Recent developments in reversible photoregulation of oligonucleotide structure and function

Light-Responsive Dynamic DNA-Origami-Based Plasmonic Assemblies

DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA‐based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non‐photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine‐based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA‐based devices and nanomaterials.

Reversible photo-regulation on the folding/unfolding of telomere G-quadruplexes with solid-state nanopores

The formation of G-quadruplexes (G4) in human telomere and other important biological regions inhibits the replication and transcription of DNA, thereby influencing further cell proliferation. The investigation of G4 formation and unfolding is vital for understanding their modulation in biological processes and life science. Photo regulation is a facile and sensitive approach for monitoring the structures of biomacromolecules and material surface properties. The nanopore-based technique is also prevalent for label-free single-molecule characterization with high accuracy. This study provides a combination of solid-state nanopore technology with light-switch as a platform for the modulation of human telomere G4 formation and splitting under switchable light exposure. The introduction of molecular switch, namely azobenzene moiety at different positions of the DNA sequence influences the formation and stability of G4. Three azobenzenes immobilized on each of the G-quartet plane (hTelo-3azo-p) or four azobenzenes on the same plane (hTelo-4azo-4p) of the human telomere G4 sequence realized the reversible control of G4 folding/unfolding at the temporal scale upon photo regulation, and the formation and splitting of G4 with hTelo-4azo-4p is slower and not thorough compared to that with hTelo-3azo-p due to the coplanar steric hindrance. Moreover, the G4 formation recorded with the combined nanopore and photo-responsive approach was also characterized with fluorescence, and the variation in the fluorescence intensity of the NMM and G4 complex exhibited a different tendency under reverse light irradiation due to the distinct interactions of NMM with the azobenzene-modified G4. Our study demonstrated a controllable and sensitive way for the manipulation of G4 structures, which will be inspiring for the intervention of G4-related cell senescence, cancer diagnosis and drug exploration.

Reductive stability evaluation of 6-azopurine photoswitches for the regulation of CKIα activity and circadian rhythms

6-Azopurines were evaluated for their reductive stability, and the ability to modulate CKIα activity and cellular circadian rhythms, revealing key challenges for long-term activity modulation utilizing chronophotopharmacology.

Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials

Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.

Hierarchical Synthesis, Structure, and Photophysical Properties of Gallium- and Ruthenium-Porphyrins with Axially Bonded Azo Ligands

The hierarchical synthesis of three porphyrin and four bisporphyrin derivatives is presented. This strategy relies on the incorporation of linkers based on azo moieties appended with pyridyl and/or acetylenic groups that facilitate axial coordination to Ga- and Ru-metalloporphyrins. These porphyrinic systems allow for a quantitative analysis of the effects of diamagnetic anisotropy (DA) by using ¹ H NMR spectroscopic and X-ray crystallographic analyses. A simple power-law relationship between the proton chemical shift and the distance from the porphyrin core is experimentally outlined, which confirms previous theoretical predictions and shows that the limit of DA is about 2 nm. Photophysical properties of the azo-linked porphyrins are analyzed by UV/Vis spectroscopy, showing that significant cis-trans isomerization is not observed for azo ligands bound only to Ga-porphyrins. Incorporation of Ru-porphyrins to an azo ligand facilitates photoswitching behavior, but the process faces competition from decarbonylation of the Ru-porphyrin, and appreciable switching is only documented for GaL1Ru.

Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex

Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus facilitate the photoisomerization reaction between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after trans-cis isomerization occurring in a longer time dynamics, in agreement with the experimental findings. The QM/MM simulations of the absorption spectra indicated that the thermal fluctuation plays a more crucial role in the main absorption band of the azobenzene derivatives than the inclusion of the G-quadruplex, implying that the influence of the G-quadruplex environment is minimal. We propose that the latter is attributed to the position of the azobenzene linkers in the G-quadruplexes, i.e. the edgewise loops containing the azobenzene moieties that are located above the G-quartets, not being fully embedded inside or involved in the stacked structure. Our theoretical findings provide support to a recent study of the photoresponsive formation of photoswitchable G-quadruplex motifs.

