A Photon-Fueled DNA Nanodevice that Contains Two Different Photoswitches

Orthogonal Photoswitching in a Porous Organic Framework

The development of photoresponsive systems with non-invasive orthogonal control by distinct wavelengths of light is still in its infancy. In particular, the design of photochemically triggered-orthogonal systems integrated into solid materials that enable multiple dynamic control over their properties remains a longstanding challenge. Here, we report the orthogonal and reversible control of two types of photoswitches in an integrated solid porous framework, that is, visible-light responsive o-fluoroazobenzene and nitro-spiropyran motifs. The properties of the constructed material can be selectively controlled by different wavelengths of light thus generating four distinct states providing a basis for dynamic multifunctional materials. Solid-state NMR spectroscopy demonstrated the selective transformation of the azobenzene switch in the bulk, which in turn modulates N2 and CO2 adsorption.

Site-Selective Photo-Crosslinking of Stilbene Pairs in a DNA Duplex Mediated by Ruthenium Photocatalyst

We herein report a method for site-selective photo-crosslinking of a DNA duplex. A stilbene pair was introduced into a DNA duplex and a ruthenium complex was conjugated with a triplex-forming oligonucleotide. We demonstrated that [2+2] photocycloaddition of the stilbene pair occurred upon irradiation with visible light when the ruthenium complex was in close proximity due to triplex formation. No reaction occurred when the ruthenium complex was not in proximity to the stilbene pair. The wavelength of visible light used was of lower energy than the wavelength of UV light necessary for direct excitation of stilbene. Quantum chemical calculation indicated that ruthenium complex catalyzed the photocycloaddition via triplet-triplet energy transfer. Site selectivity of this photo-crosslinking system was evaluated using a DNA duplex bearing two stilbene pairs as a substrate; we showed that the site of crosslinking was precisely regulated by the sequence of the oligonucleotide linked to the ruthenium complex. Since this method does not require orthogonal photoresponsive molecules, it will be useful in construction of complex photoresponsive DNA circuits, nanodevices and biological tools.

Azobenzene-containing surfactant directs small features of DNA thermotropic liquid crystals via bottom-up and top-down strategies

Compared to classical block copolymers, the self-assembly of small molecules shows an advantage in addressing small features. As a new type of solvent-free ionic complexes, azobenzene-containing DNA thermotropic liquid crystals (TLCs) form an assembly as block copolymers when using small DNA. However, the self-assembly behavior of such biomaterials has not been fully investigated. In this study, photoresponsive DNA TLCs are fabricated by employing an azobenzene-containing surfactant with double flexible chains. For these DNA TLCs, the self-assembly behavior of DNA and surfactants could be guided by the factors of the molar ratio of azobenzene-containing surfactant, dsDNA/ssDNA, and presence or absence of water, which addresses the bottom-up control on domain spacing of mesophase. Meanwhile, such DNA TLCs also gain top-down control on morphology via photoinduced phase change. This work would provide a strategy for regulating the small features of solvent-free biomaterials, facilitating the development of patterning templates based on photoresponsive biomaterials. STATEMENT OF SIGNIFICANCE: The relationship between nanostructure and function is attractive in the science of biomaterials. With biocompatibility and degradability, photoresponsive DNA materials in solutions have been widely studied in biological and medical areas, but they are still hard to obtain in a condensed state. The complex created with designed azobenzene-containing surfactants paves the way for obtaining condensed photoresponsive DNA materials. However, fine control of the small features of such biomaterials has not yet been achieved. In this study, we present a bottom-up strategy of controlling the small features of such DNA materials and, simultaneously, the top-down control of morphology via photoinduced phase change. This work provides a bi-directional approach to controlling the small features of condensed biomaterials.

