Photoswitching of DNA Hybridization Using a Molecular Motor

Bimodal DNA self-origami material with nucleic acid function enhancement

BACKGROUND

The design of DNA materials with specific nanostructures for biomedical tissue engineering applications remains a challenge. High-dimensional DNA nanomaterials are difficult to prepare and are unstable; moreover, their synthesis relies on heavy metal ions. Herein, we developed a bimodal DNA self-origami material with good biocompatibility and differing functions using a simple synthesis method. We simulated and characterized this material using a combination of oxDNA, freeze-fracture electron microscopy, and atomic force microscopy. Subsequently, we optimized the synthesis procedure to fix the morphology of this material.

RESULTS

Using molecular dynamics simulation, we found that the bimodal DNA self-origami material exhibited properties of spontaneous stretching and curling and could be fixed in a single morphology via synthesis control. The application of different functional nucleic acids enabled the achievement of various biological functions, and the performance of functional nucleic acids was significantly enhanced in the material. Consequently, leveraging the various functional nucleic acids enhanced by this material will facilitate the attainment of diverse biological functions.

CONCLUSION

The developed design can comprehensively reveal the morphology and dynamics of DNA materials. We thus report a novel strategy for the construction of high-dimensional DNA materials and the application of functional nucleic acid-enhancing materials.

Light-Activated Assembly of DNA Origami into Dissipative Fibrils

Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif-protonated, self-complementary poly(adenine) sequences-can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.

A visible-light-driven molecular motor based on barbituric acid

We present a class of visible-light-driven molecular motors based on barbituric acid. Due to a serendipitous reactivity we observed during their synthesis, these motors possess a tertiary stereogenic centre on the upper half, characterised by a hydroxy group. Using a combination of femto- and nanosecond transient absorption spectroscopy, molecular dynamics simulations and low-temperature 1H NMR experiments we found that these motors operate similarly to push-pull second-generation overcrowded alkene-based molecular motors. Interestingly, the hydroxy group at the stereocentre enables a hydrogen bond with the carbonyl groups of the barbituric acid lower half, which drives a sub-picosecond excited-state isomerisation, as observed spectroscopically. Computational simulations predict an excited state "lasso" mechanism where the intramolecular hydrogen bond pulls the molecule towards the formation of the metastable state, with a high predicted quantum yield of isomerisation (68%) in gas phase.

Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations

DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is necessary, both in simple solvents as well as more complex and diverse anisotropic environments. Here we analyse an archetypal six-duplex DNA nanoarchitecture with single-particle cryo-electron microscopy and molecular dynamics simulations in solvents of tunable ionic strength and within the anisotropic environment of biological membranes. Outside lipid bilayers, the six-duplex bundle lacks the designed symmetrical barrel-type architecture. Rather, duplexes are arranged in non-hexagonal fashion and are disorted to form a wider, less elongated structure. Insertion into lipid membranes, however, restores the anticipated barrel shape due to lateral duplex compression by the bilayer. The salt concentration has a drastic impact on the stability of the inserted barrel-shaped DNA nanopore given the tunable electrostatic repulsion between the negatively charged duplexes. By synergistically combining experiments and simulations, we increase fundamental understanding into the environment-dependent structural dynamics of a widely used nanoarchitecture. This insight will pave the way for future engineering and biosensing applications.

Accounts of applied molecular rotors and rotary motors: recent advances

Molecular machines are nanoscale devices capable of performing mechanical works at molecular level. These systems could be a single molecule or a collection of component molecules that interrelate with one another to produce nanomechanical movements and resulting performances. The design of the components of molecular machine with bioinspired traits results in various nanomechanical motions. Some known molecular machines are rotors, motors, nanocars, gears, elevators, and so on based on their nanomechanical motion. The conversion of these individual nanomechanical motions to collective motions via integration into suitable platforms yields impressive macroscopic output at varied sizes. Instead of limited experimental acquaintances, the researchers demonstrated several applications of molecular machines in chemical transformation, energy conversion, gas/liquid separation, biomedical use, and soft material fabrication. As a result, the development of new molecular machines and their applications has accelerated over the previous two decades. This review highlights the design principles and application scopes of several rotors and rotary motor systems because these machines are used in real applications. This review also offers a systematic and thorough overview of current advancements in rotary motors, providing in-depth knowledge and predicting future problems and goals in this area.