Chloro- and BF2bdk-substituted dithienylethene: Synthesis, photophysical properties, and optical switching behavior

A novel chloro- and BF2bdk-substituted dithienylethene derivative, in which a chlorine atom and a difluoroboron β-diketonate (BF2bdk) group are appended at the termini of the dithienylethene core, is developed. The structure was confirmed by 1H NMR, 13C NMR, and high-resolution mass spectrometry (electrospray ionization). It displayed solvent-dependent photophysical properties, and blue/red light-triggered optical switching behavior in nonpolar or less polar solvents.

A hydrogen peroxide activatable nanoprobe for light-controlled "double-check" multi-colour fluorescence imaging

A new probe for precise and accurate bioimaging contributes significantly to advancing biomedical research for early disease diagnosis and treatment monitoring. Through wrapping a photochromic molecule (SP-Np-B) within a polymer nanoparticle, a new light-controlled multicolour fluorescence nanoprobe (Poly-SP-Np-B) is developed for precise fluorescence subcellular bioimaging. Poly-SP-Np-B shows an "OFF-ON" red-emitting fluorescence response upon alternate UV/Vis light irradiation. After activation by hydrogen peroxide (H2O2), a green-emitting Poly-SP-Np nanoparticle is generated, thus allowing light-controlled fluorescence response simultaneously, i.e., green and yellow switch upon alternate UV/Vis light irradiation for 10 and 20 s, respectively. Such a "blinking" fluorescence signal change is not possible by only using a photochromic molecule probe (SP-Np-B) with alternate UV/vis light irradiation for over 5 min. Poly-SP-Np-B has large isomerization kinetic constants (kSP-MR = 0.4543 s-1 and kMR-SP = 0.0809 s-1), excellent biocompatibility and lysosome distribution capability, enabling multicolour fluorescence imaging in live cells. With exo-/endogenous H2O2 activation in lysosomes, light-controlled "double-check" fluorescence imaging at the subcellular level is successfully achieved. More specifically, the change in fluorescence imaging is reversible in green, red and yellow channels in live cells upon excitation under alternate UV and visible light. This work thus provides a new strategy to develop switchable photochromic probes for precise fluorescence bioassay and bioimaging.

Controlling Gene-Silencing with Azobenzene-Containing siRNAs (siRNAzos)

This article contains the detailed biophysical characterization, biological testing, and photo-switching protocols of azobenzene containing siRNAs (siRNAzos), which have photoswitchable properties that can be controlled with light. First, the siRNAzos are characterized by annealing the sense and anti-sense strands together and then measuring the circular dichroism (CD) profile, and the melting temperatures (T_m ) of the duplexes. Second, the biological testing of the siRNAzos in cell culture is done to determine their gene silencing efficacy. Finally, their gene-silencing activities are measured after exposure to ultraviolet (UV) light in order to inactivate the siRNAzo, and then broadband visible light, which re-activates the siRNAzo. This inactivation/reactivation protocol can be done in real time, and is reversible and robust and can be performed multiple times on the same sample if desired. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Bio-physical characterization of siRNAzo duplexes Basic Protocol 2: Evaluation of azobenzene gene-silencing using Firefly Luciferase Basic Protocol 3: Evaluation of azobenzene gene-silencing using reverse transcriptase-polymerase chain reaction (RT-PCR).

Proton-Gated Ring-Closure of a Negative Photochromic Azulene-Based Diarylethene

Proton-responsive photochromic molecules are attractive for their ability to react on non-invasive rapid optical stimuli and the importance of protonation/deprotonation processes in various fields. Conventionally, their acidic/basic sites are on hetero-atoms, which are orthogonal to the photo-active π-center. Here, we incorporate azulene, an acid-sensitive pure hydrocarbon, into the skeleton of a diarylethene-type photoswitch. The latter exhibits a novel proton-gated negative photochromic ring-closure and its optical response upon protonation in both open and closed forms is much more pronounced than those of diarylethene photoswitches with hetero-atom based acidic/basic moieties. The unique behavior of the new photoswitch can be attributed to direct protonation on its π-system, supported by 1H NMR and theoretical calculations. Our results demonstrate the great potential of integrating non-alternant hydrocarbons into photochromic systems for the development of multi-responsive molecular switches.