Photoreversible DNA nanoswitch-based eluent-free strategy for the direct and effective isolation of highly-active thrombin from whole blood

This study proposes an eluent-free isolation strategy for the direct isolation of thrombin from whole blood via tandem temperature/pH dual-responsive polyether sulfone monolith and photoreversible DNA nanoswitch-functionalized metal-organic framework (MOF) aerogel. Temperature/pH dual-responsive microgel immobilized on polyether sulfone monolith was adopted to remove the matrix complexity of blood sample via size/charge screening effect. Photoreversible DNA nanoswitches, comprising thrombin aptamer, aptamer complementary ssDNA (cDNA) and the azobenzene-modified ssDNA (control DNA), were functionalized on MOF aerogel to offer efficient capturing of thrombin under irradiation of ultraviolet light (365 nm), driven by electrostatic and hydrogen bond interactions. The release of captured thrombin was easily achieved by changing the complementary behaviors of DNA strands via blue light (450 nm) irradiation. Thrombin with purity higher than 95 % can be directly obtained from whole blood using this tandem isolation procedure. Fibrin production and substrate chromogenic tests showed that the released thrombin possessed high biological activity. The photoreversible thrombin capturing-release strategy is merited with eluent-free, avoiding the loss of activity of thrombin in chemical circumstances and undesired dilution, providing a robust guarantee for subsequent application.

Sulfur and Azobenzenes, a Profitable Liaison: Straightforward Synthesis of Photoswitchable Thioglycosides with Tunable Properties

Azobenzene photoswitches are valuable tools for controlling properties of molecular systems with light. We have been investigating azobenzene glycoconjugates to probe carbohydrate-protein interactions and to design glycoazobenzene macrocycles with chiroptical and physicochemical properties modulated by light irradiation. To date, direct conjugation of glycosides to azobenzenes was performed by reactions providing target compounds in limited yields. We therefore sought a more effective and reliable coupling method. In this paper, we report on a straightforward thioarylation of azobenzene derivatives with glycosyl thiols as well as other thiols, thereby increasing the scope of azobenzene conjugation. Even challenging unsymmetrical conjugates can be achieved in good yields via sequential or one-pot procedures. Importantly, red-shifted azoswitches, which are addressed with visible light, were easily functionalized. Additionally, by oxidation of the sulfide bridge to the respective sulfones, both the photochromic and the thermal relaxation properties of the core azobenzene can be tuned. Utilizing this option, we realized orthogonal three-state photoswitching in mixtures containing two distinct azobenzene thioglycosides.

Dynamics of Excitons in Conjugated Molecules and Organic Semiconductor Systems

The exciton, an excited electron-hole pair bound by Coulomb attraction, plays a key role in photophysics of organic molecules and drives practically important phenomena such as photoinduced mechanical motions of a molecule, photochemical conversions, energy transfer, generation of free charge carriers, etc. Its behavior in extended π-conjugated molecules and disordered organic films is very different and very rich compared with exciton behavior in inorganic semiconductor crystals. Due to the high degree of variability of organic systems themselves, the exciton not only exerts changes on molecules that carry it but undergoes its own changes during all phases of its lifetime, that is, birth, conversion and transport, and decay. The goal of this review is to give a systematic and comprehensive view on exciton behavior in π-conjugated molecules and molecular assemblies at all phases of exciton evolution with emphasis on rates typical for this dynamic picture and various consequences of the above dynamics. To uncover the rich variety of exciton behavior, details of exciton formation, exciton transport, exciton energy conversion, direct and reverse intersystem crossing, and radiative and nonradiative decay are considered in different systems, where these processes lead to or are influenced by static and dynamic disorder, charge distribution symmetry breaking, photoinduced reactions, electron and proton transfer, structural rearrangements, exciton coupling with vibrations and intermediate particles, and exciton dissociation and annihilation as well.

