A DNA nanomachine powered by light irradiation

G-Quadruplex-Stimulated Optical and Electrocatalytic DNA Switches

The K(+) /18-crown-6-(or [2.2.2] cryptand)-stimulated formation and dissociation of G-quadruplex nanostructures lead to the cyclic and switchable photonic and electrocatalytic molecular devices.

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.

A two-ring interlocked DNA catenane rotor undergoing switchable transitions across three states

A two-ring (α/β) interlocked DNA catenane rotor system is described. Using appropriate fuel and anti-fuel strands, the triggered switchable rotation across three states S1, S2 and S3 associated with the circular track of ring α is demonstrated.

DNA-based machines

The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

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.

RNA-regulated molecular tweezers for sensitive fluorescent detection of microRNA from cancer cells

We describe here the construction of the DNA self-assembled molecular tweezers and the application of the tweezers for the monitoring of microRNA (miR-141) from human prostate cancer cells. The self-assembly formation of the DNA tweezers and the regulation of the tweezers upon alternative addition of the fuel miR-141 and the anti-fuel strands are characterized by native polyacrylamide gel electrophoresis. The addition of miR-141 to the DNA tweezers turns "off" the tweezers, while subsequent introduction of the anti-fuel strands switches the tweezers back to the "on" state, which verifies the regulatory ability of the tweezers. The miR-141-regulated DNA tweezers are concentration dependent and can be employed for sensitive detection of miR-141 down to 0.6 pM. The DNA tweezers also show high selectivity toward the fuel strand and can be used to monitor miR-141 expression in cancer cells, which provides new opportunities for the application of the dynamic DNA devices in clinical diagnostics.

Light-driven reversible strand displacement using glycerol azobenzene inserted DNA

Tethered with bistable 2′,6′-dimethylazobenzene via a glycerol linker, an artificial 35 nt-long DNA has performed photoresponsive hybridization and reversible light-driven strand displacement.

DNA switches: from principles to applications

The base sequence of nucleic acid encodes structural and functional properties into the biopolymer. Structural information includes the formation of duplexes, G-quadruplexes, i-motif, and cooperatively stabilized assemblies. Functional information encoded in the base sequence involves the strand-displacement process, the recognition properties by aptamers, and the catalytic functions of DNAzymes. This Review addresses the implementation of the information encoded in nucleic acids to develop DNA switches. A DNA switch is a supramolecular nucleic acid assembly that undergoes cyclic, switchable, transitions between two distinct states in the presence of appropriate triggers and counter triggers, such as pH value, metal ions/ligands, photonic and electrical stimuli. Applications of switchable DNA systems to tailor switchable DNA hydrogels, for the controlled drug-release and for the activation of switchable enzyme cascades, are described, and future perspectives of the systems are addressed.

Synthesis and evaluation of a photoresponsive quencher for fluorescent hybridization probes

Nowadays, most nucleic acid detections using fluorescent probes rely on quenching of fluorescence by energy transfer from one fluorophore to another or to a non-fluorescent molecule (quencher). The most widely used quencher in fluorescent probes is 4-((4-(dimethylamino)phenyl)azo)benzoic acid (DABCYL). We targeted a nucleoside-DABCYL analogue which could be incorporated anywhere in an oligonucleotide sequence and in any number, and used as a quencher in different hybridization sensitive probes. Specifically, we introduced a 5-(4-((dimethylamino)phenyl)azo)benzene)-2'-deoxy-uridine (dU(DAB)) quencher. The photoisomerization and dU(DAB)'s ability to quench fluorescein emission have been investigated. We incorporated dU(DAB) into a series of oligonucleotide (ON) probes including strand displacement probes, labeled with both fluorescein (FAM) and dU(DAB), and TaqMan probes bearing one or two dU(DAB) and a FAM fluorophore. We used these probes for the detection of a DNA target in real-time PCR (RT-PCR). All probes showed amplification of targeted DNA. A dU(DAB) modified TaqMan RT-PCR probe was more efficient as compared to a DABCYL bearing probe (93% vs. 87%, respectively). Furthermore, dU(DAB) had a stabilizing effect on the duplex, causing an increase in Tm up to 11 °C. In addition we showed the photoisomerisation of the azobenzene moiety of dU(DAB) and the dU(DAB) triply-labeled oligonucleotide upon irradiation. These findings suggest that dU(DAB) modified probes are promising probes for gene quantification in real-time PCR detection and as photoswitchable devices.