Spectroscopic Properties of Two 5'-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides

The synthesis of two 5'-end (4-dimethylamino)azobenzene conjugated G-quadruplex forming aptamers, the thrombin binding aptamer (TBA) and the HIV-1 integrase aptamer (T30695), was performed. Their structural behavior was investigated by means of UV, CD, fluorescence spectroscopy, and gel electrophoresis techniques in K+-containing buffers and water-ethanol blends. Particularly, we observed that the presence of the 5'-(4-dimethylamino)azobenzene moiety leads TBA to form multimers instead of the typical monomolecular chair-like G-quadruplex and almost hampers T30695 G-quadruplex monomers to dimerize. Fluorescence studies evidenced that both the conjugated G-quadruplexes possess unique fluorescence features when excited at wavelengths corresponding to the UV absorption of the conjugated moiety. Furthermore, a preliminary investigation of the trans-cis conversion of the dye incorporated at the 5'-end of TBA and T30695 showed that, unlike the free dye, in K+-containing water-ethanol-triethylamine blend the trans-to-cis conversion was almost undetectable by means of a standard UV spectrophotometer.

UV Accelerated Assemblies Constructed Using Calixpyridinium in Aqueous Solution

In this work, an irregular calixpyridinium-suramin sodium supramolecular assembly was constructed by the strong host-guest electrostatic interactions. More interestingly, a novel regular spherical supramolecular assembly was also fabricated by the hydrogen bonding interactions between suramin sodium and the UV accelerated addition product of deprotonated calixpyridinium in water. The same principle was also applied to construct a UV accelerated regular spherical self-assembly by the addition product of deprotonated calixpyridinium in water. Compared with the complicated and irreversible covalent connection of the light-responsive groups to the building block, which is one of the common means of obtaining light-responsive supramolecular systems, this finding not only provides a smart, facile, and universally applicable method to construct deprotonated calixpyridinium-based light-responsive host-guest systems but also provides a new idea for the development of other novel light-responsive building blocks.

Bioorthogonal Turn-On BODIPY-Peptide Photosensitizers for Tailored Photodynamic Therapy

Photodynamic therapy (PDT) leads to cancer remission via the production of cytotoxic species under photosensitizer (PS) irradiation. However, concomitant damage and dark toxicity can both hinder its use. With this in mind, we have implemented a versatile peptide-based platform of bioorthogonally activatable BODIPY-tetrazine PSs. Confocal microscopy and phototoxicity studies demonstrated that the incorporation of the PS, as a bifunctional module, into a peptide enabled spatial and conditional control of singlet oxygen (1 O2 ) generation. Comparing subcellular distribution, PS confined in the cytoplasmic membrane achieved the highest toxicities (IC50 =0.096±0.003 μm) after activation and without apparent dark toxicity. Our tunable approach will inspire novel probes towards smart PDT.

Spectroscopic Study of the E/Z Photoisomerization of a New Cyrhetrenyl Acylhydrazone: A Potential Photoswitch and Photosensitizer†

The new cyrhetrenyl acylhydrazone [(CO)₃ Re(η⁵ -C₅ H₄ )-C(O)-NH-N = C(CH₃ )-(2-C₄ H₂ S-5-NO₂ )] (E-CyAH) has been designed, synthesized and fully characterized to study the effect of having a cyrhetrenyl fragment (sensitizer) covalently bonded to an acylhydrazone moiety (switch), on its photophysical and photochemical properties. The crystal structure reveals that E-CyAH adopts an E-configuration around the iminic moiety [-N = C(CH₃ )]. The absorption spectrum of E-CyAH displays two bands at 270 and 380 nm, which are mainly ascribed to π → π* intraligand (IL) and d_π  → π* metal-to-ligand charge transfer (MLCT) transitions, being consistent with DFT/TD-DFT calculations. Upon 365 nm irradiation, E-CyAH photoisomerizes to Z-CyAH, as evidenced by UV-Vis and ¹ H-NMR spectral changes, with a quantum yield value Φ_{E -CyAH → Z -CyAH} of 0.30. Z-CyAH undergoes a first-order thermal back-isomerization process, with a relatively short half-life τ_1/2 of 277 min. Consequently, E-CyAH was quantitatively recovered after 24 h, making it a fully reversible T-type molecular photoswitch. This remarkable behavior allows us to measure the individual photophysical properties for both isomers. In addition, E-CyAH and Z-CyAH efficiently photosensitize the generation of singlet oxygen (O₂ (¹ Δ_g )) with good yield (Φ_Δ  = 0.342).

