Chemo‐Enzymatic Synthesis of Position‐Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy

The investigation of non‐coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo‐enzymatic RNA synthesis containing photoactivatable or ¹³C,¹⁵N‐labelled nucleosides. All four ribonucleotides containing ortho‐nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C‐nucleotides and ¹³C,¹⁵N‐labelled nucleotides were incorporated position‐specifically in high yields. We applied this approach for the synthesis of light‐inducible 2′dG‐sensing riboswitch variants and detected ligand‐induced structural reorganization upon irradiation by NMR spectroscopy. This chemo‐enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid‐phase synthesis.     

Optogenetic Apoptosis: Light‐Triggered Cell Death

An optogenetic Bax has been designed that facilitates light‐induced apoptosis. We demonstrate that mitochondrial recruitment of a genetically encoded light‐responsive Bax results in the release of mitochondrial proteins, downstream caspase‐3 cleavage, changes in cellular morphology, and ultimately cell death. Mutagenesis of a key phosphorylatable residue or modification of the C‐terminus mitigates background (dark) levels of apoptosis that result from Bax overexpression. The mechanism of optogenetic Bax‐mediated apoptosis was explored using a series of small molecules known to interfere with various steps in programmed cell death. Optogenetic Bax appears to form a mitochondrial apoptosis‐induced channel analogous to that of endogenous Bax.     

G‐Quartet‐Based Nanostructure for Mimicking Light‐Harvesting Antenna

Artificial light‐harvesting systems have received great attention for use in photosynthetic and optoelectronic devices. Herein, a system involving G‐quartet‐based hierarchical nanofibers generated from the self‐assembly of guanosine 5′‐monophosphate (GMP) and a two‐step Förster resonance energy transfer (FRET) is presented that mimics natural light‐harvesting antenna. This solid‐state property offers advantages for future device fabrication. The generation of photocurrent under visible light shows it has potential for use as a nanoscale photoelectric device. The work will be beneficial for the development of light‐harvesting systems by the self‐assembly of supramolecular nanostructures.     

Spatiotemporal Control of CRISPR/Cas9 Function in Cells and Zebrafish using Light‐Activated Guide RNA

We developed a new method for the conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos using photochemically activated, caged guide RNAs (gRNAs). Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5′‐protospacer region with caged nucleobases during synthesis. Caging confers complete suppression of gRNA:dsDNA‐target hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation. This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off‐to‐on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes. Caged gRNAs are novel tools for the conditional control of gene editing, thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.     

Copying of RNA Sequences without Pre‐Activation

Template‐directed incorporation of nucleotides at the terminus of a growing complementary strand is the basis of replication. For RNA, this process can occur in the absence of enzymes, if the ribonucleotides are first converted to an active species with a leaving group. Thus far, the activation required a separate chemical step, complicating prebiotically plausible scenarios. Here we show that a combination of a carbodiimide and an organocatalyst induces near‐quantitative incorporation of any of the four ribonucleotides. Upon in situ activation, adenosine monophosphate was found to also form oligomers in aqueous solution. So, both de novo strand formation and sequence‐specific copying can occur without an artificial synthetic step.     

Cell Fixation by Light‐Triggered Release of Glutaraldehyde

Chemical fixation of living cells for microscopy is commonly achieved by crosslinking of intracellular proteins with dialdehydes prior to examination. We herein report a photocleavable protecting group for glutaraldehyde that results in a light‐triggered and membrane‐permeable fixative, which is nontoxic prior to photocleavage. Lipophilic ester groups allow for diffusion across the cell membrane and intracellular accumulation after enzymatic hydrolysis. Irradiation with UV light releases glutaraldehyde. The in situ generated fixative crosslinks intracellular proteins and preserves and stabilizes the cell so that it is ready for microscopy. In contrast to conventional glutaraldehyde fixation, tissue autofluorescence does not increase after fixation. Caged glutaraldehyde may in future enable functional experiments on living cells under a light microscope in which events of interest can be stopped in spatially confined volumes at defined time points. Samples with individually stopped events could then later be analyzed in ultrastructural studies.     

Rapid UV Light‐Triggered Macromolecular Click Conjugations via the Use of o‐Quinodimethanes

Shining a light on click chemistry: The use of UV‐radiation as trigger signal provides a facile means to obtain spatial and temporal control over polymer conjugation reactions in addition to providing a further means of achieving orthogonality in click transformations. In the current contribution, UV‐radiation was employed to induce a highly efficient Diels–Alder conjugation of polymeric building blocks via the photo‐induced in situ formation of highly reactive cis‐dienes from a 2‐methylbenzophenone precursor.