Light-driven DNA nanomachine with a photoresponsive molecular engine

CONSPECTUS: DNA is regarded as an excellent nanomaterial due to its supramolecular property of duplex formation through A-T and G-C complementary pairs. By simply designing sequences, we can create any desired 2D or 3D nanoarchitecture with DNA. Based on these nanoarchitectures, motional DNA-based nanomachines have also been developed. Most of the nanomachines require molecular fuels to drive them. Typically, a toehold exchange reaction is applied with a complementary DNA strand as a fuel. However, repetitive operation of the machines accumulates waste DNA duplexes in the solution that gradually deteriorate the motional efficiency. Hence, we are facing an "environmental problem" even in the nanoworld. One of the direct solutions to this problem is to use clean energy, such as light. Since light does not contaminate the reaction system, a DNA nanomachine run by a photon engine can overcome the drawback of waste that is a problem with molecular-fueled engines. There are several photoresponsive molecules that convert light energy to mechanical motion through the change of geometry of the molecules; these include spiropyran, diarylethene, stilbene, and azobenzene. Although each molecule has both advantages and drawbacks, azobenzene derivatives are widely used as "molecular photon engines". In this Account, we review light-driven DNA nanomachines mainly focusing on the photoresponsive DNAs that we have developed for the past decade. The basis of our method is installation of an azobenzene into a DNA sequence through a d-threoninol scaffold. Reversible hybridization of the DNA duplex, triggered by trans-cis isomerization of azobenzene in the DNA sequences by irradiation with light, induces mechanical motion of the DNA nanomachine. Moreover we have successfully developed azobenzene derivatives that improve its photoisomerizaition properties. Use of these derivatives and techniques have allowed us to design various DNA machines that demonstrate sophisticated motion in response to lights of different wavelengths without a drop in photoregulatory efficiency. In this Account, we emphasize the advantages of our methods including (1) ease of preparation, (2) comprehensive sequence design of azobenzene-tethered DNA, (3) efficient photoisomerization, and (4) reversible photocontrol of hybridization by irradiation with appropriate wavelengths of light. We believe that photon-fueled DNA nanomachines driven by azobenzene-derivative molecular photon-fueled engines will be soon science rather than "science fiction".

Hydrophobic actuation of a DNA origami bilayer structure

Amphiphilic compounds have a strong tendency to form aggregates in aqueous solutions. It is shown that such aggregation can be utilized to fold cholesterol-modified, single-layered DNA origami structures into sandwich-like bilayer structures, which hide the cholesterol modifications in their interior. The DNA bilayer structures unfold after addition of the surfactant Tween 80, and also in the presence of lipid bilayer membranes, with opening kinetics well described by stretched exponentials. It is also demonstrated that by combination with an appropriate lock and key mechanism, hydrophobic actuation of DNA sandwiches can be made conditional on the presence of an additional molecular input such as a specific DNA sequence.

DNA nanotechnology: from sensing and DNA machines to drug-delivery systems

DNA/nanoparticle hybrid systems combine the unique electronic and optical properties of nanomaterials with the recognition and catalytic properties of nucleic acids. These materials hold great promise for the development of new sensing platforms, the programmed organization of nanoparticles, the switchable control of plasmonic phenomena in the nanostructures, and the controlled delivery of drugs. In this Perspective, we summarize recent advances in the application of DNA/nanoparticle (NP) hybrids in these different disciplines. Nucleic acid-semiconductor quantum dot hybrids are implemented to develop multiplexed sensing platforms for targeted DNA. The chemiluminescence resonance energy transfer mechanism is introduced as a new transduction signal, and the amplified detection of DNA targets through the biocatalytic regeneration of analytes is demonstrated. DNA machines consisting of catenanes or tweezers, and modified with fluorophore/Au NP pairs are used as functional devices for the switchable "mechanical" control of the fluorescence properties of the fluorophore. Also, nucleic acid nanostructures act as stimuli-responsive caps for trapping drugs in the pores of mesoporous SiO2 nanoparticles. In the presence of appropriate biomarker triggers, the pores are unlocked, leading to the controlled release of anticancer drugs. Selective cancer-cell death is demonstrated with the stimuli-responsive SiO2 nanoparticles.