Photocaged functional nucleic acids for spatiotemporal imaging in biology

Imaging of species in living organisms with high spatiotemporal resolution is essential for understanding biological processes. While functional nucleic acids (FNAs), such as catalytic nucleic acids and aptamers, have emerged as effective sensors for a wide range of molecules, photocaged control of these FNAs has played a key role in translating them into bioimaging agents with high spatiotemporal control. In this review, we summarize methods and results of photocaged FNAs based on photolabile modifications, photoisomerization, and photothermal activation. Future directions, including strategies to improve the performance of these photocaged FNAs, are also described.

Photorelaxation Pathways of 4-(N,N-Dimethylamino)-4'-nitrostilbene Upon S1 Excitation Revealed by Conical Intersection and Intersystem Crossing Networks

Multi-state n-electron valence state second order perturbation theory (MS-NEVPT2) was utilized to reveal the photorelaxation pathways of 4-(N,N-dimethylamino)-4′-nitrostilbene (DANS) upon S₁ excitation. Within the interwoven networks of five S₁/S₀ and three T₂/T₁ conical intersections (CIs), and three S₁/T₂, one S₁/T₁ and one S₀/T₁ intersystem crossings (ISCs), those competing nonadiabatic decay pathways play different roles in trans-to-cis and cis-to-trans processes, respectively. After being excited to the Franck–Condon (FC) region of the S₁ state, trans-S₁-FC firstly encounters an ultrafast conversion to quinoid form. Subsequently, the relaxation mainly proceeds along the triplet pathway, trans-S₁-FC → ISC-S₁/T₂-trans → CI-T₂/T₁-trans → ISC-S₀/T₁-twist → trans- or cis-S₀. The singlet relaxation pathway mediated by CI-S₁/S₀-twist-c is hindered by the prominent energy barrier on S₁ surface and by the reason that CI-S₁/S₀-trans and CI-S₁/S₀-twist-t are both not energetically accessible upon S₁ excitation. On the other hand, the cis-S₁-FC lies at the top of steeply decreasing potential energy surfaces (PESs) towards the CI-S₁/S₀-twist-c and CI-S₁/S₀-DHP regions; therefore, the initial twisting directions of DN and DAP moieties determine the branching ratio between α_C=C twisting (cis-S₁-FC → CI-S₁/S₀-twist-c → trans- or cis-S₀) and DHP formation relaxation pathways (cis-S₁-FC → CI-S₁/S₀-DHP → DHP-S₀) on the S₁ surface. Moreover, the DHP formation could also take place via the triplet relaxation pathway, cis-S₁-FC → ISC-S₁/T₁-cis → DHP-T₁ → DHP-S₀, however, which may be hindered by insufficient spin-orbit coupling (SOC) strength. The other triplet pathways for cis-S₁-FC mediated by ISC-S₁/T₂-cis are negligible due to the energy or geometry incompatibility of possible consecutive stepwise S₁ → T₂ → T₁ or S₁ → T₂ → S₁ processes. The present study reveals photoisomerization dynamic pathways via conical intersection and intersystem crossing networks and provides nice physical insight into experimental investigation of DANS.

Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine-quinolizinium conjugates

Two new spiroindolinonaphthoxazine derivatives with an electron-accepting styrylquinolizinium or styrylcoralyne unit, respectively, were synthesized, and the influence of such an arylvinyl substituent on the chemical and photochemical properties of the compounds was investigated. Specifically, these spirooxazines turned out to be resistant towards the photoinduced merocyanine formation, and the irradiation with light mainly led to photodegradation of the substrates. However, it was shown by colorimetric and fluorimetric screening assays as well as by detailed NMR spectroscopic and mass spectrometric studies that the addition of particular metal ions (Cu2+, Fe3+, and to a certain extent Hg2+) initially induced a ring-opening reaction that was irreversibly followed by a fast ring closure-deprotonation-oxidation sequence to give styryl-substituted naphthoxazole derivatives as the products quantitatively. For the quinolizinium-substituted spirooxazine derivative, the formation of the respective oxidation product caused the development of a broad absorption band between 425 nm and 500 nm and a new emission band at λfl = 628 nm, so that it may be employed as a selective chemosensor or chemodosimeter for the colorimetric and fluorimetric detection of Cu2+ and Fe3+.