Systematic investigation of the influence of electronic substituents on dinuclear gold(I) amidinates: synthesis, characterisation and photoluminescence studies

Dinuclear gold(I) compounds are of great interest due to their aurophilic interactions that influence their photophysical properties. Herein, we showcase that gold-gold interactions can be influenced by tuning the electronic properties of the ligands. Therefore, various para substituted (R) N,N'-bis(2,6-dimethylphenyl)formamidinate ligands (pRXylForm; Xyl = 2,6-dimethylphenyl and Form = formamidinate) were treated with Au(tht)Cl (tht = tetrahydrothiophene) to give via salt metathesis the corresponding gold(I) compounds [pRXylForm₂Au₂] (R = -OMe, -Me, -Ph, -H, -SMe, and -CO₂Me). All complexes showed intense luminescence properties at low temperatures. Alignment with the Hammett parameter σ_p revealed the trends in the ¹H and ¹³C NMR spectra. These results showed the influence of the donor-acceptor abilities of different substituents on the ligand system which were confirmed with calculated orbital energies. Photophysical investigations showed their lifetimes in the millisecond range indicating phosphorescence processes and revealed a redshift with the decreasing donor ability of the substituents in the solid state.

Photoregulative phase change biomaterials showing thermodynamic and mchanical stabilities

Azobenzenes are great photochromic molecules for switching the physical properties of various materials via trans-cis isomerization. However, the UV light resulted cis-azobenzene is metastable and thermodynamically gets back to trans-azobenzene after ceasing UV irradiation, which causes an unwanted property change of azobenzene-containing materials. Additionally, thermal and mechanical conditions would accelerate this process dramatically. In this present work, a new type of azobenzene-containing surfactant is designed for the fabrication of photoresponsive phase change biomaterials. With a "locked" cis-azobenzene conformation, the resulting biomaterials could maintain their disordered state after ceasing UV light, which exhibit great resistance to thermal and piezo conditions. Interestingly, the "locked" cis-azobenzene could be unlocked by Vis light in high efficiency, which opens a new way for the design of phase change materials only responding to light. By showing stable cis-azobenzene maintained physical state, the newly fabricated biomaterials provide new potential for the construction of advanced materials, like self-healing materials, with less use of long time UV irradiation for maintaining their disordered states.

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.

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

Light-Regulated Liquid-Liquid Phase Separation for Spatiotemporal Protein Recruitment and Cell Aggregation

We have previously shown that the upper critical solution temperature-type thermoresponsive ureido polymers such as polyallylurea and poly(2-ureidoethylmethacrylate) derivatives show liquid-liquid phase separation (LLPS), also known as simple coacervation, under physiological conditions below their phase-separation temperatures (T_p). The addition of the polymer-rich coacervate droplets that result from LLPS to a monolayer cell culture induced aggregation of cells into multicellular spheroids. In this study, we prepared a ureido copolymer, poly(vinylamine-co-vinylurea), with azobenzene substituents (Azo-PVU) and demonstrated light-guided assembly and disassembly of LLPS coacervates. Azo-PVUs with T_p values ranging from 10 to 52 °C were prepared by changing the azobenzene content. Ultraviolet light caused a decrease in the T_p of Azo-PVU because of trans-to-cis photoisomerization of the azobenzene and irradiation with visible light increased the T_p. Thus, LLPS of Azo-PVU was reversibly controlled. The coacervate droplets deposited on a dish surface were immediately dissolved by targeted UV irradiation (owing to a decrease in the T_p). Spatially controlled recruitment of proteins on the dish surface was achieved when protein solution was added to the light-patterned surface. Furthermore, the light-guided deposition of coacervates resulted in the spatiotemporal transformation of monolayer cells to aggregates. This light-controlled LLPS will allow the preparation of novel liquid-based materials for biomolecular and cellular engineering.

