Nucleoside-based diarylethene photoswitches and their facile incorporation into photoswitchable DNA

Synthesis and Development of Inverse-Type Nucleoside Diarylethene Photoswitches

Nucleosidic diarylethenes (DAEs) have evolved from an emerging class of photochromes into a well-established option for integrating photochromic functionalities into biological systems. However, a comprehensive understanding of how chemical structure influences their photochromic properties remains essential. While structural features, such as an inverse connection between the aryl residues and the ethene bridge, are well-documented for classical DAEs, their application to nucleosidic DAEs has been underexplored. In this study, we address this gap by developing three distinct types of inverse nucleosidic DAEs-semi-inverse thiophenes, semi-inverse uridines and inverse uridines. We successfully synthesized these compounds and conducted comprehensive analyses of their photostationary states, thermal stability, reversibility, and reaction quantum yields. Additionally, we conducted an in-depth comparison of their photochromic properties with those of their normal-type counterparts. Among the synthesized compounds, seven semi-inverse thiophenes exhibited the most promising characteristics. Notably, these compounds demonstrated excellent fatigue resistance, with up to 96 % retention of photochromic activity over 40 switching cycles, surpassing the performance of all comparable nucleosidic DAEs reported to date. These findings hold significant promise for future applications in various fields.

Orthogonal Control of Nucleic Acid Function via Chemical Caging-Decaging Strategies

The ability to precisely control the function of nucleic acids plays an important role in biosensing and biomedicine. In recent years, novel strategies employing biological, physical, and chemical triggers have been developed to modulate the function of nucleic acids spatiotemporally. These approaches commonly involve the incorporation of stimuli-responsive groups onto nucleic acids to block their functions until triggers-induced decaging restore activity. These inventive strategies deepen our comprehension of nucleic acid molecules' dynamic behavior and provide new techniques for precise disease diagnosis and treatment. Focusing on the spatiotemporal regulation of nucleic acid molecules through the chemical caging-decaging strategy, we here present an overview of the innovative triggered control mechanisms and accentuate their implications across the fields of chemical biology, biomedicine, and biosensing.

DNA liquid crystals with AIE effect toward humidity-indicating biomaterials

In this study, by fabricating DNA doped with tetraphenylethene-containing ammonium surfactant, the resulting solvent-free DNA ionic complex could undergo a humidity-induced phase change that could be well tracked by the fluorescence signal of the surfactant. Taking advantage of the humidity-induced change in fluorescence, the reported ionic DNA complex could accurately indicate the humidity in real time.

Photochromic Nucleosides and Oligonucleotides

Photochromism is a reversible phenomenon wherein a material undergoes a change in color upon exposure to light. In organic photochromes, this effect often results from light-induced isomerization reactions, leading to alterations in either the spatial orientation or electronic properties of the photochrome. The incorporation of photochromic moieties into biomolecules, such as proteins or nucleic acids, has become a prevalent approach to render these biomolecules responsive to light stimuli. Utilizing light as a trigger for the manipulation of biomolecular structure and function offers numerous advantages compared to other stimuli, such as chemical or electrical treatments, due to its non-invasive nature. Consequently, light proves particularly advantageous in cellular and tissue applications. In this review, we emphasize recent advancements in the field of photochromic nucleosides and oligonucleotides. We provide an overview of the design principles of different classes of photochromes, synthetic strategies, critical analytical challenges, as well as structure-property relationships. The applications of photochromic nucleic acid derivatives encompass diverse domains, ranging from the precise photoregulation of gene expression to the controlled modulation of the three-dimensional structures of oligonucleotides and the development of DNA-based fluorescence modulators. Moreover, we present a future perspective on potential modifications and applications.

