Recent developments in reversible photoregulation of oligonucleotide structure and function

Optical Control of the GTP Affinity of K-Ras(G12C) by a Photoswitchable Inhibitor

Photocontrol of protein activity is an emerging field in biomedicine. For optical control of a mutant small GTPase K-Ras(G12C), we developed small-molecule inhibitors with photoswitchable efficacy, where one configuration binds the target protein and exert different pharmacological effects upon light irradiation. The compound design was based on the structure feature of a previously identified allosteric pocket of K-Ras(G12C) and the chemical structure of covalent inhibitors, and resulted in the synthesis and characterization of two representative azobenzene-containing compounds. Nucleotide exchange assays demonstrated the different efficacy to control the GTP affinity by photoswitching of one potent compound PS-C2, which would be a useful tool to probe the conformation of mutational K-Ras. Our study demonstrated the feasibility of designing photoswitchable modulators from allosteric covalent inhibitor of small GTPases.

Blue-/NIR Light-Excited Fluorescence Switch Based on a Carbazole-Dithienylethene-BF2bdk Triad

The development of novel solid-state fluorescence switches, particularly triggered by visible light, is of increasing interest for the potential application in optical data storage and super-resolution fluorescence microscopies. In this study, two carbazole-dithienylethene-BF₂bdk triads CDB1 and CDB2, suspending carbazole and BF₂bdk moieties on both sides of dithienylethene unit, have been developed. They exhibit blue-/NIR light-controlled photochromism with solvent-dependent characteristics. Moreover, CDB1 (o) reveals blue-/NIR light-induced reversible fluorescent switching behaviors in toluene, chloroform, poly(methyl methacrylate) (PMMA) film, and powder state, while its analogue CDB2 (o) in the powder state exhibits no fluorescence due to a strong intermolecular π-π stacking interaction, and the fluorescent switching performance is observed only in toluene and PMMA film. The density functional theory calculations further validate the differences in their optical properties in the solution and powder states.

Hybrid Azo-fluorophore Organic Nanoparticles as Emissive Turn-on Probes for Cellular Endocytosis

The development of fluorescent organic nanoparticles, serving as bioimaging agents or drug cargos, represents a buoyant field of investigations. Nevertheless, their ulterior fate and structural integrity after cell uptake remain elusive. Toward this aim, we have elaborated original photoactive organic nanoparticles (d_TEM ∼ 35-50 nm wide) with an off-on signal upon cellular internalization. Such nanoparticles are based on the noncovalent association of red-emitting benzothiadiazole (BDZ) derivatives and azo dyes, acting as fluorescence quenchers. Upon varying the azo/BDZ ratio, we found that quantitative emission quenching could be obtained with only a 0.2:1 azo/BDZ ratio and originated from exergonic oxidative and reductive photoinduced electron transfer from the azo units (Δ_elG⁰ = -0.21 and -0.29 eV, respectively). Such results revisited the origin of emission quenching, often confusedly ascribed to Förster resonance energy transfer. A nonlinear and sharp drop of the emission intensity with the increase in the azo unit density n was observed and presents comparable evolution to a n^-1/3 mathematical law. Thorough biological examinations involving cancer cells prove a receptor-independent endocytosis pathway, leading to progressive cell lighting upon nanoparticle accumulation in the late endosomal/lysosomal compartments. Complete emission recovery of the initially quenched azo/BDZ nanosystems could be achieved by using mefloquine, which caused endosomal/lysosomal disruption, and release of their content in the cytoplasm. Such results demonstrate that the dotlike emission from endosomes actually stems from fully dissociated individual dyes and not integer nanoparticles. They conclude on the high spatial confinement promoted by organelles and finally question its severe impact on functional compounds or nanoparticles whose properties are strongly distance dependent.

Introducing LNAzo: More Rigidity for Improved Photocontrol of Oligonucleotide Hybridization

Oligonucleotide-based therapeutics have made rapid progress in clinical treatment of a variety of disease indications. Since most therapeutic oligonucleotides serve more than just one function and tend to have a prolonged lifetime, spatio-temporal control of these functions would be desirable. Photoswitches like azobenzene have proven themselves as useful tools in this matter. Upon irradiation, the photoisomerization of the azobenzene moiety causes destabilization in adjacent base pairs, leading to a decreased hybridization affinity. Since the way the azobenzene is incorporated in the oligonucleotide is of utmost importance, we synthesized locked azobenzene C-nucleosides and compared their photocontrol capabilities to established azobenzene C-nucleosides in oligonucleotide test-sequences by means of fluorescence-, UV/Vis-, and CD-spectroscopy.