Synthesis, Derivatization and Photochemical Control of ortho-Functionalized Tetrachlorinated Azobenzene-Modified siRNAs

We report the chemical synthesis and derivatization of an ortho-functionalized tetrachlorinated azobenzene diol. A 4',4-dimethoxytrityl (DMT) phosphoramidite was synthesized for its site-specific incorporation within the sense strand of an siRNA duplex to form ortho-functionalized tetrachlorinated azobenzene-containing siRNAs (Cl-siRNAzos). Compared to a non-halogenated azobenzene, ortho-functionalized tetrachlorinated azobenzenes are capable of red-shifting the π→π* transition from the ultraviolet (UV) portion of the electromagnetic spectrum into the visible range. Within this visible range, the azobenzene molecule can be reliably converted from trans to cis with red light (660 nm), and converted back to trans with violet wavelength light (410 nm) and/or thermal relaxation. We also report the gene-silencing ability of these Cl-siRNAzos in cell culture as well as their reversible control with visible light for up to 24 hours.

Electrostatically PEGylated DNA enables salt-free hybridization in water

Chemically modified nucleic acids have long served as a very important class of bio-hybrid structures. In particular, the modification with PEG has advanced the scope and performance of oligonucleotides in materials science, catalysis and therapeutics. Most of the applications involving pristine or modified DNA rely on the potential of DNA to form a double-stranded structure. However, a substantial requirement for metal-cations to achieve hybridization has restricted the range of applications. To extend the applicability of DNA in salt-free or low ionic strength aqueous medium, we introduce noncovalent DNA-PEG constructs that allow canonical base-pairing between individually PEGylated complementary strands resulting in a double-stranded structure in salt-free aqueous medium. This method relies on grafting of amino-terminated PEG polymers electrostatically onto the backbone of DNA, which results in the formation of a PEG-envelope. The specific charge interaction of PEG molecules with DNA, absolute absence of metal ions within the PEGylated DNA molecules and formation of a double helix that is significantly more stable than the duplex in an ionic buffer have been unequivocally demonstrated using multiple independent characterization techniques.

Precise Cross-Dimensional Regulation of the Structure of a Photoreversible DNA Nanoswitch

In this study, an accurately and digitally regulated allosteric nanoswitch based on the conformational control of two DNA hairpins was developed. By switching between UV irradiation and blue light conditions, the second molecular beacon (H#2) would bind/separate with a repression sequence (RES) via the introduced PTG molecules (a photosensitive azobenzene derivative), resulting in the target aptamer sequence in the first molecular beacon (H#1) not being able/being able to hold the stem-loop configuration, hence losing/regaining the ability to bind with the target. Importantly, we successfully monitor conformation changes of the nanoswitch by an elegant mathematical model for connecting K_i (the dissociation constant between RES and H#2) with K_d (the overall equilibrium constant of the nanoswitch binding the target), hence realizing "observing" DNA structure across dimensions from "structural visualization" to digitization and, accurately, digitally regulating DNA structure from digitization to "structural visualization".

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.

A toolbox of molecular photoswitches to modulate the CXCR3 chemokine receptor with light

We report a detailed structure-activity relationship for the scaffold of VUF16216, a compound we have previously communicated as a small-molecule efficacy photoswitch for the peptidergic chemokine GPCR CXCR3. A series of photoswitchable azobenzene ligands was prepared through various synthetic strategies and multistep syntheses. Photochemical and pharmacological properties were used to guide the design iterations. Investigations of positional and substituent effects reveal that halogen substituents on the ortho-position of the outer ring are preferred for conferring partial agonism on the cis form of the ligands. This effect could be expanded by an electron-donating group on the para-position of the central ring. A variety of efficacy differences between the trans and cis forms emerges from these compounds. Tool compounds VUF15888 (4d) and VUF16620 (6e) represent more subtle efficacy switches, while VUF16216 (6f) displays the largest efficacy switch, from antagonism to full agonism. The compound class disclosed here can aid in new photopharmacology studies of CXCR3 signaling.

Photo-regulatable DNA isothermal amplification by template-mediated ligation

By combining azobenzene-tethered oligonucleotides as modulators and poly(l-lysine)-graft-dextran (PLL-g-Dex), a chaperone polymer, to facilitate strand displacement, we successfully developed a photo-regulatable DNA isothermal amplification method. By alternating UV and visible irradiation, linear amplification was achieved. The method enables photo-regulatability and mismatch discrimination in linear amplification of the DNA target.