Encoding quantized fluorescence states with fractal DNA frameworks

Signal amplification in biological systems is achieved by cooperatively recruiting multiple copies of regulatory biomolecules. Nevertheless, the multiplexing capability of artificial fluorescent amplifiers is limited due to the size limit and lack of modularity. Here, we develop Cayley tree-like fractal DNA frameworks to topologically encode the fluorescence states for multiplexed detection of low-abundance targets. Taking advantage of the self-similar topology of Cayley tree, we use only 16 DNA strands to construct n-node (n = 53) structures of up to 5 megadalton. The high level of degeneracy allows encoding 36 colours with 7 nodes by site-specifically anchoring of distinct fluorophores onto a structure. The fractal topology minimises fluorescence crosstalk and allows quantitative decoding of quantized fluorescence states. We demonstrate a spectrum of rigid-yet-flexible super-multiplex structures for encoded fluorescence detection of single-molecule recognition events and multiplexed discrimination of living cells. Thus, the topological engineering approach enriches the toolbox for high-throughput cell imaging.

Though DNA framework-based scaffolds for biomolecular assembly are attractive for bioimaging applications, realizing super-multiplex fluorescent amplifiers remains a challenge. Here, the authors report a topological engineering approach to designing fractal DNA frameworks for multiplexed amplifiers.

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.

Switching the recognition ability of a photoswitchable receptor towards phosphorylated anions

An azobenzene based photoswitchable macrocyclic receptor displays different binding affinities in its E and Z forms towards various phosphorylated coenzymes under physiological conditions with remarkable selectivity for ATP in the E-form and selectivity towards GTP in the photoisomerized Z-form. Linear discriminant analysis clearly separated the analytes using the E-form. An application of this method enabled monitoring the progress of enzymatic phosphorylation using a tyrosine kinase enzyme.

A donor-acceptor type macrocycle: toward photolyzable self-assembly

A water-soluble macrocyclic host is reported, composed of alkoxyanthracene as the donor (D), and 4,4-bipyridinium as the acceptor (A). The intramolecular D-A structure renders the host highly photostable. However, the introduction of a strong electron-donating guest promotes the photodecomposition of alkoxyanthracene, yielding photolyzable host-guest complexes or aggregates.

Metal ions-triggered photo-induced fluorescence change in rhodamine B-based photo-responsive complexes

Photo-responsive materials with tunable properties by multiple stimuli have been widely used as molecular machines, molecular logic gates, optical data storages, etc. In this work, we report a rhodamine B-based photo-responsive system, whose properties could be facilely modulated by metal ions (Zn(II), Ni(II) and Hg(II)). These metal ions endow the complexes (L-Zn, L-Ni and L-Hg) with similar photochromic property but distinctly different photo-induced fluorescence change. Upon UV light irradiation, the spirolactam ring in rhodamine B moiety turned from a close form to an open form, along with enlarged conjugated structure with intense absorbance. Interestingly, fluorescence "turn off", "no change" and "turn on" responses were induced by Zn(II), Ni(II) and Hg(II) respectively upon UV light irradiation. Taking advantage of the prominently different characteristics caused by metal ions, different logic gates were designed by simply varying the inputs of metal ions and UV light. This work provided a new strategy for developing multifunctional photo-responsive materials, which were further beneficial for constructing photo-controlled logic gates with tunable performance.

AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides

We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.

Integrating 808 nm Light-Excited Upconversion Luminescence Powering with DNA Tetrahedron Protection: An Exceptionally Precise and Stable Nanomachine for Intracelluar MicroRNA Tracing

Although plentiful advanced fluorescence sensors have achieved to analyze microRNAs (miRNAs) in living cells, the prerequisite relating to nucleic acids specific recognition based sensing principle compels them lack favorable accurancy and stability in such complicated biological mediums. Here, we make a double breakthrough for the two challenges by combining a near-infrared (NIR) light powering process with a DNA tetrahedron (DNAT)-based protection concept. In this sensing system, a special nanomachine is first engineered by conjugating a core-shell-structured upconversion nanoparticle capable of highly converting 808 nm NIR photons into ultraviolet ones with self-assembling DNATs. The newly developed nanostructure not only prevents the sensing pathway from triggering during the intracellular delivery as well as reducing the adverse thermal effect for cell viability but also significantly enhances the enzyme resistance to avoid degradation to produce false signals. Furthermore, a fluorescence resonance energy transfer sensing strategy is rationally designed on this nanomachine. Upon using the powering light to excite the upconversion luminescence to activate the nanomachine in living cells, it can stably trace the precise level changes of miRNA-21 sequences at the reaching position with an "off-on" mode of fluorescence outputs.