On photokinetics under monochromatic light

The properties of photokinetics under monochromatic light have not yet been fully described in the literature. In addition, for the last 120 years or so, explicit, handy model equations that can map out the kinetic behaviour of photoreactions have been lacking. These gaps in the knowledge are addressed in the present paper. Several general features of such photokinetics were investigated, including the effects of initial reactant concentration, the presence of spectator molecules, and radiation intensity. A unique equation, standing for a pseudo-integrated rate law, capable of outlining the kinetic behaviour of any photoreaction is proposed. In addition, a method that solves for quantum yields and absorption coefficients of all species of a given photoreaction is detailed. A metric (the initial velocity) has been adopted, and its reliability for the quantification of several effects was proven by theoretical derivation, Runge-Kutta numerical integration calculations and through the model equation proposed. Overall, this study shows that, under monochromatic light, photoreaction kinetics is well described by Φ -order kinetics, which is embodied by a unifying model equation. This paper is aimed at contributing to rationalising photokinetics via reliable, easy-to-use mathematical tools.

Covalent Modification of Nucleobases using Water-Soluble Palladium Catalysts

Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.

Light responsive nucleic acid for biomedical application

Nucleic acids are widely used in biomedical applications because of their programmability and biocompatibility. The light responsive nucleic acids have attracted wide attention due to their remote control and high spatiotemporal resolution. In this review, we summarized the latest developments in biomedicine of light responsive molecules. The molecules which confer light responsive properties to nucleic acids were summarized. The binding sites of molecules to nucleic acids, the induced structural changes, and functional regulation of nucleic acids were reviewed. Then, the biomedical applications of light responsive nucleic acids were listed, such as drug delivery, biosensing, optogenetics, gene editing, etc. Finally, the challenges were discussed and possible future directions of light-responsive nucleic acids were proposed.

Ultrafast Dynamics of a Molecular Switch from Resonance Raman Spectroscopy: Comparing Visible and UV Excitation

Resonance Raman spectroscopy probes the ultrafast dynamics of a diarylethene (DAE) molecular switch following excitation into the first two optical absorption bands. Mode-specific resonance enhancements for Raman excitation at visible (750-560 nm) and near-UV (420-390 nm) wavelengths compared with the calculated and experimental off-resonance Raman spectrum at 785 nm reveal different Franck-Condon active vibrations for the two electronically excited states. The resonance enhancements at visible wavelengths are consistent with initial motion on the first excited-state that promotes the cycloreversion reaction, whereas the enhancements for excitation at near-UV wavelengths highlight motions involving conjugated backbone and phenyl ring stretching modes that are orthogonal to the reaction coordinate. The results support a mechanism involving rapid internal conversion from the higher-lying state followed by cycloreversion on the first excited state. These observations provide new information about the reactivity of DAE derivatives following excitation in the visible and near-UV.

Future-Oriented Advanced Diarylethene Photoswitches: From Molecular Design to Spontaneous Assembly Systems

Diarylethene (DAE) photoswitch is a new and promising family of photochromic molecules and has shown superior performance as a smart trigger in stimulus-responsive materials. During the past few decades, the DAE family has achieved a leap from simple molecules to functional molecules and developed toward validity as a universal switching building block. In recent years, the introduction of DAE into an assembly system has been an attractive strategy that enables the photochromic behavior of the building blocks to be manifested at the level of the entire system, beyond the DAE unit itself. This assembly-based strategy will bring many unexpected results that promote the design and manufacture of a new generation of advanced materials. Here, recent advances in the design and fabrication of diarylethene as a trigger in materials science, chemistry, and biomedicine are reviewed.

A DNA-Based Two-Component Excitonic Switch Utilizing High-Performance Diarylethenes

Nucleosidic diarylethenes (DAEs) are an emerging class of photochromes but have rarely been used in materials science. Here, we have developed doubly methylated DAEs derived from 2'-deoxyuridine with high thermal stability and fatigue resistance. These new photoswitches not only outperform their predecessors but also rival classical non-nucleosidic DAEs. To demonstrate the utility of these new DAEs, we have designed an all-optical excitonic switch consisting of two oligonucleotides: one strand containing a fluorogenic double-methylated 2'-deoxyuridine as a fluorescence donor and the other a tricyclic cytidine (tC) as acceptor, which together form a highly efficient conditional Förster-Resonance-Energy-Transfer (FRET) pair. The system was operated in liquid and solid phases and showed both strong distance- and orientation-dependent photochromic FRET. The superior ON/OFF contrast was maintained over up to 100 switching cycles, with no detectable fatigue.

