Azobenzene-tethered T7 promoter for efficient photoregulation of transcription

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

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

Reversible Control of Gene Expression by Guest-Modified Adenosines in a Cell-Free System via Host-Guest Interaction

Gene expression technology has become an indispensable tool for elucidating biological processes and developing biotechnology. Cell-free gene expression (CFE) systems offer a fundamental platform for gene expression-based technology, in which the reversible and programmable control of transcription can expand its use in synthetic biology and medicine. This study shows that CFE can be controlled via the host-guest interaction of cucurbit[7]uril (CB[7]) with N6-guest-modified adenosines. These adenosine derivatives were conveniently incorporated into the DNA strand using a post-synthetic approach and formed a selective and stable base pair with complementary thymidine in DNA. Meanwhile, alternate addition of CB[7] and the exchanging guest molecule induced the reversible formation of a duplex structure through the formation and dissociation of a bulky complex on DNA. The kinetics of the reversibility was fine-tuned by changing the size of the modified guest moieties. When incorporated into a specific region of the T7 promoter sequence, the guest-modified adenosines enabled tight and reversible control of in vitro transcription and protein expression in the CFE system. This study marks the first utility of the host-guest interaction for gene expression control in the CFE system, opening new avenues for developing DNA-based technology, particularly for precise gene therapy and DNA nanotechnology.

Photochromic Nucleosides and Oligonucleotides

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

A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower

Molecular engineering seeks to create functional entities for modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most artificial molecular motors are driven by Brownian motion, in which, with few exceptions, the generated forces are non-directed and insufficient for efficient transfer to passive second-level components. Consequently, efficient chemical-fuel-driven nanoscale driver-follower systems have not yet been realized. Here we present a DNA nanomachine (70 nm × 70 nm × 12 nm) driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates as fuel to generate a rhythmic pulsating motion of two rigid DNA-origami arms. Furthermore, we demonstrate actuation control and the simple coupling of the active nanomachine with a passive follower, to which it then transmits its motion, forming a true driver-follower pair.

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.

Reversible On-Off Photoswitching of DNA Replication Using a Dumbbell Oligodeoxynucleotide

In most organisms, DNA extension is highly regulated; however, most studies have focused on controlling the initiation of replication, and few have been done to control the regulation of DNA extension. In this study, we adopted a new strategy for azODNs to regulate DNA extension, which is based on azobenzene oligonucleotide chimeras regulated by substrate binding affinity, and the conformation of the chimera can be regulated by a light source with a light wavelength of 365 nm. The results showed that the primer was extended with Taq DNA polymerase after visible light treatment, and DNA extension could be effectively hindered with UV light treatment. We also verify the reversibility of the photoregulation of primer extension through photoswitching of dumbbell asODNs by alternate irradiation with UV and visible light. Our method has the advantages of fast and simple, green response and reversible operations, providing a new strategy for regulating gene replication.

Light responsive nucleic acid for biomedical application

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

Photochemical modifications for DNA/RNA oligonucleotides

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

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.

Chiral rhodium(III)-azobenzene complexes as photoswitchable DNA molecular locks

Chiral rhodium(III)-azobenzene complexes which are able to intercalate into DNA were developed. Upon light exposure, the azobenzene moiety of the metal complex can photoisomerize from the trans- into the cis-form...

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.

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

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

Reversible Photoswitchable Inhibitors Generate Ultrasensitivity in Out-of-Equilibrium Enzymatic Reactions

Ultrasensitivity is a ubiquitous emergent property of biochemical reaction networks. The design and construction of synthetic reaction networks exhibiting ultrasensitivity has been challenging, but would greatly expand the potential properties of life-like materials. Herein, we exploit a general and modular strategy to reversibly regulate the activity of enzymes using light and show how ultrasensitivity arises in simple out-of-equilibrium enzymatic systems upon incorporation of reversible photoswitchable inhibitors (PIs). Utilizing a chromophore/warhead strategy, PIs of the protease α-chymotrypsin were synthesized, which led to the discovery of inhibitors with large differences in inhibition constants (K_i) for the different photoisomers. A microfluidic flow setup was used to study enzymatic reactions under out-of-equilibrium conditions by continuous addition and removal of reagents. Upon irradiation of the continuously stirred tank reactor with different light pulse sequences, i.e., varying the pulse duration or frequency of UV and blue light irradiation, reversible switching between photoisomers resulted in ultrasensitive responses in enzymatic activity as well as frequency filtering of input signals. This general and modular strategy enables reversible and tunable control over the kinetic rates of individual enzyme-catalyzed reactions and makes a programmable linkage of enzymes to a wide range of network topologies feasible.

Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches

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

Protonation-Induced Enhanced Optical-Light Photochromic Properties of an Inorganic-Organic Phosphomolybdic Acid/Polyaniline Hybrid Thin Film

A phosphomolybdic acid/polyaniline (PMoA/PANI) optical-light photochromic inorganic/organic hybrid thin film was successfully synthesized by protonation between the the multiprotonic acid phosphomolybdic acid (H₃PO₄·12MoO₃) and the conductive polymer polyaniline. The stable Keggin-type structure of PMoA was maintained throughout the process. Protonation and proton transfer successfully transformed the quinone structure of eigenstate PANI into the benzene structure of single-polarized PANI in the PMoA/PANI hybridized thin film, and proton transfer transformed the benzene structure of single-polarized PANI back to the quinone structure of eigenstate PANI in the PMoA/PANI hybrid thin film, as verified by Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). The average distribution of PMoA/PANI was observed by atom force microscopy (AFM). Interestingly, protonation of PMoA caused PANI to trigger transformation of the quinone structure into the single-polarized benzene structure, which enhanced the electron delocalization ability and vastly enhanced the maximum light absorption of the PMoA/PANI hybrid thin film as confirmed by density functional theory (DFT), electrochemistry, and ultraviolet-visible spectroscopy (UV-Vis) studies. Under optical-light illumination, the pale-yellow PMoA/PANI hybrid thin film gradually turned deep blue, thus demonstrating a photochromic response, and reversible photochromism was also observed in the presence of hydrogen peroxide (H₂O₂) or oxygen (O₂). After 40 min of optical-light illumination, 36% of the Mo⁵⁺ species in PMoA was photoreduced via a protonation-induced proton transfer mechanism, and this proton transfer resulted in a structural change of PANI, as observed by XPS, generating a dominant structure with high maximum light absorption of 3.46, when compared with the literature reports.

Compatibility and Fidelity of Mirror-Image Thymidine in Transcription Events by T7 RNA Polymerase

Due to highly enzymatic d-stereoselectivity, l-nucleotides (l-2'-deoxynucleoside 5'-triphosphates [l-dNTPs]) are not natural targets of polymerases. In this study, we synthesized series of l-thymidine (l-T)-modified DNA strands and evaluated the processivity of nucleotide incorporation for transcription by T7 RNA polymerase (RNAP) with an l-T-containing template. When single l-T was introduced into the transcribed region, transcription proceeded to afford the full-length transcript with different efficiencies. However, introduction of l-T into the non-transcribed region did not exhibit a noticeable change in the transcription efficiency. Surprisingly, when two consecutive or internal l-Ts were introduced into the transcribed region, no transcripts were detected. Compared to natural template, significant lags in NTP incorporation into the template T+4/N and T+7/N (where the number corresponds to the site of l-T position, and + means downstream of the transcribed region) were detected by kinetic analysis. Furthermore, affinity of template T+4/N was almost the same with T/N, whereas affinity of T+7/N was apparently increased. Furthermore, no mismatch opposite to l-T in the template was detected in transcription reactions via gel fidelity analysis. These results demonstrate the effects of chiral l-T in DNA on the efficiency and fidelity of RNA transcription mediated by T7 RNAP, which provides important knowledge about how mirror-image thymidine perturbs the flow of genetic information during RNA transcription and development of diseases caused by gene mutation.

Photoregulation between small DNAs and reversible photochromic molecules

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

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

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

Introducing LNAzo: More Rigidity for Improved Photocontrol of Oligonucleotide Hybridization

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

Light triggered encapsulation and release of C60 with a photoswitchable TPE-based supramolecular tweezers

Stimuli responsive hosts for C₆₀ can control its binding and release on demand. A photoswitchable TPE based supramolecular host can encapsulate C₆₀ in the Z-form with a markedly different visual change in the colour. In addition, the Z-1 bound C₆₀ has been characterized by various spectroscopic methods and mass spectrometry. Upon exposure to visible light (>490 nm), the host switches to the E-form where the structural complementarity with the guest is destroyed as a result of which the C₆₀ is disassembled from the host. The results described herein reveals an actionable roadmap to pursue further advances in component self-assembly particularly light-induced association and dissociation of a guest molecule.