Modulating the Lifetime of DNA Motifs Using Visible Light and Small Molecules

Here we regulate the formation of dissipative assemblies built from DNA using a merocyanine photoacid that responds to visible light. The operation of our system and the relative distribution of species within it are controlled by irradiation time, initial pH value, and the concentration of a small-molecule binder that inhibits the reaction cycle. This approach is modular, does not require DNA modification, and can be used for several DNA sequences and lengths. Our system design allows for waste-free control of dissipative DNA nanotechnology, toward the generation of nonequilibrium, life-like nanodevices.

Martini 3 Coarse-Grained Model for Second-Generation Unidirectional Molecular Motors and Switches

Artificial molecular motors (MMs) and switches (MSs), capable of undergoing unidirectional rotation or switching under the appropriate stimuli, are being utilized in multiple complex and chemically diverse environments. Although thorough theoretical work utilizing QM and QM/MM methods have mapped out many of the critical properties of MSs and MMs, as the experimental setups become more complex and ambitious, there is an ever increasing need to study the behavior and dynamics of these molecules as they interact with their environment. To this end, we have parametrized two coarse-grained (CG) models of commonly used MMs and a model for an oxindole-based MS, which can be used to study the ground state behavior of MMs and MSs in large simulations for significantly longer periods of time. We also propose methods to perturb these systems which can allow users to approximate how such systems would respond to MMs rotating or the MSs switching.

Controllable DNA hybridization by host-guest complexation-mediated ligand invasion

Dynamic regulation of nucleic acid hybridization is fundamental for switchable nanostructures and controllable functionalities of nucleic acids in both material developments and biological regulations. In this work, we report a ligand-invasion pathway to regulate DNA hybridization based on host-guest interactions. We propose a concept of recognition handle as the ligand binding site to disrupt Watson-Crick base pairs and induce the direct dissociation of DNA duplex structures. Taking cucurbit[7]uril as the invading ligand and its guest molecules that are integrated into the nucleobase as recognition handles, we successfully achieve orthogonal and reversible manipulation of DNA duplex dissociation and recovery. Moreover, we further apply this approach of ligand-controlled nucleic acid hybridization for functional regulations of both the RNA-cleaving DNAzyme in test tubes and the antisense oligonucleotide in living cells. This ligand-invasion strategy establishes a general pathway toward dynamic control of nucleic acid structures and functionalities by supramolecular interactions.

Chemically Driven Rotatory Molecular Machines

Molecular machines are at the frontier of biology and chemistry. The ability to control molecular motion and emulating the movement of biological systems are major steps towards the development of responsive and adaptive materials. Amazing progress has been seen for the design of molecular machines including light-induced unidirectional rotation of overcrowded alkenes. However, the feasibility of inducing unidirectional rotation about a single bond as a result of chemical conversion has been a challenging task. In this Review, an overview of approaches towards the design, synthesis, and dynamic properties of different classes of atropisomers which can undergo controlled switching or rotation under the influence of a chemical stimulus is presented. They are categorized as molecular switches, rotors, motors, and autonomous motors according to their type of response. Furthermore, we provide a future perspective and challenges focusing on building sophisticated molecular machines.

Intrinsically unidirectional chemically fuelled rotary molecular motors

Biological systems mainly utilize chemical energy to fuel autonomous molecular motors, enabling the system to be driven out of equilibrium¹. Taking inspiration from rotary motors such as the bacterial flagellar motor² and adenosine triphosphate synthase³, and building on the success of light-powered unidirectional rotary molecular motors^4-6, scientists have pursued the design of synthetic molecular motors solely driven by chemical energy^7-13. However, designing artificial rotary molecular motors operating autonomously using a chemical fuel and simultaneously featuring the intrinsic structural design elements to allow full 360° unidirectional rotary motion like adenosine triphosphate synthase remains challenging. Here we show that a homochiral biaryl Motor-3, with three distinct stereochemical elements, is a rotary motor that undergoes repetitive and unidirectional 360° rotation of the two aryl groups around a single-bond axle driven by a chemical fuel. It undergoes sequential ester cyclization, helix inversion and ring opening, and up to 99% unidirectionality is realized over the autonomous rotary cycle. The molecular rotary motor can be operated in two modes: synchronized motion with pulses of a chemical fuel and acid-base oscillations; and autonomous motion in the presence of a chemical fuel under slightly basic aqueous conditions. This rotary motor design with intrinsic control over the direction of rotation, simple chemical fuelling for autonomous motion and near-perfect unidirectionality illustrates the potential for future generations of multicomponent machines to perform mechanical functions.

Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation.

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks.

Controlling rotary motion of molecular motors based on oxindole

Molecular motors are essential components of artificial molecular machines, which can be used to manipulate and amplify mechanical motion at the nanoscale to create machine-like function. Since the discovery of light-driven rotary molecular motors, the field has been widely developed, including the introduction of molecular motors based on oxindole by our group in 2019. The rotational properties of molecular motors, e.g. absorption wavelength, quantum yield and rotation speed, often critically depend on substituent effects. Up to now, the substituent effects of oxindole-based molecular motors have not yet been investigated. Herein, we present a family of oxindole-based molecular motors functionalised at three different positions on the motor core, with either CN or OMe groups. The motors prepared in this work retain the favourable features of oxindole-based motors, i.e. simple synthesis and visible light addressability. We find that functionalisation has substantial effects on the absorption wavelength of the motors, meanwhile the rotation speed is unaffected. Furthermore, we found that functionalisation of the oxindole molecular motors increases their quantum efficiency considerably in comparison to previous motors of their class.

We present a new family of oxindole-based functionalised at three positions on the upper and lower halves, with methoxy or cyano groups. We find that this allows the absorption wavelength and quantum yields of these motors to be tuned.

Photoswitchable single-stranded DNA-peptide coacervate formation as a dynamic system for reaction control

In cells, segregation allows for diverse biochemical reactions to take place simultaneously. Such intricate regulation of cellular processes is achieved through the dynamic formation and disassembly of membraneless organelles via liquid-liquid phase separation (LLPS). Herein, we demonstrate the light-controlled formation and disassembly of liquid droplets formed from a complex of polylysine (pLys) and arylazopyrazole (AAP)-conjugated single-stranded DNA. Photoswitchablility of droplet formation was also shown to be applicable to the control of chemical reactions; imine formation and a DNAzyme-catalyzed oxidation reaction were accelerated in the presence of droplets. These outcomes were reversed upon droplet disassembly. Our results demonstrate that the photoswitchable droplet formation system is a versatile model for the regulation of reactions through dynamic LLPS.

•

Incorporating AAP enabled light-controlled droplet formation with ssDNA and pLys

•

Droplets were reversibly formed or disassembled without altering sample composition

•

Photoswitchability depended on sequence and ionic interactions but not flexibility

•

Photoswitchable droplet formation accelerated uncatalyzed and catalyzed reactions

Synthesis and Functionality Study of Photoswitchable Hydrazone Oligodeoxynucleotides

This article provides a detailed procedure for the chemical synthesis and characterization of photoswitchable hydrazone phosphoramidite and its incorporation into oligodeoxynucleotides. The synthesis starts with commercially available deoxyuridine, followed by conversion of the 4-oxo into a 4-chloro moiety via Appel reaction to install the key hydrazone group in the absence of base. The hydrazone phosphoramidite building block is compatible with the conventional amidite chemistry protocols for solid-phase synthesis of oligodeoxynucleotides. Our method expands the current nucleotide pool by adding a novel, functional DNA building block that is suitable for a broad spectrum of applications, including the regulation of DNA-enzyme interactions and DNA synthesis by irradiation with cell-friendly blue light. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of photoswitchable hydrazone phosphoramidite Basic Protocol 2: Synthesis and purification of oligodeoxynucleotides containing the hydrazone photoswitch Basic Protocol 3: Primer extension assay for functionality studies of hydrazone cytidine.

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.

Photoresponsive Control of G-Quadruplex DNA Systems

G-quadruplex (G4) oligonucleotide secondary structures have recently attracted significant attention as therapeutic targets owing to their occurrence in human oncogene promoter sequences and the genome of pathogenic organisms. G4s also demonstrate interesting catalytic activities in their own right, as well as the ability to act as scaffolds for the development of DNA-based materials and nanodevices. Owing to this diverse range of opportunities to exploit G4 in a variety of applications, several strategies to control G4 structure and function have emerged. Interrogating the role of G4s in biology requires the delivery of small-molecule ligands that promote its formation under physiological conditions, while exploiting G4 in the development of responsive nanodevices is normally achieved by the addition and sequestration of the metal ions required for the stabilization of the folded structure. Although these strategies prove successful, neither allows the system in question to be controlled externally. Meanwhile, light has proven to be an attractive means for the control of DNA-based systems as it is noninvasive, can be delivered with high spatiotemporal precision, and is orthogonal to many chemical and biological processes. A plethora of photoresponsive DNA systems have been reported to date; however, the vast majority deploy photoreactive moieties to control the stability and assembly of duplex DNA hybrids. Despite the unique opportunities afforded by the regulation of G-quadruplex formation in biology, catalysis, and nanotechnology, comparatively little attention has been devoted to the design of photoresponsive G4-based systems. In this Perspective, we consider the potential of photoresponsive G4 assemblies and examine the strategies that may be used to engineer these systems toward a variety of applications. Through an overview of the main developments in the field to date, we highlight recent progress made toward this exciting goal and the emerging opportunities that remain ripe for further exploration in the coming years.