Metal nanoparticle-functionalized DNA tweezers: from mechanically programmed nanostructures to switchable fluorescence properties

DNA tweezers are modified with two 10-nm sized Au NPs and one 5-nm sized Au NP. Upon treatment of the tweezers with fuel and antifuel nucleic acid strands, the switchable closure and opening of the tweezers proceed, leading to the control of programmed nanostructures of the tethered NPs. The tweezers are further modified with a single 10-nm sized nanoparticle, and a fluorophore unit (Cy3), positioned at different distinct sites of the tweezers. The reversible and cyclic fluorescence quenching or fluorescence enhancement phenomena, upon the dynamic opening/closure of the different tweezers, are demonstrated.

Smart nanomachines based on DNA self-assembly

DNA-based nanomachines are self-assembled DNA superstructures that harness chemical free energy to perform mechanical work. The development of DNA machines has benefited greatly from the achievements in both structural and dynamic DNA nanotechnology. In this review, the configurations of DNA machines, fuel systems, and operations are discussed to outline the evolving paths of DNA machines. The focus is on the smart mechanical behavior of DNA machines, from the standpoint of upgrading the complexity of DNA nanostructures, cooperative activation of multimachinary systems, and the establishment of a network of the mechanical states. In the end, the challenges are highlighted and possible solutions are proposed to push forward smart DNA nanomachines, with the goal of creating biomimicking systems. Insights are also provided into the potential applications of the DNA machines with designable intelligence.

Effect of the steric molecular structure of azobenzene on the formation of self-assembled monolayers with a photoswitchable surface morphology

The growth processes of self-assembled monolayers (SAMs) of two azobenzene disulfides formed on flat gold surfaces were studied to confirm the effect of the intermolecular interactions between azobenzene molecules on the light-triggered surface morphologies of the SAMs. Scanning tunneling microscopy (STM), atomic force microscopy (AFM), thermal desorption spectroscopy (TDS), X-ray photoelectron spectroscopy (XPS), and ultraviolet-visible (UV-vis) absorption spectroscopy were employed to study the SAMs and their growth processes. The SAMs studied were of bulky-substituted azobenzene disulfide (Et-2S), and nonsubstituted azobenzene disulfide (Me-2S), formed on a gold-covered substrate, and had a twisted and a planar structure, respectively. STM-based imaging of the initial stage of the self-assembly of the Et-2S molecules revealed that cleavage of the disulfide bond occurred on the gold surface, and phase-separated domains composed of azobenzenethiolate and dodecanethiolate were formed. Time-dependent AFM-based imaging illustrated the mechanism through which the Et-2S SAM grew-it was through the formation of dendritic aggregates and islands-eventually resulting in phase-separated domains with a wormlike structure. This wormlike structure showed noticeable changes in its surface morphology upon irradiation with UV and visible light. On the other hand, while the growth process for the Me-2S SAM was similar to that of the Et-2S SAM, the final Me-2S SAM had smooth domains whose morphology did not exhibit photoswitchability. The TD and XP spectra of the SAMs showed that the number of adsorbed Et-2S molecules reached a point of saturation after a 24 h long immersion while the number of Me-2S molecules increased even after a 336 h long immersion. Furthermore, the area occupied by the azobenzene moiety in the Et-2S SAM was constant regardless of the immersion time, whereas that in the Me-2S SAM decreased with the immersion time. These results indicated that the strength of the interactions between the azobenzene molecules significantly influenced the aggregate-forming ability in SAMs.

Pseudo-complementary PNA actuators as reversible switches in dynamic DNA nanotechnology

The structural reorganization of nanoscale DNA architectures is a fundamental aspect in dynamic DNA nanotechnology. Commonly, DNA nanoarchitectures are reorganized by means of toehold-expanded DNA sequences in a strand exchange process. Here we describe an unprecedented, toehold-free switching process that relies on pseudo-complementary peptide nucleic acid (pcPNA) by using a mechanism that involves double-strand invasion. The usefulness of this approach is demonstrated by application of these peptide nucleic acids (PNAs) as switches in a DNA rotaxane architecture. The monomers required for generating the pcPNA were obtained by an improved synthesis strategy and were incorporated into a PNA actuator sequence as well as into a short DNA strand that subsequently was integrated into the rotaxane architecture. Alternate addition of a DNA and PNA actuator sequence allowed the multiple reversible switching between a mobile rotaxane macrocycle and a stationary pseudorotaxane state. The switching occurs in an isothermal process at room temperature and is nearly quantitative in each switching step. pcPNAs can potentially be combined with light- and toehold-based switches, thus broadening the toolbox of orthogonal switching approaches for DNA architectures that open up new avenues in dynamic DNA nanotechnology.