Photochemical modifications for DNA/RNA oligonucleotides

Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.

Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution

Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.

Photoresponsive DNA materials and their applications

Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.

Development of Red-Shifted and Fluorogenic Nucleoside and Oligonucleotide Diarylethene Photoswitches

The reversible modulation of fluorescence signals by light is of high interest for applications in super‐resolution microscopy, especially on the DNA level. In this article we describe the systematic variation of the core structure in nucleoside‐based diarylethenes (DAEs), in order to generate intrinsically fluorescent photochromes. The introduction of aromatic bridging units resulted in a bathochromic shift of the visible absorption maximum of the closed‐ring form, but caused reduced thermal stability and switching efficiency. The replacement of the thiophene aryl unit by thiazol improved the thermal stability, whereas the introduction of a benzothiophene unit led to inherent and modulatable turn‐off fluorescence. This feature was further optimized by introducing a fluorescent indole nucleobase into the DAE core, resulting in an effective photoswitch with a fluorescence quantum yield of 0.0166 and a fluorescence turn‐off factor of 3.2. The site‐specific incorporation into an oligonucleotide resulted in fluorescence‐switchable DNA with high cyclization quantum yields and switching efficiency, which may facilitate future applications.

Polymerase Synthesis of DNA Containing Iodinated Pyrimidine or 7-Deazapurine Nucleobases and Their Post-synthetic Modifications through the Suzuki-Miyaura Cross-Coupling Reactions

All four iodinated 2'-deoxyribonucleoside triphosphates (dNTPs) derived from 5-iodouracil, 5-iodocytosine, 7-iodo-7-deazaadenine and 7-iodo-7-deazaguanine were prepared and studied as substrates for KOD XL DNA polymerase. All of the nucleotides were readily incorporated by primer extension and by PCR amplification to form DNA containing iodinated nucleobases. Systematic study of the Suzuki-Miyaura cross-coupling reactions with two bulkier arylboronic acids revealed that the 5-iodopyrimidines were more reactive and gave cross-coupling products both in the terminal or internal position in single-stranded oligonucleotides (ssONs) and in the terminal position of double-stranded DNA (dsDNA), whereas the 7-iodo-7-deazapurines were less reactive and gave cross-coupling products only in the terminal position. None of the four iodinated bases reacted in an internal position of dsDNA. These findings are useful for the use of the iodinated nucleobases for post-synthetic modification of DNA with functional groups for various applications.

Molecular photoswitches in aqueous environments

Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.

Molecular platforms based on biocompatible photoreactions for photomodulation of biological targets

Photoirradiation provides a convenient and biocompatible approach for spatiotemporal modulation of biological systems with photoresponsive components. The construction of molecular platforms with a photoresponse to be integrated into biomolecules for photomodulation has been of great research interest in optochemical biology. In this review, we summarize typical molecular platforms that are integratable with biomolecules for photomodulation purposes. We categorize these molecular platforms according to their excitation light source, namely ultraviolet (UV), visible (Vis) or near-infrared (NIR) light. The protype chemistry of these molecular platforms is introduced along with an overview of their most recent applications for spatiotemporal regulation of biomolecular function in living cells or mice models. Challenges and the outlook are also presented. We hope this review paper will contribute to further progress in the development of molecular platforms and their biomedical use.

Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch

Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5'-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson-Crick base-pairing. We show that 5'-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5'-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.

"Click-switch" - one-step conversion of organic azides into photochromic diarylethenes for the generation of light-controlled systems