Photoswitchable peptides for spatiotemporal control of biological functions

Light is unsurpassed in its ability to modulate biological interactions. Since their discovery, chemists have been fascinated by photosensitive molecules capable of switching between isomeric forms, known as photoswitches. Photoswitchable peptides have been recognized for many years; however, their functional implementation in biological systems has only recently been achieved. Peptides are now acknowledged as excellent protein-protein interaction modulators and have been important in the emergence of photopharmacology. In this review, we briefly explain the different classes of photoswitches and summarize structural studies when they are incorporated into peptides. Importantly, we provide a detailed overview of the rapidly increasing number of examples, where biological modulation is driven by the structural changes. Furthermore, we discuss some of the remaining challenges faced in this field. These exciting proof-of-principle studies highlight the tremendous potential of photocontrollable peptides as optochemical tools for chemical biology and biomedicine.

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.

Visible-range hemi-indigo photoswitch: ON-OFF fluorescent binder for HIV-1 RNA

A proof-of-principle for the application of hemi-indigo derivatives as RNA binders with photocontrollable fluorescence is presented. The photoswitch binds to the human immunodeficiency virus type 1 (HIV-1) RNA with a significant light-up effect. The fluorescence of the RNA-bound ligand can be reversibly switched ON and OFF by light without destroying the ligand-RNA associates.

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.

Light-controlled thrombin catalysis and clot formation using a photoswitchable G-quadruplex DNA aptamer

The reversible photocontrol of an enzyme governing blood coagulation is demonstrated. The thrombin binding aptamer (TBA), was rendered photochromic by modification with two anthracene groups. Light-triggered anthracene photodimerisation distorts its structure, inhibiting binding of the enzyme thrombin, which in turn triggers catalysis and the resulting clotting process.

Photoswitchable Fluorescent Crystals Obtained by the Photoreversible Coassembly of a Nucleobase and an Azobenzene Intercalator

Self-assembled nucleobases, such as G-quartets or quadruplexes, have numerous applications, but light-responsive structures are limited to small, noncrystalline motifs. In addition, the assembly of the widely exploited azobenzene photochromic compounds can produce fluorescent crystals of extended dimensions but at the prize of sacrificing their photoswitchability. Here, we overcome inherent limitations of self-assembly with a new concept of supramolecular coassembly leading to materials with unprecedented properties. We show that the coassembly of guanosine monophosphate (GMP) with an azobenzene-containing DNA intercalator produces supramolecular crystals arranged through a combination of π-π, electrostatic, and hydrogen-bond interactions. The resulting crystals are 100 μm long, pH-sensitive, fluorescent, and can be photoreversibly disassembled/reassembled upon UV/blue irradiation. This allows us to perform operations such as dynamic photocontrol of a single-crystal growth, light-gated permeability in membrane-like materials, and photoswitchable fluorescence. We believe this concept critically expands the breadth of multifunctional materials attainable by self-assembly.

Synthesis and properties of dithienylethene-functionalized switchable antibacterial agents

Photopharmacology involving azobenzene has offered a viable alternative for combating bacterial resistance. However, the degradation and potential toxicity of azobenzene limit its further study in vivo. Therefore, searching for an appropriate photoswitch for further clinical application is highly desirable. Herein a series of dithienylethene-functionalized switchable antibacterial agents have been designed and prepared by the introduction of the dithienylethene scaffold into fluoroquinolones. And it was found that these switchable antibacterial agents displayed good photochromism and fluorescence switching behaviors upon irradiation with UV/Vis light in DMSO. Surprisingly, methoxy-substituted dithienylethenes 3a and 3b exhibited fluorescence turn-on behavior. Furthermore, it was found that all of the open-isomers showed partial antibacterial activity on E. coli and S. aureus compared with the native drugs. Apart from 2a and 2b, the other switchable antibacterial agents showed a large difference in antibacterial activity on Gram-negative E. coli between the open and closed forms, in which the antimicrobial activity of the ring-closed isomers for 1b and 3b was 16 times that of the corresponding ring-open isomers. DFT calculations showed that the ring-closed isomers of 1b and 3b presented a rigid "S-type" conformation, which may be conducive to forming more stable complexes with the DNA gyrase of E. coli.