Highly efficient remote controlled release system based on light-driven DNA nanomachine functionalized mesoporous silica

An intelligent photoswitchable single-molecule nanomachine with DNA hairpin-loop structure was designed by the incorporation of azobenzene groups in DNA sequences, which was studied by fluorescence resonance energy transfer (FRET) and attached onto the surface of mesoporous silica. Based on the photo-induced conformational transformation of DNA, highly efficient controlled release was realized.

Reversible light switch for macrocycle mobility in a DNA rotaxane

A recent trend in DNA nanotechnology consists of the assembly of architectures with dynamic properties that can be regulated by employing external stimuli. Reversible processes are important for implementing molecular motion into DNA architectures as they allow for the regeneration of the original state. Here we describe two different approaches for the reversible switching of a double-stranded DNA rotaxane architecture from a stationary pseudorotaxane mode into a state with movable components. Both states only marginally differ in their respective topologies but their mechanical properties are fundamentally different. In the two approaches, the switching operation is based on strand-displacement reactions. One of them employs toehold-extended oligodeoxynucleotides whereas in the other one the switching is achieved by light-irradiation. In both cases, multiple back and forth switching between the stationary and the mobile states was achieved in nearly quantitative fashion. The ability to reversibly operate mechanical motion in an interlocked DNA nanostructure opens exciting new avenues in DNA nanotechnology.

Photon-manipulated drug release from a mesoporous nanocontainer controlled by azobenzene-modified nucleic acid

Herein a photon-manipulated mesoporous release system was constructed based on azobenzene-modified nucleic acids. In this system, the azobenzene-incorporated DNA double strands were immobilized at the pore mouth of mesoporous silica nanoparticles. The photoisomerization of azobenzene induced dehybridization/hybridization switch of complementary DNA, causing uncapping/capping of pore gates of mesoporous silica. This nanoplatform permits holding of guest molecules within the nanopores under visible light but releases them when light wavelength turns to the UV range. These DNA/mesoporous silica hybrid nanostructures were exploited as carriers for the cancer cell chemotherapy drug doxorubicin (DOX) due to its stimuli-responsive property as well as good biocompatibility via MTT assay. It is found that the drug release behavior is light-wavelength-sensitive. Switching of the light from visible to the UV range uncapped the pores, causing the release of DOX from the mesoporous silica nanospheres and an obvious cytotoxic effect on cancer cells. We envision that this photocontrolled drug release system could find potential applications in cancer therapy.

Diarylethene-modified nucleotides for switching optical properties in DNA

Diarylethenes were attached to the 5-position of 2’-deoxyuridine in order to yield three different photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These results open the way for the use of diarylethenes as photochromic compounds in DNA-based architectures.

Photoswitchable oligonucleotide-modified gold nanoparticles: controlling hybridization stringency with photon dose

We describe a new class of stimulus-responsive DNA-functionalized gold nanoparticles that incorporate azobenzene-modified oligonucleotides. Beyond the classic directed assembly and sensing behaviors associated with oligonucleotide-modified nanoparticles, these particles also exhibit reversible photoswitching of their assembly behavior. Exposure to UV light induces a trans-cis isomerization of the azobenzene which destabilizes the DNA duplex, resulting in dissociation of the nanoparticle assemblies. The isomerization is reversible upon exposure to blue light, resulting in rehybridization and reassembly of the DNA-linked nanoparticle clusters. We show that perfectly complementary and partially mismatched strands exhibit clearly distinguishable photoinduced melting properties, and we demonstrate that photon dose can thus be used in place of temperature or ionic strength to control hybridization stringency with the ability to discriminate single-base mismatches.