Development of Visible-Light-Responsive RNA Scissors Based on a 10-23 DNAzyme

The 10-23 DNAzyme is an artificially developed functional oligonucleotide that can cleave RNA in a sequence-specific manner. In this study, we designed a new photo-driven DNAzyme incorporating a photoresponsive DNA overhang complementary to the catalytic core region. The photoresponsive overhang region of the DNAzyme included either azobenzene components (Azos) or 2,6-dimethyl-4-(methylthio)azobenzene units (SDM-Azos) each attached to a d-threoninol linker. When the Azos or SDM-Azos were in the trans form, the photoresponsive DNA overhang hybridized with the DNAzyme, and the RNA cleavage activity was suppressed. cis Isomerization of Azos or SDM-Azos, induced by 365 or 400 nm light, respectively, destabilized the duplex between the photoresponsive overhang and the catalytic core, and the DNAzyme recovered RNA cleavage activity. Reversible photoswitching of the DNAzyme activity was achieved by use of specific light irradiation. Further, light-dependent photoswitching of protein expression in the presence of the DNAzyme was demonstrated. Thus, this photo-driven DNAzyme has potential for application as a photocontrolled gene silencing system and a photoactivatable gene expression system.

Simultaneous complementary photoswitching of hemithioindigo tweezers for dynamic guest relocalization

Remote control of complex molecular behavior and function is one key problem in modern chemistry. Using light signaling for this purpose has many advantages, however the integration of different photo processes into a wholesome yet complex system is highly challenging. Here we report an alternative approach to increase complexity of light control-simultaneous complementary photoswitching-in which spectral overlap is used as an advantage to drastically reduce the signaling needed for controlling multipart supramolecular assemblies. Two photoswitchable molecular tweezers respond to the same light signals with opposite changes in their binding affinities. In this way the configuration of two host tweezers and ultimately the dynamic relocation of a guest molecule can be trigged by only one signal reversibly in the same solution. This approach should provide a powerful tool for the construction of sophisticated, integrated, and multi-responsive smart molecular systems in any application driven field of chemistry.

Controlling complex photoresponsive systems while minimizing light input is highly challenging. Here, the authors report two photoswitchable molecular tweezers responding to the same light signals with opposite changes in their binding affinities towards a guest molecule allowing for its “light-economic” relocation.

Recent developments in reversible photoregulation of oligonucleotide structure and function

There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.

Supramolecular aptamer nano-constructs for receptor-mediated targeting and light-triggered release of chemotherapeutics into cancer cells

Platforms for targeted drug-delivery must simultaneously exhibit serum stability, efficient directed cell internalization, and triggered drug release. Here, using lipid-mediated self-assembly of aptamers, we combine multiple structural motifs into a single nanoconstruct that targets hepatocyte growth factor receptor (cMet). The nanocarrier consists of lipidated versions of a cMet-binding aptamer and a separate lipidated GC-rich DNA hairpin motif loaded with intercalated doxorubicin. Multiple 2',6'-dimethylazobenzene moieties are incorporated into the doxorubicin-binding motif to trigger the release of the chemotherapeutics by photoisomerization. The lipidated DNA scaffolds self-assemble into spherical hybrid-nanoconstructs that specifically bind cMet. The combined features of the nanocarriers increase serum nuclease resistance, favor their import into cells presumably mediated by endocytosis, and allow selective photo-release of the chemotherapeutic into the targeted cells. cMet-expressing H1838 tumor cells specifically internalize drug-loaded nanoconstructs, and subsequent UV exposure enhances cell mortality. This modular approach thus paves the way for novel classes of powerful aptamer-based therapeutics.