Kinetics of photo-isomerization of azobenzene containing surfactants

We report on photoisomerization kinetics of azobenzene containing surfactants in aqueous solution. The surfactant molecule consists of a positively charged trimethylammonium bromide head group, a hydrophobic spacer connecting via 6 to 10 CH₂ groups to the azobenzene unit, and the hydrophobic tail of 1 and 3CH₂ groups. Under exposure to light, the azobenzene photoisomerizes from more stable trans- to metastable cis-state, which can be switched back either thermally in dark or by illumination with light of a longer wavelength. The surfactant isomerization is described by a kinetic model of a pseudo first order reaction approaching equilibrium, where the intensity controls the rate of isomerization until the equilibrated state. The rate constants of the trans-cis and cis-trans photoisomerization are calculated as a function of several parameters such as wavelength and intensity of light, the surfactant concentration, and the length of the hydrophobic tail. The thermal relaxation rate from cis- to trans-state is studied as well. The surfactant isomerization shows a different kinetic below and above the critical micellar concentration of the trans isomer due to steric hindrance within the densely packed micelle but does not depend on the spacer length.

Imidazole diarylethene switches: an alternative to acid-gated photochromism

Improving the photoactivity of imidazole diarylethenes by modifying their response sites in imidazole instead of appended aryl units is accomplished.

Visible-light photoswitching of ligand binding mode suggests G-quadruplex DNA as a target for photopharmacology

A pyridinium-decorated photoresponsive dithienylethene selectively targets G-quadruplex DNA, allowing binding mode and toxicity to be controlled exclusively with visible light.

Reversible control of RNA interference by siRNAzos

In this study, we report the reversible control of RNA interference using siRNAzos, a class of siRNAs that contain azobenzene.

The chemistry and applications of RNA 2'-OH acylation

RNA is a versatile biomolecule with a broad range of biological functions that go far beyond its initially described role as a simple information carrier. The development of chemical methods to control, manipulate and modify RNA has the potential to yield new insights into its many functions and properties. Traditionally, most of these methods involved the chemical modification of RNA structure using solid-state synthesis or enzymatic transformations. However, over the past 15 years, the direct functionalization of RNA by selective acylation of the 2'-hydroxyl (2'-OH) group has emerged as a powerful alternative that enables the simple modification of both synthetic and transcribed RNAs. In this Review, we discuss the chemical properties and design of effective reagents for RNA 2'-OH acylation, highlighting the unique problem of 2'-OH reactivity in the presence of water. We elaborate on how RNA 2'-OH acylation is being exploited to develop selective chemical probes that enable interrogation of RNA structure and function, and describe new developments and applications in the field.

Tunable Spreading and Shrinking on Photocontrolled Liquid Substrate

Droplets of n-hexadecane were observed to shrink under ultraviolet (365 nm) and spread under blue light (475 nm) irradiation on an aqueous solution of photosensitive surfactant AzoTAB. We demonstrate that the change of wettability of n-hexadecane droplet on the solution depends on the change of oil-water interface tension. According to the addition of ethanol into the substrate, the change of relative diameter ΔD/D exceeds 20%, much larger than the system without ethanol. With light-emitting diode (LED) light as a sole power source, without any other triggers, we provide a contactless and isothermal method to realize photocontrolled alternative spreading and shrinking of a droplet on a liquid surface, which provides a basis for a chromocapillary-based optical zoom liquid lens.

Synthesis of 5-Alkyl- and 5-Phenylamino-Substituted Azothiazole Dyes with Solvatochromic and DNA-Binding Properties

A series of new 5-mono- and 5,5'-bisamino-substituted azothiazole derivatives was synthesized from the readily available diethyl azothiazole-4,4'-dicarboxylate. This reaction most likely comprises an initial Michael-type addition by the respective primary alkyl and aromatic amines at the carbon atom C5 of the substrate. Subsequently, the resulting intermediates are readily oxidized by molecular oxygen to afford the amino-substituted azothiazole derivatives. The latter exhibit remarkably red-shifted absorption bands (λabs =507-661 nm) with high molar extinction coefficients and show a strong positive solvatochromism. As revealed by spectrometric titrations and circular and linear dichroism studies, the water-soluble, bis-(dimethylaminopropylamino)-substituted azo dye associates with duplex DNA by formation of aggregates along the phosphate backbone at high ligand-DNA ratios (LDR) and by intercalation at low LDR, which also leads to a significant increase of the otherwise low emission intensity at 671 nm.