Diarylethenes (DAEs) are an established class of photochromic molecules, but their effective incorporation into pre-existing targets is synthetically difficult. Here we describe a new class of DAEs in which one of the aryl rings is a 1,2,3-triazole that is formed by “click” chemistry between an azide on the target and a matching alkyne–cyclopentene–thiophene component. This late-stage zero-length linking allows for tight integration of the DAE with the target, thereby increasing the chances for photomodulation of target functions. Nineteen different DAEs were synthesized and their properties investigated. All showed photochromism. Electron-withdrawing groups, and in particular −M-substituents at the triazole and/or thiophene moiety resulted in DAEs with high photo- and thermostability. Further, the chemical nature of the cyclopentene bridge had a strong influence on the behaviour upon UV light irradiation. Incorporation of perfluorinated cyclopentene led to compounds with high photo- and thermostability, but the reversible photochromic reaction was restricted to halogenated solvents. Compounds containing the perhydrogenated cyclopentene bridge, on the other hand, allowed the reversible photochromic reaction in a wide range of solvents, but had on average lower photo- and thermostabilities. The combination of the perhydrocyclopentene bridge and electron-withdrawing groups resulted in a DAE with improved photostability and no solvent restriction. Quantum chemical calculations helped to identify the photoproducts formed in halogenated as well as non-halogenated solvents. For two optimized DAE photoswitches, photostationary state composition and reaction quantum yields were determined. These data revealed efficient photochemical ring closure and opening. We envision applications of these new photochromic diarylethenes in photonics, nanotechnology, photobiology, photopharmacology and materials science.

New photochromic diarylethenes are reported in which one aryl ring is a 1,2,3-triazole that is formed by “click” chemistry between an azide on the target and a matching alkyne–cyclopentene–thiophene component.

Optochemical control of transcription by the use of 7-deaza-adenosine-based diarylethenes

Out of nine different 7-deaza-adenosine diarylethenes, we identified a high-performance photoswitch, suitable for the synthesis of photochromic DNA. By using solid phase synthesis, a photoresponsive T7 promotor was generated which allowed reversibly modulating the rate of enzymatic RNA synthesis in vitro.

"On-The-Fly" Non-Adiabatic Dynamics Simulations on Photoinduced Ring-Closing Reaction of a Nucleoside-Based Diarylethene Photoswitch

Nucleoside-based diarylethenes are emerging as an especial class of photochromic compounds that have potential applications in regulating biological systems using noninvasive light with high spatio-temporal resolution. However, relevant microscopic photochromic mechanisms at atomic level of these novel diarylethenes remain to be explored. Herein, we have employed static electronic structure calculations (MS-CASPT2//M06-2X, MS-CASPT2//SA-CASSCF) in combination with non-adiabatic dynamics simulations to explore the related photoinduced ring-closing reaction of a typical nucleoside-based diarylethene photoswitch, namely, PS-IV. Upon excitation with UV light, the open form PS-IV can be excited to a spectroscopically bright S₁ state. After that, the molecule relaxes to the conical intersection region within 150 fs according to the barrierless relaxed scan of the C1–C6 bond, which is followed by an immediate deactivation to the ground state. The conical intersection structure is very similar to the ground state transition state structure which connects the open and closed forms of PS-IV, and therefore plays a crucial role in the photochromism of PS-IV. Besides, after analyzing the hopping structures, we conclude that the ring closing reaction cannot complete in the S₁ state alone since all the C1–C6 distances of the hopping structures are larger than 2.00 Å. Once hopping to the ground state, the molecules either return to the original open form of PS-IV or produce the closed form of PS-IV within 100 fs, and the ring closing quantum yield is estimated to be 56%. Our present work not only elucidates the ultrafast photoinduced pericyclic reaction of the nucleoside-based diarylethene PS-IV, but can also be helpful for the future design of novel nucleoside-based diarylethenes with better performance.

Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches

Nucleosidic and oligonucleotidic diarylethenes (DAEs) are an emerging class of photochromes with high application potential. However, their further development is hampered by the poor understanding of how the chemical structure modulates the photochromic properties. Here we synthesized 26 systematically varied deoxyuridine- and deoxycytidine-derived DAEs and analyzed reaction quantum yields, composition of the photostationary states, thermal and photochemical stability, and reversibility. This analysis identified two high-performance photoswitches with near-quantitative, fully reversible back-and-forth switching and no detectable thermal or photochemical deterioration. When incorporated into an oligonucleotide with the sequence of a promotor, the nucleotides maintained their photochromism and allowed the modulation of the transcription activity of T7 RNA polymerase with an up to 2.4-fold turn-off factor, demonstrating the potential for optochemical control of biological processes.