ortho-Fluoroazobenzene derivatives as DNA intercalators for photocontrol of DNA and nucleosome binding by visible light

We report a high-affinity photoswitchable DNA binder, which displays different nucleosome-binding capacities upon visible-light irradiation. Both photochemical and DNA-recognition properties were examined by UV-Vis, HPLC, CD spectroscopy, NMR, FID assays, EMSA and DLS. Our probe sets the basis for developing new optoepigenetic tools for conditional modulation of nucleosomal DNA accessibility.

A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA

The polymorphic nature of G-quadruplex (G4) DNA structures points to a range of potential applications in nanodevices and an opportunity to control G4 in biological settings. Light is an attractive means for the regulation of oligonucleotide structure as it can be delivered with high spatiotemporal precision. However, surprisingly little attention has been devoted towards the development of ligands for G4 that allow photoregulation of G4 folding. We report a novel G4-binding chemotype derived from stiff-stilbene. Surprisingly however, whilst the ligand induces high stabilization in the potassium form of human telomeric DNA, it causes the unfolding of the same G4 sequence in sodium buffer. This effect can be reversed on demand by irradiation with 400 nm light through deactivation of the ligand by photo-oxidation. By fuelling the system with the photolabile ligand, the conformation of G4 DNA was switched five times.

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.

Design, Synthesis, Investigation, and Application of a Macromolecule Photoswitch

Azobenzene (AZO) has attracted increasing interest due to its reversible structural change upon a light stimulus. However, poor fatigue durability and the photobleaching phenomenon restricts its further application. Herein, the AZO domain as a pendent group, was incorporated into copolymers, which was synthesized by radical copolymerization in the research. Structure-properties of synthesized copolymer can be adjusted by monomer ratios. Emphatically, responsive properties of copolymer in different solutions were investigated. In the DMSO solution, copolymer exhibited effective structural change, stable rapid responsive time (1 min) upon UV light at room temperature, stable relative acceptable recovery time (100 min) upon white light at room temperature, and good fatigue resistance property. In an aqueous solution, even more controllable responsive properties and fatigue resistance properties for copolymer were verified by results. More pervasively, the recovery process could be controlled by light density and temperature. In order to clarify reasons for the difference between the AZO molecule and the AZO domain of copolymer, energy barrier or interactions between single atoms or even structural units was calculated using the density functional theory (DFT). Furthermore, the status of copolymer was characterized by dynamic light scattering (DLS) and transmission electron microscope (TEM). Finally, copolymer was further functionalized with bioactive protein (concanavalin, ConA) to reduce the cytotoxicity of the AZO molecule.

New Acylhydrazone Photoswitches with Quantitative Conversion and High Quantum Yield but without Hydrogen Bond Stabilizing ( Z)-Isomer

Hydrazones are recently attracting increasing interest because of their facile synthesis and high addressability, fatigue resistance, and modifiability as molecular switches. However, this new class of switches generally suffers from low conversion from E- to Z-configuration. Here, novel benzoylhydrazones were synthesized by condensation of 2-methoxynaphthaldhyde and benzoylhydrazine. In this hydrazone system, both sides of the imine double bond had large steric hindrance, so that the ( E)-isomer of the benzoylhydrazones was less stable and easily converted into the ( Z)-isomer even without an intramolecular hydrogen bond. Up to 99% conversion efficiency and 89% quantum yield were obtained, in addition to excellent addressability and high fatigue resistance. Outstandingly, the crystal structure of one ( Z)-isomer disclosed no intermolecular hydrogen bonds between the molecules of the ( Z)-isomer but strong and sequential hydrogen bonds between those of the ( E)-isomer. Therefore, the ( E)-isomer was less soluble in solvents than the ( Z)-isomer. This molecular switch system could be easily modified by both hydrophilic pentaethylene glycol chains and hydrophobic octyl chains. Under light irradiation, the resultant amphiphilic acylhydrazone could be transferred from ( E)-isomer to ( Z)-isomer in more than 90% yield even in water after light irradiation. Meanwhile, the self-assembled big nanospheres could rearrange into much smaller vesicles because of the solubility difference of ( Z)- and ( E)-isomers. After the anticancer drug procarbazine was loaded by this kind of acylhydrazone in water, it could be released by light irradiation, showing potential application in photocontrollable drug release.

