Control of DNA hybridization by photoswitchable molecular glue

Photoswitchable molecular glue for RNA: reversible photocontrol of structure and function of the ribozyme

Single-stranded RNA folds into a variety of secondary and higher-order structures. Distributions and dynamics of multiple RNA conformations are responsible for the biological function of RNA. We here developed a photoswitchable molecular glue for RNA, which could reversibly control the association of two unpaired RNA regions in response to light stimuli. The photoswitchable molecular glue, NCTA, is an RNA-binding ligand possessing a photoisomerizable azobenzene moiety. Z-NCTA is an active ligand for the target RNA containing 5'-WGG-3'/5'-WGG-3' (W = U or A) site and stabilizes its hybridized state, while its isomer E-NCTA is not. Photoreversible isomerization of NCTA enabled control of the secondary and tertiary structure of the target RNA. The RNA-cleaving activity of hammerhead ribozyme, where appropriate RNA folding is necessary, could be reversibly regulated by photoirradiation in cells treated with NCTA, demonstrating precise photocontrol of RNA structure and function by the photoswitchable molecular glue.

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.

Possibilities and challenges of small molecule organic compounds for the treatment of repeat diseases

The instability of repeat sequences in the human genome results in the onset of many neurological diseases if the repeats expand above a certain threshold. The transcripts containing long repeats sequester RNA binding proteins. The mechanism of repeat instability involves metastable slip-out hairpin DNA structures. Synthetic organic chemists have focused on the development of small organic molecules targeting repeat DNA and RNA sequences to treat neurological diseases with repeat-binding molecules. Our laboratory has studied a series of small molecules binding to mismatched base pairs and found molecules capable of binding CAG repeat DNA, which causes Huntington's disease upon expansion, CUG repeat RNA, a typical toxic RNA causing myotonic dystrophy type 1, and UGGAA repeat RNA causing spinocerebellar ataxia type 31. These molecules exhibited significant beneficial effects on disease models in vivo, suggesting the possibilities for small molecules as drugs for treating these neurological diseases.

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.

A novel naphthyridine tetramer that recognizes tandem G–G mismatches by the formation of an interhelical complex

A novel naphthyridine tetramer, p-NCTB, was reported to bind two distal CGGG/CGGG via noncovalent binding forming inter- and intrastrand complexes.

Programmable DNA switches and their applications

DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.

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.

Self-assembly of a redox-active bolaamphiphile into supramolecular vesicles

Self-assembly of a redox-active bolaamphiphile leads to the formation of narrow-bandgap supramolecular vesicles.

Copper(II)-Controlled Molecular Glue for Mismatched DNA

Isothermal hybridization of two DNA strands bearing three thymine-thymine (T:T) mismatches can be brought about in the presence of a stoichiometric amount of a bis-naphthalene macrocycle, 2,7-BisNP-NH. This process can be reverted by addition of a Cu^II salt due to formation of a dinuclear metal complex which does not bind to DNA. Subsequent sequestration of Cu^II releases the macrocycle and restores the hybridization state of DNA strands, thus allowing implementation of a fast fluorescent two-state DNA switch.

Synthesis of Responsive Two-Dimensional Polymers via Self-Assembled DNA Networks

Despite a growing interest in two-dimensional polymers, their rational synthesis remains a challenge. The solution-phase synthesis of a two-dimensional polymer is reported. A DNA-based monomer self-assembles into a supramolecular network, which is further converted into the covalently linked two-dimensional polymer by anthracene dimerization. The polymers appear as uniform monolayers, as shown by AFM and TEM imaging. Furthermore, they exhibit a pronounced solvent responsivity. The results demonstrate the value of DNA-controlled self-assembly for the formation of two-dimensional polymers in solution.

pH-Stimulated Reconfiguration and Structural Isomerization of Origami Dimer and Trimer Systems

Reversible pH-responsive dimer or trimer origami structures are assembled by bridging origami frames with pH-responsive units. The cyclic pH-stimulated separation and reassembly of dimer origami structures is demonstrated using i-motif or Hoogsteen-type (C-G·C⁺ or T-A·T) interactions. The duplex-bridged dimer T₁-T₂ is separated by the pH-induced formation of an i-motif structure (pH = 4.5), and the dimer is reassembled at pH = 7.0. The duplex-bridged dimer, T₃-T₄, is separated at pH = 4.5 through the formation of C-G·C⁺ triplex structures and is reassembled to the dimer at pH = 7.0. Similarly, the T-A·T triplex-bridged dimer, T₅-T₆, is separated at pH = 9.5 and is reassembled at neutral pH. Finally, a trimer, T₃-T₇-T₆, that includes C-G·C⁺ and T-A·T pH-responsive bridges reveals pH-programmed cleavage to selectively yield the dimers T₃-T₇ or T₇-T₆, which reassemble to the trimer at pH = 7.0. A linear three-frame origami structure bridged by duplexes including caged i-motif units undergoes pH-stimulated isomerization to a bent structure (pH = 4.5) through the formation of i-motif complex and bridging T-A·T triplex units.

Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base

A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the sequence 5'-T-3'/5'-GG-3' (T/GG) with the formation of a 1:1 complex, which is one of possible structural elements involved in the higher order structures of (TGG)n repeat DNA triggering the genome microdeletion. Surface plasmon resonance assay also showed the binding of CMBL4: with TGG repeat DNA. Potassium permanganate oxidation studies of CMBL4: -bound duplex containing the T/GG site showed that the CMBL4: -binding accelerated the oxidation of thymine at that site, which suggests the flipping out of the thymine base from a π-stack. Preferential binding was observed for CMBL4: compared with its acyclic variants, which suggests the marked significance of the macrocyclic structure for the recognition of the T/GG site.

Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease

The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.

DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles

Dimers of origami tiles are bridged by the Pb(2+)-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1-T2 and T3-T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb(2+)-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb(2+)-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1-T5-T4. In the presence of Pb(2+)-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb(2+) or histidine as trigger cleaves the trimer to yield T5-T4 and T1 or the dimer T1-T5 and T4, respectively. In the presence of Pb(2+)-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging.

DNA gated photochromism and fluorescent switch in a thiazole orange modified diarylethene

Thiazole orange-modified diarylethene (1) shows weak fluorescence but no photochromism in aqueous solution. When binding with DNA, the fluorescence of 1 is enhanced drastically and the photochromic reactivity is unlocked. This kind of DNA-responsive photoswitchable system can be used for imaging nucleic acids within cells.

Engineering structure and function using thermoresponsive biopolymers

Self-assembly enables exquisite control at the smallest scale and generates order among macromolecular-building blocks that remain too small to be manipulated individually. Environmental cues, such as heating, can trigger the organization of these materials from individual molecules to multipartixcle assemblies with a variety of compositions and functions. Synthetic as well as biological polymers have been engineered for these purposes; however, biological strategies can offer unparalleled control over the composition of these macromolecular-building blocks. Biologic polymers are macromolecules composed of monomeric units that can be precisely tailored at the genetic level; furthermore, they can often utilize endogenous biodegradation pathways, which may enhance their potential clinical applications. DNA (nucleotides), polysaccharides (carbohydrates), and proteins (amino acids) have all been engineered to self-assemble into nanostructures in response to a change in temperature. This focus article reviews the growing body of literature exploring temperature-dependent nano-assembly of these biological macromolecules, summarizes some of their physical properties, and discusses future directions.

Photoswitching properties of hairpin ODNs with azobenzene derivatives at the loop position

Photoisomerization of an azobenzene moiety modulates the thermodynamic stability of hairpin ODNs by interfering with stacking interation between azobenzene and neighbouring base pair and dihedral angle of the neighbouring base pair.

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.

A modular LHC built on the DNA three-way junction

A light-harvesting complex composed of a π-stacked multichromophoric array in a DNA three-way junction is described. The modular design allows for a ready exchange of non-covalently attached energy acceptors.

Observation of the rare chrysene excimer

Formation of the so far elusive chrysene excimer in solution is achieved by using DNA as a supramolecular scaffold.

Molecular recognition: from solution science to nano/materials technology

In the 25 years since its Nobel Prize in chemistry, supramolecular chemistry based on molecular recognition has been paid much attention in scientific and technological fields. Nanotechnology and the related areas seek breakthrough methods of nanofabrication based on rational organization through assembly of constituent molecules. Advanced biochemistry, medical applications, and environmental and energy technologies also depend on the importance of specific interactions between molecules. In those current fields, molecular recognition is now being re-evaluated. In this review, we re-examine current trends in molecular recognition from the viewpoint of the surrounding media, that is (i) the solution phase for development of basic science and molecular design advances; (ii) at nano/materials interfaces for emerging technologies and applications. The first section of this review includes molecular recognition frontiers, receptor design based on combinatorial approaches, organic capsule receptors, metallo-capsule receptors, helical receptors, dendrimer receptors, and the future design of receptor architectures. The following section summarizes topics related to molecular recognition at interfaces including fundamentals of molecular recognition, sensing and detection, structure formation, molecular machines, molecular recognition involving polymers and related materials, and molecular recognition processes in nanostructured materials.