Posttranscriptional Suzuki-Miyaura Cross-Coupling Yields Labeled RNA for Conformational Analysis and Imaging

Chemical labeling of RNA by using chemoselective reactions that work under biologically benign conditions is increasingly becoming valuable in the in vitro and in vivo analysis of RNA. Here, we describe a modular RNA labeling method based on a posttranscriptional Suzuki-Miyaura coupling reaction, which works under mild conditions and enables the direct installation of various biophysical reporters and tags. This two-part procedure involves the incorporation of a halogen-modified UTP analog (5-iodouridine-5'-triphosphate) by a transcription reaction. Subsequent posttranscriptional coupling with boronic acid/ester substrates in the presence of a palladium catalyst provides access to RNA labeled with (a) fluorogenic environment-sensitive nucleosides for probing nucleic acid structure and recognition, (b) fluorescent probes for microscopy, and (3) affinity tags for pull-down and immunoassays. It is expected that this method could also become useful for imaging nascent RNA transcripts in cells if the nucleotide analog can be metabolically incorporated and coupled with reporters by metal-assisted cross-coupling reactions.

Nucleic Acid Conformation Influences Postsynthetic Suzuki-Miyaura Labeling of Oligonucleotides

Chemoselective transformations that work under physiological conditions have emerged as powerful tools to label nucleic acids in cell-free and cellular environments. However, detailed studies investigating the influence of nucleic acid conformation on the performance of such chemoselective nucleic labeling methods are less explored. Given that nucleic acids adopt complex structures, it is highly important to study the scope of the chemical modification method in the context of nucleic acid conformations. Here we report a systematic study on the effect of local conformation on the postsynthetic Suzuki-Miyaura functionalization of human telomeric (H-Telo) DNA repeat oligonucleotide (ON) sequences, which form multiple G-quadruplex (GQ) structures. 5-Iodo-2'-deoxyuridine (IdU)-modified H-Telo ONs were synthesized by the solid-phase method, and when subjected to Suzuki-Miyaura cross-coupling reaction, its efficiency was found to depend on the type of conformation and the position of IdU label in different loops of the GQ structure. IdU-labeled GQs gave better yields as compared to single-stranded random coil structures. However, the IdU-labeled duplex under different ionic conditions did not undergo the coupling reaction. Further, using this method, we directly installed an environment-sensitive fluorescent probe, which photophysically reported the formation as well as distinguished different GQ topologies of telomeric repeat. Collectively, this systematic study underscores the influence of nucleic acid conformation, which has to be taken into account when establishing postsynthetic chemoselective functionalization strategies.

Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state

To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.

Synthesis strategies for non-symmetric, photochromic diarylethenes

Diarylethenes (DAEs) represent an important class of photochromes with notable characteristics, like thermally irreversible photoisomerization and high fatigue resistance. Structural diversification of the DAE scaffold has enabled further refinement of photochromic properties and realization of new applications, ranging from advanced materials to tools for studying biological systems. In particular, methods for synthesizing non-symmetric DAE scaffolds, which are typically more challenging to synthesize than their symmetric counterparts, have grown over the past 20 years. These developments are surveyed in this review, with discussion of how access to these compounds has contributed to the improvement of photochromic properties and paved the way for exploring new applications of DAEs. First, non-symmetric DAE structures are classified and their uses and applications are overviewed. Subsequent sections discuss the main strategies that have been used to access non-symmetric DAEs with examples illustrating the impact of non-symmetric DAEs in the growing field of light-controlled molecular systems.

Transition-Metal-Mediated Modification of Biomolecules

The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.

Norbornadiene-bridged diarylethenes and their conversion into turn-off fluorescent photoswitches

We describe the synthesis and characterization of novel diarylethene photoswitches that contain a norbornadiene bridge and operate as p-type positive photochromes. One of the double bonds of norbornadiene is furthermore utilized to attach a fluoresceine tetrazine by an iEDDA cascade reaction, thereby forming a turn-off mode fluorescent photoswitch.