Steric Effects on the Thermal Processes of Hemithioindigo Based Molecular Motor Rotation

Tuning the thermal behavior of light driven molecular motors is fundamentally important for their future rational design. In many molecular motors thermal ratcheting steps are comprised of helicity inversions, energetically stabilizing the initial photoproducts. In this work we investigated a series of five hemithioindigo (HTI) based molecular motors to reveal the influence of steric hindrance in close proximity to the rotation axle on this process. Applying a high yielding synthetic procedure, we synthesized constitutional isomeric derivatives to distinguish between substitution effects at the aromatic and aliphatic position on the rotor fragment. The kinetics of thermal helix inversions were elucidated using low temperature 1 H NMR spectroscopy and an in situ irradiation technique. In combination with a detailed theoretical description, a comparative analysis of substituent effects on the thermal helix inversions of the rotation cycle is now possible. Such deeper understanding of the rotational cycle of HTI molecular motors is essential for speed regulation and future applications of visible light triggered nanomachines.

Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer

Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA-ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs.

DNA Assembly-Based Stimuli-Responsive Systems

Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.

A 2-(benzothiazol-2-yl)-phenolato platinum(II) complex as potential photosensitizer for combating bacterial infections in lung cancer chemotherapy†

Cancer and antibiotic resistance are two global health threats that usually hamper clinical chemotherapeutic efficacy. Particularly for lung cancer, bacterial infections frequently arise thereby complicating the course of cancer treatment. In this sense, three new neutral luminescent cycloplatinated(II) photosensitizers of the type [Pt(dmba)(L)] (dmba = N,N-dimethylbenzylamine-κN,κC; L = 2-(benzo[d]oxazol-2-yl)-phenolato-κN,κO1, 2-(benzo[d]thiazol-2-yl)-phenolato-κN,κO2, and 2-(1-methyl-1H-benzo[d]imidazole-2-yl)phenolato-κN,κO3) have been characterized and developed to potentially eliminate both resistant bacteria and lung cancer cells. The phototherapeutic effects of complex 2 have been evaluated using low doses of blue light irradiation. Complex 2 exerted promising photoactivity against pathogenic Gram-positive bacteria strains of clinical interest, displaying a phototoxic index (PI) of 15 for methicillin-resistant Staphylococcus aureus, one of the major microorganisms predominating lung infections. Likewise, the anticancer activity of 2 was also increased upon light irradiation in human lung A549 cancer cells (PI = 36). Further in vitro experiments with this platinum(II) complex suggest that ROS-generating photodynamic reactions were involved upon light irradiation, thus providing a reasonable mechanism for its dual anticancer and antibacterial activities.

Fluorinated Azobenzenes Switchable with Red Light

Molecular photoswitches triggered with red or NIR light are optimal for photomodulation of complex biological systems, including efficient penetration of the human body for therapeutic purposes ("therapeutic window"). Yet, they are rarely reported, and even more rarely functional under aqueous conditions. In this work, fluorinated azobenzenes are shown to exhibit efficient E→Z photoisomerization with red light (PSS660nm >75 % Z) upon conjugation with unsaturated substituents. Initially demonstrated for aldehyde groups, this effect was also observed in a more complex structure by incorporating the chromophore into a cyclic dipeptide with propensity for self-assembly. Under physiological conditions, the latter molecule formed a supramolecular material that reversibly changed its viscosity upon irradiation with red light. Our observation can lead to design of new photopharmacology agents or phototriggered materials for in vivo use.