Recent Implementations of Molecular Photoswitches into Smart Materials and Biological Systems

Light is a nearly ideal stimulus for molecular systems. It delivers information encoded in the form of wavelengths and their intensities with high precision in space and time. Light is a mild trigger that does not permanently contaminate targeted samples. Its energy can be reversibly transformed into molecular motion, polarity, or flexibility changes. This leads to sophisticated functions at the supramolecular and macroscopic levels, from light-triggered nanomaterials to photocontrol over biological systems. New methods and molecular adapters of light are reported almost daily. Recently reported applications of photoresponsive systems, particularly azobenzenes, spiropyrans, diarylethenes, and indigoids, for smart materials and photocontrol of biological setups are described herein with the aim to demonstrate that the 21st century has become the Age of Enlightenment-"Le siècle des Lumières"-in molecular sciences.

Tuning the photochromic properties of chromophores containing a nitrile-rich acceptor: a novel branch in the investigation of negative photochromes

High photoswitching contrast and variation of the thermal stability of the photoinduced form for a novel group of reverse photochromes are described for the first time.

Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra

DNA intercalation and groove binding of two photoswitching dithienylethene derivatives have been studied and characterized by means of molecular dynamics and electronic circular dichroism.

Controlling interfacial interactions of supramolecular assemblies by light-responsive overcrowded alkenes

A light-responsive supramolecular polymer was constructed by an AB-type monomer containing a light-responsive overcrowded alkene. The primary assemblies of the supramolecular polymer can further undertake secondary self-assembly by interfacial host-guest connections, which can be manipulated by light stimuli to convert into discrete primary assemblies.

Reversible Photocontrol of DNA Melting by Visible-Light-Responsive F4-Coordinated Azobenzene Compounds

Spatiotemporal control over the regulation of intra- and intermolecular motions in naturally occurring systems is systematically studied to expand the toolbox of mechanical operations in multicomponent nanoarchitectures. DNA is ideally suited for programming light-powered processes that are based on a minimalist molecular design. Here, the noncovalent incorporation of bistable photoswitches into B-like DNA moieties is shown to trigger the thermal transition midpoint of the duplexes by converting visible light into directed mechanical work by orchestrating the collective actions of the photoresponsive chromophores and the host DNA nanostructures. Besides its practical applications, the resulting hybrid nanosystem bears unique features of modulability, biocompatibility, reversibility, and addressability, which are key components for developing molecular photon-controlled programmed materials.

Aldehyde-Substituted Donor–Acceptor-Type Dithienylethenes as Novel Building Blocks for Photochromic Materials

Two novel donor–π–acceptor-type dithienylethene derivatives, in which the triphenylamine group acts as electron donor and the formyl group functions as electron acceptor, have been developed. Their structures were confirmed by 1H NMR, 13C NMR and HRMS (ESI). Investigation of their photochromic properties indicated that they had good photochromic behaviour and excellent fatigue resistance on irradiation with UV or visible light. DFT calculations further validated these experimental results for photochromic behaviour. Moreover, these compounds can be utilised as versatile building blocks to construct novel near-infrared photochromic materials.