Reversible single-crystal-to-single-crystal conversion of a photoreactive coordination network for rewritable optical memory storage

Reversible single-crystal-to-single-crystal photoreaction of a coordination network exhibits switchable fluorescence for rewritable optical memory storage.

Photoregulation between small DNAs and reversible photochromic molecules

Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

Photoswitchable oligonucleotides can determine specific biological outcomes by light-induced conformational changes. In particular, artificial probes activated by visible-light irradiation are highly desired in biological applications. Here, we report two novel types of visible-light photoswitchable peptide nucleic acids (PNAs) based on the molecular transducers: hemithioindigo and tetra-ortho-fluoroazobenzene. Our study reveals that the tetra-ortho-fluoroazobenzene-PNA conjugates have promising properties (fast reversible isomerization, exceptional thermal stability, high isomer conversions and sensitivity to visible-light irradiation) as reversible modulators to control oligonucleotide hybridization in biological contexts. Furthermore, we verified that this switchable modification delivers a slightly different hybridization behavior in the PNA. Thus, both melting experiments and strand-displacement assays showed that in all the cases the trans-isomer is the one with superior binding affinities. Alternative versions, inspired by our first compounds here reported, may find applications in different fields such as chemical biology, nanotechnology and materials science.

Photoswitchable Oligonucleotides Containing Different Diarylethene-Modified Nucleotides

Diarylethenes are a well-studied class of photoswitches and have often been linked to partner molecules to render them photoresponsive. Earlier, our lab developed a new type of diarylethenes in which the purine or pyrimidine base of a nucleoside or oligonucleotide serves as one of the two aryl residues of the photochromic system. Here, we report the synthesis of three different diarylethene-deoxyuridine phosphoramidites and their site-specific incorporation into oligodeoxynucleotides by solid-phase synthesis. Various DNA sequences carrying single or multiple, identical or different photoswitchable moieties are synthesized with high yield and purity. Upon UV irradiation, these DNA strands form a colored closed-ring isomer. The combination of different diarylethenes within one strand leads to an additive absorption spectrum. The photochromic DNA oligonucleotides are thermostable and photoreversible.

Ultrafast ring closing of a diarylethene-based photoswitchable nucleoside

Deoxyuridine nucleosides embodied into diarylethenes form an especial class of photoswitchable compounds that are designed to stack and pair with DNA bases. The molecular geometry can be switched between "open" and "closed" isomers by a pericyclic reaction that affects the stability of the surrounding double helix. This potentially enables light-induced control of DNA hybridization at microscopic resolution. Despite its importance for the optimization of DNA photoswitches, the ultrafast photoisomerization mechanism of these diarylethenes is still not well understood. In this work, femtosecond transient absorption spectroscopy is applied to study the ring closing reaction upon UV excitation with 45 fs pulses. Excited-state absorption decays rapidly and gives rise to the UV-Vis difference spectrum of the "closed" form within ≈15 ps. Time constants of 0.09, 0.49 and 6.6 ps characterize the multimodal dynamics, where a swift recurrence in the signal anisotropy indicates transient population of the intermediate 21A-like state.

An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases

The excitonic circuitry found in photosynthetic organisms suggests an alternative to electronic circuits, but the assembly of optically active molecules to fabricate even simple excitonic devices has been hampered by the limited availability of suitable molecular scale assembly technologies. Here we have designed and operated a hybrid all-optical excitonic switch comprised of donor/acceptor chromophores and photochromic nucleotide modulators assembled with nanometer scale precision using DNA nanotechnology. The all-optical excitonic switch was operated successfully in both liquid and solid phases, exhibiting high ON/OFF switching contrast with no apparent cyclic fatigue through nearly 200 cycles. These findings, combined with the switch's small footprint and volume, estimated low energy requirement, and potential ability to switch at speeds in the 10s of picoseconds, establish a prospective pathway forward for all-optical excitonic circuits.

Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection

Background

Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response.

Results

In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2'-deoxycytidine, an FDA-approved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment.

Conclusion

As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.