Photoresponsive Self-Assembled DNA Nanomaterials: Design, Working Principles, and Applications

Photoresponsive DNA nanomaterials represent a new class of remarkable functional materials. By adjusting the irradiation wavelength, light intensity, and exposure time, various photocontrolled DNA-based systems can be reversibly or irreversibly regulated in respect of their size, shape, conformation, movement, and dissociation/association. This Review introduces the most updated progress in the development of photoresponsive DNA-based system and emphasizes their advantages over other stimuli-responsive systems. Their design and mechanisms to trigger the photoresponses are shown and discussed. The potential application of these photon-responsive DNA nanomaterials in biology, biomedicine, materials science, nanophotonic and nanoelectronic are also covered and described. The challenges faced and further directions of the development of photocontrolled DNA-based systems are also highlighted.

A novel photosensitive dual-sensor for simultaneous detection of nucleic acids and small chemical molecules

Sensors that can rapidly and specifically detect nucleic acids and chemical molecules can revolutionize the diagnosis and treatment of diseases by allowing molecular-level informations to be used during the routine medicines. In this study, we demonstrated a novel dual-sensor that can be used to simultaneously detect any nucleic acids and chemical molecules whose binding aptamers can be found or synthesized. In the developed dual-sensor, the specifically designed PTG (a photosensitive azobenzene derivative carrying one photoisomerizable azobenzene moiety, one threoninol terminal and one guanidinium terminal) molecules are introduced into the unwinding region of two T7 promoters, and two DNA bubbles are introduced upstream of the two T7 promoters. Without the target, the indicating gene in the dual-tensor would not be expressed since the binding with RNAPs (RNA polymerases) cannot melt the T7 promoter for the indicating gene due to the integration of the DNA double strands via the PTG molecules, manifesting the absence of the target nucleic acid and chemical molecule. While with the presence of the target nucleic acid and/or chemical molecule, the indicating gene would be expressed as the T7 promoter contained in the enlarged DNA bubble can be melted and transcribed by the bound RNAPs as the enlarged DNA bubble can help the separation of the two DNA strands, demonstrating the existence of target nucleic acid and/or chemical molecule.

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.

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

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

Photochromism into nanosystems: towards lighting up the future nanoworld

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

Light-patterning of synthetic tissues with single droplet resolution

Synthetic tissues can be generated by forming networks of aqueous droplets in lipid-containing oil. Each droplet contains a cell-free expression system and is connected to its neighbor through a lipid bilayer. In the present work, we have demonstrated precise external control of such networks by activating protein expression within single droplets, by using light-activated DNA to encode either a fluorescent or a pore-forming protein. By controlling the extent of activation, synthetic tissues were generated with graded levels of protein expression in patterns of single droplets. Further, we have demonstrated reversible activation within individual compartments in synthetic tissues by turning a fluorescent protein on-and-off. This is the first example of the high-resolution patterning of droplet networks, following their formation. Single-droplet control will be essential to power subsets of compartments within synthetic tissues or to stimulate subsets of cells when synthetic tissues are interfaced with living tissues.

Chirality on Amorphous High-Tg Polymeric Nanofilms: Optical Activity Amplification by Thermal Annealing

The chiroptical properties of amorphous chiral polymers functionalized with conjugated trans-azoaromatic chromophore linked to the backbone through a chiral cyclic pyrrolidine moiety of one single configuration at the solid state, as thin films, were investigated. For the first time nanometric thin films of amorphous polymers (not liquid crystals) showed a remarkable chiral amplification upon thermal treatment at a temperature close to their Tg. The side-chain azobenzene chromophores rearrangement driven by the enhanced chain mobility seems to favor the formation of nanodomains of conformationally ordered macromolecular chains with one prevailing helical handedness whose optical activity depends on the configuration of the intrinsic chirality of the monomeric units and which as a result are stable at room temperature for a long time.

Artificial Base zT as Functional "Element" for Constructing Photoresponsive DNA Nanomolecules

In contrast to small molecules, DNA and RNA macromolecules can be accurately formulated with base "elements" abbreviated as A, T, U, C, and G. However, the development of functionally artificial bases can result in the generation of new biomaterials with unique properties and applications. Therefore, we herein report the design and synthesis of a photoresponsive base as a new functional or molecular "element" for constructing DNA nanomolecules. The new base is made by fusion of an azobenzene with a natural T base (zT). zT, a new molecular element, is not only the most size-expanded T analogue but also a photoresponsive base capable of specific self-assembly through hydrogen bonding. Our results showed that stable and selective self-assembly of double-stranded DNAs occurred through zT-A base pairing, but it could still be efficiently dissociated by light irradiation. The photoresponsive DNA bases will provide the versatility required for constructing desired DNA nanomolecules and nanodevices.