Orthogonal Operation of Constitutional Dynamic Networks Consisting of DNA-Tweezer Machines

Overexpression or down-regulation of cellular processes are often controlled by dynamic chemical networks. Bioinspired by nature, we introduce constitutional dynamic networks (CDNs) as systems that emulate the principle of the nature processes. The CDNs comprise dynamically interconvertible equilibrated constituents that respond to external triggers by adapting the composition of the dynamic mixture to the energetic stabilization of the constituents. We introduce a nucleic acid-based CDN that includes four interconvertible and mechanically triggered tweezers, AA', BB', AB' and BA', existing in closed, closed, open, and open configurations, respectively. By subjecting the CDN to auxiliary triggers, the guided stabilization of one of the network constituents dictates the dynamic reconfiguration of the structures of the tweezers constituents. The orthogonal and reversible operations of the CDN DNA tweezers are demonstrated, using T-A·T triplex or K⁺-stabilized G-quadruplex as structural motifs that control the stabilities of the constituents. The implications of the study rest on the possible applications of input-guided CDN assemblies for sensing, logic gate operations, and programmed activation of molecular machines.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA

Azobenzene incorporated into DNA has a photoisomerization quantum yield that depends on the DNA sequence near the azobenzene attachment site. We use Molecular Dynamics computer simulations to elucidate which physical properties of the modified DNA determine the quantum yield. We show for a wide range of DNA sequences that the photoisomerization quantum yield is strongly correlated with the variance of the number of atoms in close proximity to the outer phenyl ring of the azobenzene group. We infer that quantum yield is controlled by the availability of fluctuations that enable the conformational change. We demonstrate that these simulations can be used as a qualitative predictive tool by calculating the quantum yield for several novel DNA sequences, and confirming these predictions using UV-vis spectroscopy. Our results will be useful for the development of a wide range of applications of photoresponsive DNA nanotechnology.

Orthogonal photoswitching in a multifunctional molecular system

The wavelength-selective, reversible photocontrol over various molecular processes in parallel remains an unsolved challenge. Overlapping ultraviolet-visible spectra of frequently employed photoswitches have prevented the development of orthogonally responsive systems, analogous to those that rely on wavelength-selective cleavage of photo-removable protecting groups. Here we report the orthogonal and reversible control of two distinct types of photoswitches in one solution, that is, a donor-acceptor Stenhouse adduct (DASA) and an azobenzene. The control is achieved by using three different wavelengths of irradiation and a thermal relaxation process. The reported combination tolerates a broad variety of differently substituted photoswitches. The presented system is also extended to an intramolecular combination of photoresponsive units. A model application for an intramolecular combination of switches is presented, in which the DASA component acts as a phase-transfer tag, while the azobenzene moiety independently controls the binding to α-cyclodextrin.

Red, far-red, and near infrared photoswitches based on azonium ions

Azonium ions formed by p-amino substituted azo compounds with both ortho- and meta-methoxy substituents exhibit strong absorbance in far-red and near infrared spectral region. The compounds undergo robust photoswitching in aqueous solution and exhibit a range of thermal relaxation rates from 10 μs-100 ms.

Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures

We report the stepwise assembly of supramolecular daisy chain rotaxanes (DCR) made of double-stranded DNA: Small dsDNA macrocycles bearing an axle assemble into a pseudo-DCR precursor that was connected to rigid DNA stoppers to form DCR with the macrocycles hybridized to the axles. In presence of release oligodeoxynucleotides (rODNs), the macrocycles are released from their respective hybridization sites on the axles, leading to stable mechanically interlocked DCRs. Besides the expected threaded DCRs, certain amounts of externally hybridized structures were observed, which dissociate into dumbbell structures in presence of rODNs. We show that the genuine DCRs have significantly higher degrees of freedom in their movement along the thread axle than the hybridized DCR precursors. Interlocking of DNA in DCRs might serve as a versatile principle for constructing functional DNA nanostructures where the movement of the subunits is restricted within precisely confined tolerance ranges.

Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif

The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+)  ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z isomerization.

Stiff-stilbene photoswitch ruptures bonds not by pulling but by local heating

The forces generated by stiff-stilbene during photoswitching are too low to cause bond rupture, which is instead initiated by heating.