Tuning Optical Absorption and Emission Using Strongly Coupled Dimers in Programmable DNA Scaffolds

Molecular materials for light harvesting, computing, and fluorescence imaging require nanoscale integration of electronically active subunits. Variation in the optical absorption and emission properties of the subunits has primarily been achieved through modifications to the chemical structure, which is often synthetically challenging. Here, we introduce a facile method for varying optical absorption and emission properties by changing the geometry of a strongly coupled Cy3 dimer on a double-crossover (DX) DNA tile. Leveraging the versatility and programmability of DNA, we tune the length of the complementary strand so that it "pushes" or "pulls" the dimer, inducing dramatic changes in the photophysics including lifetime differences observable at the ensemble and single-molecule level. The separable lifetimes, along with environmental sensitivity also observed in the photophysics, suggest that the Cy3-DX tile constructs could serve as fluorescence probes for multiplexed imaging. More generally, these constructs establish a framework for easily controllable photophysics via geometric changes to coupled chromophores, which could be applied in light-harvesting devices and molecular electronics.

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.

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.

Effect of high pressure on the typical supramolecular structure of guanidinium methanesulfonate

We report the high-pressure response of guanidinium methanesulfonate (C(NH(2))(3)(+)·CH(3)SO(3)(-), GMS) using in situ Raman spectroscopy and synchrotron X-ray diffraction (XRD) techniques up to the pressures of ~11 GPa. GMS exhibits the representative supramolecular structure of two-dimensional (2D) hydrogen-bonded bilayered motifs under ambient conditions. On the basis of the experimental results, two phase transitions were identified at 0.6 and 1.5 GPa, respectively. The first phase transition, which shows the reconstructive feature, is ascribed to the rearrangements of hydrogen-bonded networks, resulting in the symmetry transformation from C2/m to Pnma. The second one proves to be associated with local distortions of methyl groups, accompanied by the symmetry transformation from Pnma to Pna2(1). The cooperativity of hydrogen bonding, electrostatic, and van der Waals interactions, as well as mechanisms for the phase transitions is discussed by means of the local nature of the structure.

Design and assembly of rotaxane-based molecular switches and machines

Mechanically interlocked molecules, such as catenanes and rotaxanes, are at the heart of the development of molecular machines chemistry. They are able to self-organize, self-assemble, and self-control themselves into new materials with potential application as molecular devices. In this review, an overview of some recent progress on molecular machines is given, including new methodologies for their synthesis and self-assembly and their recent applications as dual or multilevel fluorescent molecular switches, as potential sensors, and even as a molecular-level transporter. In one development, a molecular machine containing a charge-transfer chromophore was designed to generate controllable aggregate structures through the reversible movement of a macrocycle over a thread; this was done in order to better understand the application of a molecular shuttle in solid state. Light is shed on how the novel properties and functions of molecular machines are extended, and examples of the ways in which molecular machines have been applied to the design and process of intelligentized systems are provided.

Molecular-glue-triggered DNA assembly to form a robust and photoresponsive nano-network

A robust and photoresponsive DNA network has been designed and constructed from branched DNA and molecular glue. The molecular glue is photoswitchable and can specifically bind to G-G mismatched double-stranded DNA. The assembly process can be reversibly controlled by manipulating the wavelength of light. The approach is flexible, allowing tuning of the size, morphology as well as the cavity of the network by variation of the molar ratio and the isotropic/anisotropic character of the branched building blocks. The assembled architectures are versatile and heat tolerant. These properties should allow the use of the network in further applications.