DNA Functionality with Photoswitchable Hydrazone Cytidine*

A new family of hydrazone modified cytidine phosphoramidite building block was synthesized and incorporated into oligodeoxynucleotides to construct photoswitchable DNA strands. The E-Z isomerization triggered by the irradiation of blue light with a wavelength of 450 nm was investigated and confirmed by ¹ H NMR spectroscopy and HPLC in the contexts of both nucleoside and oligodeoxynucleotide. The light activated Z form isomer of this hydrazone-cytidine with a six-member intramolecular hydrogen bond was found to inhibit DNA synthesis in the primer extension model by using Bst DNA polymerase. In addition, the hydrazone modification caused the misincorporation of dATP together with dGTP into the growing DNA strand with similar selectivity, highlighting a potential G to A mutation. This work provides a novel functional DNA building block and an additional molecular tool that has potential chemical biology and biomedicinal applications to control DNA synthesis and DNA-enzyme interactions using the cell friendly blue light irradiation.

Theoretical investigation of a novel xylene-based light-driven unidirectional molecular motor

In this study, the working mechanism of the first light-driven rotary molecular motors used to control an eight-base-pair DNA hairpin has been investigated. In particular, this linker was reported to have promising photophysical properties under physiological conditions, which motivated our work at the quantum mechanical level. Cis-trans isomerization is triggered by photon absorption at wavelengths ranging 300 nm-400 nm, promoting the rotor to the first excited state, and it is mediated by an energy-accessible conical intersection from which the ground state is reached back. The interconversion between the resulting unstable isomer and its stable form occurs at physiological conditions in the ground state and is thermally activated. Here, we compare three theoretical frameworks, generally used in the quantum description of medium-size chemical systems: Linear-Response Time-Dependent Density Functional Theory (LR-TDDFT), Spin-Flip TDDFT (SF-TDDFT), and multistate complete active space second-order perturbation theory on state-averaged complete active space self consistent field wavefunctions (MS-CASPT2//SA-CASSCF). In particular, we show the importance of resorting to a multireference approach to study the rotational cycle of light-driven molecular motors due to the occurrence of geometries described by several configurations. We also assess the accuracy and computational cost of the SF-TDDFT method when compared to MS-CASPT2 and LR-TDDFT.

Reversible Photoswitching of Isolated Ionic Hemiindigos with Visible Light

Indigoid chromophores have emerged as versatile molecular photoswitches, offering efficient reversible photoisomerization upon exposure to visible light. Here we report synthesis of a new class of permanently charged hemiindigos (HIs) and characterization of photochemical properties in gas phase and solution. Gas-phase studies, which involve exposing mobility-selected ions in a tandem ion mobility mass spectrometer to tunable wavelength laser radiation, demonstrate that the isolated HI ions are photochromic and can be reversibly photoswitched between Z and E isomers. The Z and E isomers have distinct photoisomerization response spectra with maxima separated by 40-80 nm, consistent with theoretical predictions for their absorption spectra. Solvation of the HI molecules in acetonitrile displaces the absorption bands to lower energy. Together, gas-phase action spectroscopy and solution NMR and UV/Vis absorption spectroscopy represent a powerful approach for studying the intrinsic photochemical properties of HI molecular switches.

Coordination-Assisted Reversible Photoswitching of Spiropyran-Based Platinum Macrocycles

Control over the stimuli-responsive behavior of smart molecular systems can influence their capability to execute complex functionalities. Herein, we report the development of a suite of spiropyran-based multi-stimuli-responsive self-assembled platinum(II) macrocycles (5-7), rendering coordination-assisted enhanced photochromism relative to the corresponding ligands. 5 showed shrinking and swelling during photoreversal, while 6 and 7 are fast and fatigue-free supramolecular photoswitches. 6 turns out to be a better fatigue-resistant photoswitch and can retain an intact photoswitching ability of up to 20 reversible cycles. The switching behavior of the macrocycles can also be precisely controlled by tuning the pH of the medium. Our present strategy for the construction of rapid stimuli-responsive supramolecular architectures via coordination-driven self-assembly represents an efficient route for the development of smart molecular switches.

Design of Collective Motions from Synthetic Molecular Switches, Rotors, and Motors

Precise control over molecular movement is of fundamental and practical importance in physics, biology, and chemistry. At nanoscale, the peculiar functioning principles and the synthesis of individual molecular actuators and machines has been the subject of intense investigations and debates over the past 60 years. In this review, we focus on the design of collective motions that are achieved by integrating, in space and time, several or many of these individual mechanical units together. In particular, we provide an in-depth look at the intermolecular couplings used to physically connect a number of artificial mechanically active molecular units such as photochromic molecular switches, nanomachines based on mechanical bonds, molecular rotors, and light-powered rotary motors. We highlight the various functioning principles that can lead to their collective motion at various length scales. We also emphasize how their synchronized, or desynchronized, mechanical behavior can lead to emerging functional properties and to their implementation into new active devices and materials.