Self-Assembled Porphyrazine Nucleosides on DNA Templates: Highly Fluorescent Chromophore Arrays and Sizing Forensic Tandem Repeat Sequences

The formation of chromophore arrays using a DNA templating approach leads to the creation of supramolecular assemblies, where the optical properties of the overall system can be fine-tuned to a large extent. In particular, porphyrin derivatives have been shown to be versatile building blocks; mostly covalent chemistry was used for embedding the units into DNA strands. Self-assembly of porphyrin modified nucleosides, on the other hand, has not been investigated as a simplified approach. We report on the synthesis of a magnesium(II) tetraaza porphine (MgTAP) coupled to deoxyuridine, and array formation on DNA templates which contain well-defined oligo(dA) segments showing strong fluorescence enhancement which is significantly larger than that with a Zn-porphyrin. The use of the deep-eutectic solvent glycholine is essential for successful assembly formation. The system allows for sizing of short tandem repeat markers with multiple adenosines, thus the concept could be adaptable to in vitro forensic DNA profiling with a suitable set of different chromophores on all nucleosides.

Conformational changes of DNA induced by a trans-azobenzene derivative via non-covalent interactions

In biological environments and in aqueous solution, DNA generally adopts the canonical B conformation. Recently, an azobenzene photoswitch containing a polyamine chain with three positive charges was shown to induce a reversible conformational transition between the A and B forms of DNA, the transition being triggered by trans-cis isomerization of the photoswitch upon non-covalent intercalation. It was proposed that, in its trans conformation, azobenzene stabilizes the A form of DNA. The structural details and the mechanism upon which trans-azobenzene induces the B-to-A DNA transition remain, however, unclear. In the present work, two possible intercalating modes of trans-azobenzene, from the minor groove and from the major groove, were investigated with all-atom molecular-dynamics simulations. Intercalation from the major groove was found to be the most probable binding mode due to favorable electrostatic and π-π stacking interactions. The free-energy profile associated with the B-to-A conformational transition reveals that intercalation from the major groove leads to a conformational change of DNA, showing a slight tendency to interconvert from B- to A-DNA, in agreement with the CD spectrum obtained from the experiment. However, the presence of only one interacting azobenzene is not sufficient to lead to a global conformational change to A-DNA. The present results are expected to serve in the design of DNA switches, which can induce reversible DNA conformational changes.

Molecular Motors in Aqueous Environment

Molecular motors are Nature's solution for (supra)molecular transport and muscle functioning and are involved in most forms of directional motion at the cellular level. Their synthetic counterparts have also found a myriad of applications, ranging from molecular machines and smart materials to catalysis and anion transport. Although light-driven rotary molecular motors are likely to be suitable for use in an artificial cell, as well as in bionanotechnology, thus far they are not readily applied under physiological conditions. This results mainly from their inherently aromatic core structure, which makes them insoluble in aqueous solution. Here, the study of the dynamic behavior of these motors in biologically relevant media is described. Two molecular motors were equipped with solubilizing substituents and studied in aqueous solutions. Additionally, the behavior of a previously reported molecular motor was studied in micelles, as a model system for the biologically relevant confined environment. Design principles were established for molecular motors in these media, and insights are given into pH-dependent behavior. The work presented herein may provide a basis for the application of the remarkable properties of molecular motors in more advanced biohybrid systems.

Donor-acceptor Stenhouse adduct-grafted polycarbonate surfaces: selectivity of the reaction for secondary amine on surface

Donor-acceptor Stenhouse adducts (DASAs) are gaining attention from organic and material chemists due to their visible light-stimulated photochromic properties. In this report, we present a facile method for grafting coloured triene on polycarbonate surface, without involving any pre-treatments like plasma activation, etc. The chemoselectivity of carbonate with a primary amine and Meldrum's activated furan (MAF) with polymer bound secondary amine has been exploited to graft photoswitchable DASA on the polymer surface. Primary, secondary and tertiary amine-functionalized polycarbonate surfaces have been prepared to evaluate the reactivity of amine with MAF.

Light-driven chiroptical photoswitchable DNA assemblies mediated by bioinspired photoresponsive molecules

We show that the incorporation of chiral bioinspired photochromic compounds into inherently chiral DNA matrices enables the building of smart nanoscale photoswitchable chiroptical assemblies tunable over a wide range of wavelengths. Moreover, the use of light as external trigger affords precise control of the resulting hybrid DNA nanostructures, and their chiroptical activities can be spatially modulated without photochemical fatigue.

Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study

Azobenzene covalently attached to RNA undergoes trans-to-cis photo-switching on a time scale of ∼15 picoseconds – 30 times slower than in vacuo.