A real-time control system of gene expression using ligand-bound nucleic acid aptamer for metabolic engineering

Artificial control of bio-functions through regulating gene expression is one of the most important and attractive technologies to build novel living systems that are useful in the areas of chemical synthesis, nanotechnology, pharmacology, cell biology. Here, we present a novel real-time control system of gene regulation that includes an enhancement element by introducing duplex DNA aptamers upstream promoter and a repression element by introducing a RNA aptamer upstream ribosome binding site. With the presence of ligands corresponding to the DNA aptamers, the expression of the target gene can be potentially enhanced at the transcriptional level by strengthening the recognition capability of RNAP to the recognition region and speeding up the separation efficiency of the unwinding region due to the induced DNA bubble around the thrombin-bound aptamers; while with the presence of RNA aptamer ligand, the gene expression can be repressed at the translational level by weakening the recognition capability of ribosome to RBS due to the shielding of RBS by the formed aptamer-ligand complex upstream RBS. The effectiveness and potential utility of the developed gene regulation system were demonstrated by regulating the expression of ecaA gene in the cell-free systems. The realistic metabolic engineering application of the system has also tested by regulating the expression of mgtC gene and thrombin cDNA in Escherichia coli JD1021 for controlling metabolic flux and improving thrombin production, verifying that the real-time control system of gene regulation is able to realize the dynamic regulation of gene expression with potential applications in bacterial physiology studies and metabolic engineering.

A DNA Bubble-Mediated Gene Regulation System Based on Thrombin-Bound DNA Aptamers

We describe here a novel approach to enhance the transcription of a target gene in cell-free systems by symmetrically introducing duplex aptamers upstream to a T7 promoter in both the sense and antisense strands of double-stranded plasmids, which leads to the formation of a DNA bubble due to the none-complementary state of the ssDNA region harboring the aptamer sequences. With the presence of thrombins, the DNA bubble would be enlarged due to the binding of aptamers with thrombins. Consequently, the recognition region of the promoter contained in the DNA bubble can be more easily recognized and bound by RNA polymerases, and the separation efficiency of the unwinding region can also be significantly improved, leading to the enhanced expression of the target gene at the transcriptional level. The effectiveness of the proposed gene regulation system was demonstrated by enhancing the expression of gfp and ecaA genes in cell-free systems.

Structural stability of the photo-responsive DNA duplexes containing one azobenzene via a confined pore

Herein, the structural stability of single azobenzene modified DNA duplexes, including the trans form and cis form, has been examined separately based on their distinguishable unzipping kinetics from the mixture by an α-hemolysin nanopore.

Boosting functionality of synthetic DNA circuits with tailored deactivation

Molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. The function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. Here we introduce a mechanism to tune the nonlinearities associated with individual nodes of a synthetic network. This mechanism is based on programming deactivation laws using dedicated saturable pathways. We demonstrate this approach through the conversion of a single-node homoeostatic network into a bistable and reversible switch. Furthermore, we prove its generality by adding new functions to the library of reported man-made molecular devices: a system with three addressable bits of memory, and the first DNA-encoded excitable circuit. Specific saturable deactivation pathways thus greatly enrich the functional capability of a given circuit topology.

Nonlinearity in synthetic molecular circuits is usually achieved by manipulation of network topology or of production kinetics. Here, the authors achieve bistability and other nonlinear behaviours by manipulating the individual degradation rate laws of circuit components using saturable pathways.

Light-activated communication in synthetic tissues

We have previously used three-dimensional (3D) printing to prepare tissue-like materials in which picoliter aqueous compartments are separated by lipid bilayers. These printed droplets are elaborated into synthetic cells by using a tightly regulated in vitro transcription/translation system. A light-activated DNA promoter has been developed that can be used to turn on the expression of any gene within the synthetic cells. We used light activation to express protein pores in 3D-printed patterns within synthetic tissues. The pores are incorporated into specific bilayer interfaces and thereby mediate rapid, directional electrical communication between subsets of cells. Accordingly, we have developed a functional mimic of neuronal transmission that can be controlled in a precise way.