Comparative Study of Photoswitchable Zinc-Finger Domain and AT-Hook Motif for Light-Controlled Peptide-DNA Binding

DNA-peptide interactions are involved in key life processes, including DNA recognition, replication, transcription, repair, organization, and modification. Development of tools that can influence DNA-peptide binding non-invasively with high spatiotemporal precision could aid in determining its role in cells and tissues. Here, the design, synthesis, and study of photocontrolled tools for sequence-specific small peptide-DNA major and minor groove interactions are reported, shedding light on DNA binding by transcriptionally active peptides. In particular, photoswitchable moieties were implemented in the peptide backbone or turn region. In each case, DNA binding was affected by photochemical isomerization, as determined in fluorescent displacement assays on model DNA strands, which provides promising tools for DNA modulation.

Effects of heteroaryl ring on the photochromism of asymmetrical diarylethenes containing a naphthalene group

Photochromic asymmetrical diarylethene derivatives 1o-4o bearing different benzo-five-membered heterocyclic rings were synthesized and characterized with single-crystal X-ray diffraction microscopy. The effects of heterocyclic ring on their properties including the photochromic behaviors in solution, solid state and crystalline phase were systematically investigated. The diarylethenes bearing benzothiophene or indole ring exhibited high cyclization quantum yields in solution, and evidently enhanced the fluorescent modulation efficiency in solid state, while those containing benzofuran or thiophene ring exhibited the opposite behaviors. In addition, indole ring red-shifted the absorption maximum, and notably enhanced the fatigue resistance of the diarylethene. These results indicate that heteroaryl ring played an important role in the photoisomerization of these diarylethenes, causing the heterocyclic effect.

Design, Synthesis, and Characterization of Binaphthalene Precursors as Photoactivated DNA Interstrand Cross-Linkers

Most recently, alkylation via photogenerated carbocations has been identified as a novel mechanism for photoinduced DNA interstrand cross-link (ICL) formation by bifunctional aryl compounds. However, most compounds showed a low efficiency for DNA cross-linking. Here, we have developed a series of new 1,1'-binaphthalene analogues that efficiently form DNA ICLs upon 350 nm irradiation via generated 2-naphthalenylmethyl cations. The DNA cross-linking efficiency depends on the substituents at position 4 of the naphthalene moiety as well as the leaving groups. Compounds with NO₂, Ph, H, Br, or OMe substituents led to 2-4 times higher DNA ICL yields than those with a boronate ester group. Compounds with trimethylammonium salt as a leaving group showed slightly better cross-linking efficiency than those with bromo as a leaving group. Some of these compounds showed a better cross-linking efficiency than that of traditional alkylating agents, such as nitrogen mustard analogues or quinone methide precursors. These highly efficient photoactivated carbocation precursors allow determination and characterization of the adducts formed between the photogenerated naphthalenyl cations and four natural nucleosides, indicating that the alkylation sites for these naphthalene analogues are dG, dA, and dC.

Modification of oligodeoxynucleotides by on-column Suzuki cross-coupling reactions

The on-column functionalization of oligodeoxynucleotides via base-free Suzuki cross-coupling reactions is reported herein. These cross-coupling reactions were carried out with various boronic acids and either full-length modified oligonucleotides containing one or more 2'-deoxy-5-iodouridine (5IdU) monomer(s) or on oligonucleotide fragments immediately after incorporation of 5IdU. Five different functionalities were coupled to oligonucleotides containing one or three attachment points.

Unveiling the mechanism of the promising two-dimensional photoswitch - Hemithioindigo