     

A Novel pH/Light‐Triggered Surface for DNA Adsorption and Release

A simple strategy for the immobilization of Cy3‐labeled single strand DNA (Cy3‐ssDNA) on a Si(001) surface and its release under control of both light and pH stimuli is presented. In order to prepare a dual pH/light‐triggered surface, positively chargeable azobenzene molecules are self‐assembled on the Si(001) surface. The surface wettability of this substrate can be changed under influence of both light and pH conditions. The substrates can be positively charged under mildly acidic conditions. The pH‐sensitive behavior of the film allows binding of Cy3‐ssDNA on the functionalized Si(001) surface through e?ective electrostatic interactions with the negatively charged polynucleotide backbone. Moreover, irradiation of the film with UVA light induces trans–cis isomerization of the azobenzene units on the surface. As a result, the binding a?nity for DNA decreases due to the changing surface hydrophilicity. In order to understand and control the reversible photoswitchable mechanism of this surface, water contact angles are measured after UVA and visible light irradiation. The release of DNA from a dual pH/light‐sensitive sample is performed using fluorescence microscopy. The results show that irradiation of the film with UVA light induces trans–cis isomerization of the photoresponsive azobenzene units; this leads to significant changes in the surface hydrophilicity and reduces the binding affinity for DNA.     

Covalent Chemical 5′‐Functionalization of RNA with Diazo Reagents

Functionalization of RNA at the 5′‐terminus is important for analytical and therapeutic purposes. Currently, these RNAs are synthesized de novo starting with a chemically functionalized 5′‐nucleotide, which is incorporated into RNA using chemical synthesis or biochemical techniques. Methods for direct chemical modification of native RNA would provide an attractive alternative but are currently underexplored. Herein, we report that diazo compounds can be used to selectively alkylate the 5′‐phosphate of ribo(oligo)nucleotides to give RNA labelled through a native phosphate ester bond. We applied this method to functionalize oligonucleotides with biotin and an orthosteric inhibitor of the eukaryotic initiation factor 4E (eIF4E), an enzyme involved in mRNA recognition. The modified RNA binds to eIF4E, demonstrating the utility of this labelling technique to modulate biological activity of RNA. This method complements existing techniques and may be used to chemically introduce a broad range of functional handles at the 5′‐end of RNA.     

A Fluorescent G‐Quadruplex Sensor for Chemical RNA Copying

Non‐enzymatic RNA replication may have been one of the processes involved in the appearance of life on Earth. Attempts to recreate this process in a laboratory setting have not been successful thus far, highlighting a critical need for finding prebiotic conditions that increase the rate and the yield. Now a highly parallel assay for template directed RNA synthesis is presented that relies on the intrinsic fluorescence of a 2‐aminopurine modified G‐quadruplex. The application of the assay to examine the combined influence of multiple variables including pH, divalent metal concentrations and ribonucleotide concentrations on the copying of RNA sequences is demonstrated. The assay enables a direct survey of physical and chemical conditions, potentially prebiotic, which could enable the chemical replication of RNA.     

Endless: A Purine‐Binding RNA Motif that Can Be Expressed in Cells

It is becoming increasingly clear that nature uses RNAs extensively for regulating vital functions of the cell, and short sequences are frequently used to suppress gene expression. However, controlling the concentration of small molecules intracellularly through designed RNA sequences that fold into ligand‐binding structures is difficult. The development of “endless”, a triplex‐based folding motif that can be expressed in mammalian cells and binds the second messenger 3′,5′‐cyclic guanosine monophosphate (cGMP), is described. In vitro, DNA or RNA versions of endless show low micromolar to nanomolar dissociation constants for cGMP. To test its functionality in vivo, four endless RNA motifs arranged in tandem were co‐expressed with a fluorescent cGMP sensor protein in murine vascular smooth muscle cells. Nitric oxide induced endogenous cGMP signals were suppressed in endless‐expressing cells compared to cells expressing a control motif, which suggests that endless can act as a genetically encoded cGMP sink to modulate signal transduction in cells.     

Light‐Triggered Multifunctionality at Surfaces Mediated by Photolabile Protecting Groups

Photoremovable protecting groups (PRPGs) are applied to organic surfaces, thin polymer films, and hydrogels to achieve light‐based remote control of their (bio)chemical and physical properties. These can be localized (i.e. patterned), tunable by exposure dose, and generated on‐demand. Using PRPGs with independent response to different wavelengths, multifunctional materials with a number of individually addressable functional states can be generated. Light‐triggered polymerization, crosslinking, and degradation processes as well as release of attached molecules can be realized. Light‐responsive surfaces and materials based on PRPGs open interesting possibilities for the next generation of instructive materials for cell culture and tissue regeneration.