Reusable molecular sensor based on photonic activation control of DNA probes

We propose a photoactivatable and resettable molecular sensor using DNA probes. The functionality is achieved by reversible change of DNA structure induced via photonic signals. Based on the mechanism, the sensor can detect target molecules at a desired instant and can be returned to its initial state after detection. The experimental results demonstrate that the concentrations of the target molecules are detected correctly and repeatedly according to the light signal.

Preparation of photoresponsive DNA tethering ortho-methylated azobenzene as a supra-photoswitch

This unit describes synthetic procedures of photoresponsive DNA via a phosphoramidite monomer composed of D-threoninol as a scaffold and 4-carboxy-2',6'-dimethylazobenzene or 4-carboxy-2'-methylazobenzene that works as a photoswitch more efficiently than previous nonmodified azobenzene (4-phenylazobenzoic acid). With these newly modified-azobenzenes, photoregulatory efficiency of DNA hybridization can be greatly improved. Furthermore, thermal stability of cis-azobenzene of 4-carboxy-2',6'-dimethylazobenzene remarkably increases compared with the previous non-modified azobenzene.

Using azobenzene incorporated DNA aptamers to probe molecular binding interactions

The rational design of DNA/RNA aptamers for use as molecular probes depends on a clear understanding of their structural elements in relation to target-aptamer binding interactions. We present a simple method to create aptamer probes that can occupy two different structural states. Then, based on the difference in binding affinity between these states, target-aptamer binding interactions can be elucidated. The basis of our two-state system comes from the incorporation of azobenzene within the DNA strand. Azobenzene can be used to photoregulate the melting of DNA-duplex structures. When incorporated into aptamers, the light-regulated conformational change of azobenzene can be used to analyze how aptamer secondary structure is involved in target binding. Azobenzene-modified aptamers showed no change in target selectivity, but showed differences in binding affinity as a function of the number, position, and conformation of azobenzene modifications. Aptamer probes that can change binding affinity on demand may have future uses in targeted drug delivery and photodynamic therapy.

Photoswitches: from molecules to materials

Small organic molecules, capable of undergoing efficient and reversible photochemical reactions to switch them between (at least) two (meta)stable isomers associated with markedly different properties, continue to impact the materials world. Such photoswitches are being implemented in a variety of materials for applications ranging from optical devices to "smart" polymers. All approaches exploit the photoswitching molecular entities as gates, which translate an incoming light stimulus to trigger macroscopic property changes of the materials. In this progress report, the most promising recent examples in this field are highlighted and put in perspective. Moving from supramolecular systems in solution to surfaces and finally to bulk materials, important design concepts are discussed, emphasizing both the challenges as well as the great promise of such truly advanced materials.

Effect of the ortho modification of azobenzene on the photoregulatory efficiency of DNA hybridization and the thermal stability of its cis form

We synthesized various azobenzenes methylated at their ortho positions with respect to the azo bond for more effective photoregulation of DNA hybridization. Photoregulatory efficiency, evaluated from the change of T(m) (DeltaT(m)) induced by trans-cis isomerization, was significantly improved for all ortho-modified azobenzenes compared with non-modified azobenzene due to the more stabilized trans form and the more destabilized cis form. Among the synthesized azobenzenes, 4-carboxy-2',6'-dimethylazobenzene (2',6'-Me-Azo), in which two ortho positions of the distal benzene ring with respect to carboxyl group were methylated, exhibited the largest DeltaT(m), whereas the newly synthesized 2,6-Me-Azo (4-carboxy-2,6-dimethylazobenzene), which possesses two methyl groups on the two ortho positions of the other benzene ring, showed moderate improvement of DeltaT(m). Both NMR spectroscopic analysis and computer modeling revealed that the two methyl groups on 2',6'-Me-Azo were located near the imino protons of adjacent base pairs; these stabilized the DNA duplex by stacking interactions in the trans form and destabilized the DNA duplex by steric hindrance in the cis form. In addition, the thermal stability of cis-2',6'-Me-Azo was also greatly improved, but not that of cis-2,6-Me-Azo. Solvent effects on the half-life of the cis form demonstrated that cis-to-trans isomerization of all the modified azobenzenes proceeded through an inversion route. Improved thermal stability of 2',6'-Me-Azo but not 2,6-Me-Azo in the cis form was attributed to the retardation of the inversion process due to steric hindrance between lone pair electrons of the pi orbital of the nitrogen atom and the methyl group on the distal benzene ring.