The control of internal molecular motions by outside stimuli is a decisive task in the construction of functional molecules and molecular machines. Light-induced intramolecular rotations of photoswitches have attracted increasing research interests because of the high stability and high reversibility of photoswitches. Recently, Henry et al. reported an unprecedented two-dimensional controlled photoswitch, the hemithioindigo (HTI) derivative Z1, whose single bond rotation in dimethyl sulphoxide (DMSO) solvent and double bond rotation in cyclohexane solvent can be induced by visible light (J. Am. Chem. Soc. 2016, 138, 12,219). Here we investigate the intramolecular rotations of the HTI and Z1 in different polar solvents by time-dependent density functional theory (TDDFT) and Nonadiabatic dynamic simulations. Due to the steric hindrance between methyl and thioindigo fragment, the rotations of Z1 in the excited state are obstructed. Interestingly, the HTI exhibits two distinct rotation paths in DMSO and cyclohexane solvents at about 50fs. The intermolecular hydrogen bonds between HTI and DMSO play an important role in the rotation of HTI in DMSO solvent. Therefore, the HTI is a more promising two-dimensional photoswitch compared with the Z1. Our finding is thus of fundamental importance to understand the mechanisms of this class of photoswitches and design complex molecular behavior.

Efficiently Photocontrollable or Not? Biological Activity of Photoisomerizable Diarylethenes

Diarylethene derivatives, the biological activity of which can be reversibly changed by irradiation with light of different wavelengths, have shown promise as scientific tools and as candidates for photocontrollable drugs. However, examples demonstrating efficient photocontrol of their biological activity are still relatively rare. This concept article discusses the possible reasons for this situation and presents a critical analysis of existing data and hypotheses in this field, in order to extract the design principles enabling the construction of efficient photocontrollable diarylethene-based molecules. Papers addressing biologically relevant interactions between diarylethenes and biomolecules are analyzed; however, in most published cases, the efficiency of photocontrol in living systems remains to be demonstrated. We hope that this article will encourage further discussion of design principles, primarily among pharmacologists, synthetic and medicinal chemists.

Post-transcriptional labeling by using Suzuki-Miyaura cross-coupling generates functional RNA probes

Pd-catalyzed C-C bond formation, an important vertebra in the spine of synthetic chemistry, is emerging as a valuable chemoselective transformation for post-synthetic functionalization of biomacromolecules. While methods are available for labeling protein and DNA, development of an analogous procedure to label RNA by cross-coupling reactions remains a major challenge. Herein, we describe a new Pd-mediated RNA oligonucleotide (ON) labeling method that involves post-transcriptional functionalization of iodouridine-labeled RNA transcripts by using Suzuki-Miyaura cross-coupling reaction. 5-Iodouridine triphosphate (IUTP) is efficiently incorporated into RNA ONs at one or more sites by T7 RNA polymerase. Further, using a catalytic system made of Pd(OAc)2 and 2-aminopyrimidine-4,6-diol (ADHP) or dimethylamino-substituted ADHP (DMADHP), we established a modular method to functionalize iodouridine-labeled RNA ONs in the presence of various boronic acid and ester substrates under very mild conditions (37°C and pH 8.5). This method is highly chemoselective, and offers direct access to RNA ONs labeled with commonly used fluorescent and affinity tags and new fluorogenic environment-sensitive nucleoside probes in a ligand-controlled stereoselective fashion. Taken together, this simple approach of generating functional RNA ON probes by Suzuki-Miyaura coupling will be a very important addition to the resources and tools available for analyzing RNA motifs.

Electron donor and acceptor functionalized dithienylethenes: effects of charge density on photochromic properties

Electron-donating triphenylamine and/or electron-withdrawing pyromellitic diimide (PMDI) are functionalized on dithienylethene (DTE) and three novel photochromic materials have been designed and successfully synthesized. All the compounds display reversible photochromism due to the molecular switching between ring-closed isomers upon UV light irradiation and ring-open isomers upon exposure to visible light. Thus they can be applied as an anti-counterfeiting ink. Moreover, the study of the photoswitching kinetics reveals that both the ring-closing and ring-opening reactions are first-order reactions. Further charge population analysis discovers that the electron densities of the substituents at the DTE core have a dramatic influence on the photochromic properties. The incorporation of electron-donating triphenylamine groups at the α-position of the thiophene rings in the DTE unit facilitates the ring-closing reaction upon UV light irradiation. In contrast, the substitution of an electron-withdrawing PMDI unit in the DTE unit is beneficial to the ring-opening reaction upon irradiation of visible light. This work may help to understand the photochromism of DTE derivatives and provide a pathway for designing DTE-based photochromes with more or less sensitivity to UV or visible light.