Photodependent Melting of Unmodified DNA Using a Photosensitive Intercalator: A New and Generic Tool for Photoreversible Assembly of DNA Nanostructures at Constant Temperature

External control of DNA melting and hybridization, a key step in bio- and DNA nanotechnology, is commonly achieved with temperature. The use of light to direct this process is a challenging alternative, which has been only possible with a DNA modification, such as covalent grafting or mismatch introduction, so far. Here we describe the first photocontrol of DNA melting that relies on the addition of a molecule that noncovalently interacts with unmodified DNA and affects its melting properties in a photoreversible and highly robust manner, without any prerequisite in the length or sequence of the target DNA molecule. We synthesize azobenzene-containing guanidinium derivatives and show that a bivalent molecule with a conformation-dependent binding mode, AzoDiGua, strongly increases the melting temperature (Tm) of DNA under dark conditions because its trans isomer intercalates in the DNA double helix. Upon UV irradiation at 365 nm, the trans-cis isomerization induced the ejection of AzoDiGua from the intercalation binding sites, resulting in a decrease in Tm up to 18 °C. This illumination-dependent Tm shift is observed on many types of DNA, from self-complementary single-stranded or double-stranded oligonucleotides to long genomic duplex DNA molecules. Finally, we show that simply adding AzoDiGua allows us to photoreversibly control the assembly/disassembly of a DNA nanostructure at constant temperature, as demonstrated here with a self-hybridized DNA hairpin. We anticipate that this strategy will be the key ingredient in a new and generic way of placing DNA-based bio- and nanotechnologies under dynamic control by light.

Azobenzene-modified antisense oligonucleotides for site-specific cleavage of RNA with photocontrollable property

Photoresponsive azobenzene-modified antisense oligonucleotides for site-specific RNA cleavage by RNase H.

Non-adiabatic dynamics simulation exploration of the wavelength-dependent photoinduced relaxation mechanism of trans-N-1-methyl-2-(tolylazo) imidazole in the gas phase

A comprehensive picture of the photoinduced non-adiabatic relaxation dynamics of trans-N-1-methyl-2-(tolylazo) imidazole (trans-MTAI) in different electronic excited states has been revealed using the on-the-fly surface hopping method at the ab initio CASSCF level.

Incorporation of cyclic azobenzene into oligodeoxynucleotides for the photo-regulation of DNA hybridization

Cyclic azobenzene carboxylic acid was synthesized using a shortened route. After reaction with D-threolinol, the resulting cyclic azobenzene-D-threolinol (cAB-Thr) building block was transformed into the corresponding DMTr-protected phosphoramidite, and incorporated into oligodeoxynucleotides at various positions and frequencies by solid phase synthesis. The melting temperatures of these modified oligonucleotides were determined by UV spectrometry. Photo-regulation of cAB-Thr-modified oligonucleotides with their complementary sequence was evaluated by Fluorescence Resonance Energy Transfer experiments using a fluorescein-Black Hole Quencher pair. Results suggest that while cis-cAB destabilizes DNA duplexes, trans-cAB can be accommodated in double stranded DNA.

Reversible regulation of thrombin adsorption and desorption based on photoresponsive-aptamer modified gold nanoparticles

In the protein separation, adsorption and desorption of target protein have been using different buffer condition. Different buffer will change the structure and activity of target protein in some cases. This work describes the use of different wavelength light for remote regulation of adsorption and desorption of target protein in the same buffer solutions. A dynamic system that captured and released protein in response to light is reported. Matrix gold nanoparticles and light-responsive affinity ligand comprising thrombin aptamer (APT15), polyethylene glycol linker, and azobenzene-modified complementary sequence were used. UV light induced a trans-cis isomerization of the azobenzene that destabilized the duplex of aptamer and azobenzene-modified complementary sequence, resulting in thrombin binding to aptamer sequence. Visible light irradiation resulted in DNA duplex rehybridization and thrombin released. Our work demonstrates that different light wavelengths effectively regulated the adsorption and desorption of thrombin in the same buffer, and this system also can capture and release prothrombin from plasma with different wavelength light. Furthermore, this method can be widely applied to a variety of different protein separation process.

Synthetic gene involving azobenzene-tethered T7 promoter for the photocontrol of gene expression by visible light

In the present study, we demonstrate photoregulation of gene expression in a cell-free translation system from a T7 promoter containing two azobenzene derivatives at specific positions. As photoswitches, we prepared azobenzene-4'-carboxlyic acid (Azo) and 2,6-dimethylazobenzene-4'-carboxylic acid (DM-Azo), which were isomerized from trans to cis upon irradiation with UV light (λ < 370 nm), and 4-methylthioazobenzene-4'-carboxylic acid (S-Azo) and 2,6-dimethyl-4-(methylthio)azobenzene-4'-carobxylic acid (S-DM-Azo), which were cis-isomerized by irradiation with 400 nm visible light. Expression of green fluorescent protein from a promoter modified with S-Azo or S-DM-Azo could be induced by harmless visible light whereas that from a promoter modified with Azo or DM-Azo was induced only by UV light (340-360 nm). Thus, efficient photoregulation of green fluorescent protein production was achieved in a cell-free translation system with visible light without photodamage.