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA–azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a β-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ∼10–15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA–azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

Cell-Free Optogenetic Gene Expression System

Optogenetic tools provide a new and efficient way to dynamically program gene expression with unmatched spatiotemporal precision. To date, their vast potential remains untapped in the field of cell-free synthetic biology, largely due to the lack of simple and efficient light-switchable systems. Here, to bridge the gap between cell-free systems and optogenetics, we studied our previously engineered one component-based blue light-inducible Escherichia coli promoter in a cell-free environment through experimental characterization and mathematical modeling. We achieved >10-fold dynamic expression and demonstrated rapid and reversible activation of the target gene to generate oscillatory response. The deterministic model developed was able to recapitulate the system behavior and helped to provide quantitative insights to optimize dynamic response. This in vitro optogenetic approach could be a powerful new high-throughput screening technology for rapid prototyping of complex biological networks in both space and time without the need for chemical induction.

Photoswitching of DNA Hybridization Using a Molecular Motor

Reversible control over the functionality of biological systems via external triggers may be used in future medicine to reduce the need for invasive procedures. Additionally, externally regulated biomacromolecules are now considered as particularly attractive tools in nanoscience and the design of smart materials, due to their highly programmable nature and complex functionality. Incorporation of photoswitches into biomolecules, such as peptides, antibiotics, and nucleic acids, has generated exciting results in the past few years. Molecular motors offer the potential for new and more precise methods of photoregulation, due to their multistate switching cycle, unidirectionality of rotation, and helicity inversion during the rotational steps. Aided by computational studies, we designed and synthesized a photoswitchable DNA hairpin, in which a molecular motor serves as the bridgehead unit. After it was determined that motor function was not affected by the rigid arms of the linker, solid-phase synthesis was employed to incorporate the motor into an 8-base-pair self-complementary DNA strand. With the photoswitchable bridgehead in place, hairpin formation was unimpaired, while the motor part of this advanced biohybrid system retains excellent photochemical properties. Rotation of the motor generates large changes in structure, and as a consequence the duplex stability of the oligonucleotide could be regulated by UV light irradiation. Additionally, Molecular Dynamics computations were employed to rationalize the observed behavior of the motor–DNA hybrid. The results presented herein establish molecular motors as powerful multistate switches for application in biological environments.

QM/MM Studies on Photoisomerization Dynamics of Azobenzene Chromophore Tethered to a DNA Duplex: Local Unpaired Nucleobase Plays a Crucial Role

The photoresponsive azobenzene-tethered DNAs have received growing experimental attention because of their potential applications in biotechnology and nanotechnology; however, little is known about the initial photoisomerization of azobenzene in these systems. Herein we have employed quantum mechanics/molecular mechanics (QM/MM) methods to explore the photoisomerization dynamics of an azobenzene-tethered DNA duplex. We find that in the S₁ state the trans-cis photoisomerization path is much steeper in DNA than in vacuo, which makes the photoisomerization much faster in the DNA environment. This acceleration is primarily caused by complex steric interactions between azobenzene and the nearby unpaired thymine nucleobase, which also change the photoisomerization mechanism of azobenzene in the DNA duplex.

Orthogonal photo-switching of supramolecular patterned surfaces

We used Azo/α-CD and ipAzo/γ-CD host-guest complexes to demonstrate that four independent stable states can be orthogonally photo-switched by UV (365 nm), blue (470 nm), green (530 nm) and red light (625 nm). A supramolecular patterned surface was fabricated and orthogonally photo-switched by light with different wavelengths.

RNA Control by Photoreversible Acylation

External photocontrol over RNA function has emerged as a useful tool for studying nucleic acid biology. Most current methods rely on fully synthetic nucleic acids with photocaged nucleobases, limiting application to relatively short synthetic RNAs. Here we report a method to gain photocontrol over RNA by postsynthetic acylation of 2'-hydroxyls with photoprotecting groups. One-step introduction of these groups efficiently blocks hybridization, which is restored after light exposure. Polyacylation (termed cloaking) enables control over a hammerhead ribozyme, illustrating optical control of RNA catalytic function. Use of the new approach on a transcribed 237 nt RNA aptamer demonstrates the utility of this method to switch on RNA folding in a cellular context, and underlines the potential for application in biological studies.

