structural changes and their reversibility

Fine-structural changes are induced in Tetrahymena by exposure to 7.5% dimethyl sulfoxide (DMSO) in the presence of growth medium. Some of these changes (nucleolar, mitochondrial, peroxisomal) resemble those seen during starvation, in agreement with the previously reported inhibitory effect of DMSO on food-vacuole formation; however, changes such as helical formations of polyribosomes indicate additional internal actions of the reagent. The effects vary to some extent within the same group of cells, suggesting that sensitivity to the reagent may differ with the stage in the cell cycle. The structural changes induced by a 1-hr exposure to DMSO are reversible, but recovery of the cells after removal of the reagent is slower than that seen after starvation. The observations suggest that the recovery is associated with renewed synthesis.

Effects of DMSO on Vacuole Formation, Contractile Vacuole Function, and Nuclear Division in Tetrahymena Pyriformis GL

Increasing concentrations of dimethyl sulphoxide (DMSO) affect vacuole formation in Tetrahymena, as measured quantitatively by the uptake of carmine particles. The rate of vacuole formation decreased to about 50% of the control value in 5.0% DMSO (v/v) and to zero in 7.5%. At the latter concentration, the inhibition was expressed immediately; however, the effect of 1-h exposure was reversible after removal of DMSO by washing. In vivo observations revealed abnormal function of the contractile vacuole in 7.5% DMSO, while cell motility and cell division appeared to be unaffected. Although cell division occurred there was little or no increase in cell number, as studied over a cell generation time. Feulgen preparations showed that nuclear division was inhibited and that cell division resulted in one anucleate and one nucleate daughter cell. This effect was also observed in some dividing cells at lower concentrations of DMSO. The effect of DMSO on Tetrahymena was dependent not only on the concentration of the compound but also on the physiological state of the cells.

Induction of nucleolar and mitochondrial DNA replication in Tetrahymena pyriformis

Selective induction of replication of nucleolar and mitochondrial DNA has been demonstrated in starved-refed cultures of Tetrahymena pyriformis by different techniques. Labeling of starved cells with [(3)H]thymidine during a nutritional shift-up and analysis of the DNA in isopycnic CsCl gradients shows that the two initially labeled species of DNA are two species banding on the heavy and light side of the bulk macronuclear DNA. In isolated macronuclei the radioactivity is found only in the high density fraction, which has been shown to be of nucleolar origin. In sucrose gradients the newly replicated mitochondrial and nucleolar DNAs sediment considerably slower than the bulk DNA, as one discrete band corresponding to a molecular weight of about 3 to 4 x 10(7). Electron microscope autoradiography of cells labeled with [(3)H]thymidine as above shows that the peripheral nucleoli of the macronucleus as well as the mitochondria are labeled before any radioactivity is found in the chromatin granules of the macronucleus. The results clearly indicate that nucleolar and mitochondrial DNA replication are under a control independent of that for the replication of bulk DNA.

Deficiency of the sixth component of complement in rabbits with an inherited complement defect

A strain of rabbits with an inherited complement deficiency was shown to lack the sixth component of the hemolytic complement system. A method was elaborated for the partial purification of this component from normal rabbit serum. Upon injection of partially purified rabbit C'6 into C'6-deficient animals, an antibody was obtained which specifically inhibited the hemolytic activity of C'6. The data suggest that C'6-deficient serum either lacks the C'6 molecule or contains it in a chemically modified and inactive form.