Visible light-induced thymine dimerisation based on large localised field gradient by non-uniform optical near-field

The localised excitations of several molecular reactions utilising optical irradiation have been studied in the field of molecular physics. In particular, deoxyribonucleic acid (DNA) strands organise the genetic information of all living matter. Therefore, artificial methods for freely controlling reactions using only light irradiation are highly desirable for reactions of these strands; this in regard with artificial protein synthesis, regional genetic curing, and stochastic analysis of several genetic expressions. Generally, DNA strands have strong absorption features in the deep ultra-violet (DUV) region, which are related to the degradation and reconstruction of the strand bonding structures. However, irradiation by DUV light unavoidably induces unintended molecular reactions which can damage and break the DNA strands. In this paper, we report a photo-induced molecular reaction initiated by the irradiation of DNA strands with visible light. We utilised photo-dissociation from the vibrational levels induced by non-uniform optical near-fields surrounding nanometric Au particles to which DNA strands were attached. The results were experimentally observed by a reduction in the DUV absorbance of the DNA strands during irradiation. There was a much higher yield of molecular reactions than expected due to the absorbance of visible light, and no defects were caused in the DNA strands.

Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides

Metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, have shown promise as functional units to develop stimuli-responsive DNA materials. Although a variety of metal-mediated base pairs have been constructed with artificial ligand-type nucleotides and various metal ions, the application of such metal-mediated base pairs has been relatively poorly explored mainly due to the cumbersome chemical synthesis of artificial DNA strands. Herein we report a facile enzymatic method to synthesize DNA strands containing a ligand-type hydroxypyridone (H) nucleotide, which forms a Cu^II-mediated base pair (H-Cu^II-H). A two-step primer extension reaction using two commercially available polymerases enabled the incorporation of a H nucleotide at an internal position of oligonucleotides. The polymerase synthesis was subsequently applied to the development of metal-responsive deoxyribozymes (DNAzymes), whose catalytic activity was regulated by the formation of a single H-Cu^II-H base pair in its stem region. The DNAzyme activity was reversibly switched by the alternate addition and the removal of Cu^II ions. Furthermore, metal-dependent orthogonal activation of a Cu^II-responsive H-DNAzyme and a Hg^II-responsive T-DNAzyme was experimentally demonstrated by utilizing both H-Cu^II-H as well as widely explored T-Hg^II-T base pairs. These results suggest that the incorporation of H-Cu^II-H base pairs would facilitate the rational design of metal-responsive functional DNAs. Accordingly, the facile enzymatic synthesis of artificial ligand-bearing DNAs developed in this study would significantly expand the toolbox of DNA-based supramolecular chemistry and DNA nanotechnology.

Aldehyde-substituted acceptor-DTE-acceptor-type dithienylethene as a versatile building block for near-infrared photochromic materials

A novel aldehyde-substituted acceptor-DTE-acceptor-type dithienylethene derivative, in which the difluoroboron β-diketonate and aldehyde groups at the termini of the dithienylethene function as electron acceptors, has been developed. The structure was confirmed by 1H NMR, 13C NMR, 19F NMR, high-resolution mass spectrometry (electrospray ionization) and infrared. The derivative displays solvent-dependent photophysical properties, visible light–triggered near-infrared photochromism, and fluorescent switching behavior in solvents of different polarity. Moreover, it can be utilized as a versatile building block to construct novel near-infrared photochromic materials.

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.

Efficient green light-excited switches based on dithienylethenes with BF2-doped π-conjugated systems

A series of dithienylethenes 1a-1d with BF₂-doped π-conjugation have been successfully developed. Upon alternating irradiation with green light and red/NIR light, they show efficient photochromism and fluorescence switching behaviors in toluene and PMMA film. Moreover, the fluorescence of 1a can be switched effectively in living cells.

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.

Photolysis of a calixpyridinium-based supramolecular amphiphilic assembly and its selective turn-on fluorescence recognition of lysine in water

A new calixpyridinium-based light-responsive host-guest recognition motif was found in this work. This host-guest recognition motif was further discovered to be applied as a selective turn-on fluorescent sensor for lysine over other natural amino acids.