Synergy of Two Highly Specific Biomolecular Recognition Events: Aligning an AT-Hook Peptide in DNA Minor Grooves via Covalent Conjugation to 2'-Amino-LNA

Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes. The significant cooperative DNA duplex stabilization may pave the way toward further development of POCs with enhanced affinity and selectivity toward target sequences carrying peptide-binding genetic islands.

Real-Time and Accurate Identification of Single Oligonucleotide Photoisomers via an Aerolysin Nanopore

Identification of the configuration for the photoresponsive oligonucleotide plays an important role in the ingenious design of DNA nanomolecules and nanodevices. Due to the limited resolution and sensitivity of present methods, it remains a challenge to determine the accurate configuration of photoresponsive oligonucleotides, much less a precise description of their photoconversion process. Here, we used an aerolysin (AeL) nanopore-based confined space for real-time determination and quantification of the absolute cis/ trans configuration of each azobenzene-modified oligonucleotide (Azo-ODN) with a single molecule resolution. The two completely separated current distributions with narrow peak widths at half height (<0.62 pA) are assigned to cis/ trans-Azo-ODN isomers, respectively. Due to the high current sensitivity, each isomer of Azo-ODN could be undoubtedly identified, which gives the accurate photostationary conversion values of 82.7% for trans-to- cis under UV irradiation and 82.5% for cis-to- trans under vis irradiation. Further real-time kinetic evaluation reveals that the photoresponsive rate constants of Azo-ODN from trans-to- cis and cis-to -trans are 0.43 and 0.20 min^-1, respectively. This study will promote the sophisticated design of photoresponsive ODN to achieve an efficient and applicable photocontrollable process.

Photochromism into nanosystems: towards lighting up the future nanoworld

The ability to manipulate the structure and function of promising nanosystems via energy input and external stimuli is emerging as an attractive paradigm for developing reconfigurable and programmable nanomaterials and multifunctional devices. Light stimulus manifestly represents a preferred external physical and chemical tool for in situ remote command of the functional attributes of nanomaterials and nanosystems due to its unique advantages of high spatial and temporal resolution and digital controllability. Photochromic moieties are known to undergo reversible photochemical transformations between different states with distinct properties, which have been extensively introduced into various functional nanosystems such as nanomachines, nanoparticles, nanoelectronics, supramolecular nanoassemblies, and biological nanosystems. The integration of photochromism into these nanosystems has endowed the resultant nanostructures or advanced materials with intriguing photoresponsive behaviors and more sophisticated functions. In this Review, we provide an account of the recent advancements in reversible photocontrol of the structures and functions of photochromic nanosystems and their applications. The important design concepts of such truly advanced materials are discussed, their fabrication methods are emphasized, and their applications are highlighted. The Review is concluded by briefly outlining the challenges that need to be addressed and the opportunities that can be tapped into. We hope that the review of the flourishing and vibrant topic with myriad possibilities would shine light on exploring the future nanoworld by encouraging and opening the windows to meaningful multidisciplinary cooperation of engineers from different backgrounds and scientists from the fields such as chemistry, physics, engineering, biology, nanotechnology and materials science.

Optochemical Control of Biological Processes in Cells and Animals

Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.

Rapid Capture and Release of Nucleic Acids through a Reversible Photo-Cycloaddition Reaction in a Psoralen-Functionalized Hydrogel

Reversible immobilization of DNA and RNA is of great interest to researchers who seek to manipulate DNA or RNA in applications such as microarrays, DNA hydrogels, and gene therapeutics. However, there is no existing system that can rapidly capture and release intact nucleic acids. To meet this unmet need, we developed a functional hydrogel for rapid DNA/RNA capture and release based on the reversible photo-cycloaddition of psoralen and pyrimidines. The functional hydrogel can be easily fabricated through copolymerization of acrylamide with the synthesized allylated psoralen. The psoralen-functionalized hydrogel exhibits effective capture and release of nucleic acids spanning a wide range of lengths in a rapid fashion; over 90 % of the capture process is completed within 1 min, and circa 100 % of the release process is completed within 2 min. We observe no deleterious effects on the hybridization to the captured targets.