Encoding Carbon Nanotubes with Tubular Nucleic Acids for Information Storage

DNA has evolved to be a type of unparalleled material for storing and transmitting genetic information. Much recent attention has been drawn to translate the natural specificity of DNA hybridization reactions for information storage in vitro. In this work, we developed a new type of tubular nucleic acid (TNA) by condensing DNA chains on the surface of one-dimensional carbon nanotubes (CNTs). We find that DNA interacts with CNTs in a sequence-specific manner, resulting in different conformations including helix, i-motif, and G-quadruplex. Atomic force microscopic (AFM) imaging revealed that TNAs exhibit distinct patterns with characteristic height and distance that can be exploited for two-dimensional encoding on CNTs. We further demonstrate the use of TNA-CNT for information storage with visual output. This noncanonical, DNA hybridization-free strategy provides a new route to DNA-based data storage.

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.

Photo- and Redox-Driven Artificial Molecular Motors

Directed motion at the nanoscale is a central attribute of life, and chemically driven motor proteins are nature's choice to accomplish it. Motivated and inspired by such bionanodevices, in the past few decades chemists have developed artificial prototypes of molecular motors, namely, multicomponent synthetic species that exhibit directionally controlled, stimuli-induced movements of their parts. In this context, photonic and redox stimuli represent highly appealing modes of activation, particularly from a technological viewpoint. Here we describe the evolution of the field of photo- and redox-driven artificial molecular motors, and we provide a comprehensive review of the work published in the past 5 years. After an analysis of the general principles that govern controlled and directed movement at the molecular scale, we describe the fundamental photochemical and redox processes that can enable its realization. The main classes of light- and redox-driven molecular motors are illustrated, with a particular focus on recent designs, and a thorough description of the functions performed by these kinds of devices according to literature reports is presented. Limitations, challenges, and future perspectives of the field are critically discussed.

Remote control of charge transport and chiral induction along a DNA-metallohelicate

Herein we present a new strategy to achieve chiral induction and redox switching along the backbone of metallohelicate architectures, wherein a DNA duplex directs the handedness and charge transport properties of a metal-organic assembly more than 60 bonds away (a distance of >10 nm). The quantitative and site-specific binding of copper(i) ions to DNA-templated coordination sites imparts enhanced thermodynamic stability to the assembly, while the DNA duplex transfers its natural right-handed helicity to the proximal and distal metal centers of the helicates. When copper(ii) ions are employed instead of copper(i) ions, spontaneous DNA-mediated reduction occurs, which we propose is followed by a slower change in coordination environment (from pentacoordinate CuII to tetrahedral CuI) to generate copper(i) helicates. We demonstrate that the reduction of the adjacent and distal bis-phenanthroline sites is dependent on their proximity to DNA guanine bases (which act as the electron source). The kinetics of helical charge transport can thus be tuned based on guanine-CuII separation, resulting in a sequence- and distance-dependent redox switch that transfers electronic information from DNA to multiple linearly-arranged metal centers.

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.

Iminothioindoxyl as a molecular photoswitch with 100 nm band separation in the visible range

Light is an exceptional external stimulus for establishing precise control over the properties and functions of chemical and biological systems, which is enabled through the use of molecular photoswitches. Ideal photoswitches are operated with visible light only, show large separation of absorption bands and are functional in various solvents including water, posing an unmet challenge. Here we show a class of fully-visible-light-operated molecular photoswitches, Iminothioindoxyls (ITIs) that meet these requirements. ITIs show a band separation of over 100 nm, isomerize on picosecond time scale and thermally relax on millisecond time scale. Using a combination of advanced spectroscopic and computational techniques, we provide the rationale for the switching behavior of ITIs and the influence of structural modifications and environment, including aqueous solution, on their photochemical properties. This research paves the way for the development of improved photo-controlled systems for a wide variety of applications that require fast responsive functions.

The design of photoswitches which operate in the visible light regime, show a large separation of absorption bands and are functional in various solvents is challenging. Here the authors report Iminothioindoxyls as visible-light operated photoswitches with a band separation of 100 nm.

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.

A hemithioindigo molecular motor for metal surface attachment

We report on the synthesis of a hemithioindigo molecular motor bearing thioether feet for metal surface attachment and a comprehensive study of its light induced unidirectional motion in solution.

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.