Molecular "light switch" for G-quadruplex DNA: cycling the switch on and off

We report a new G-quadruplex DNA "light switch", where the light switch can be cycled on and off through the successive introduction of G-quadruplex DNA and [Fe(CN)(6)](4-) ions.     

Molecular Design for Reversing the Photoswitching Mode of Turning ON and OFF DNA Hybridization

A new photoswitch for DNA hybridization involving para‐substituted azobenzenes (such as isopropyl‐ or tert‐butyl‐substituted derivatives) with L ‐threoninol as a linker was synthesized. Irradiation of the modified DNA with visible light led to dissociation of the duplex owing to the destabilization effect of the bulky substituent on the trans‐azobenzene. In contrast, trans‐to‐cis isomerization (UV light irradiation) facilitated duplex formation. The direction of this photoswitching mode was entirely reversed relative to the previous system with an unmodified azobenzene on D ‐threoninol whose trans form turned on the hybridization, and cis form turned it off. Such reversed and reversible photoswitching of DNA hybridization was directly demonstrated by using fluorophore‐ and quencher‐attached oligonucleotides. Furthermore, it was revealed that the cis‐to‐trans thermal isomerization was greatly suppressed in the presence of the complementary strand owing to the formation of the more‐stable duplex in the cis form.     

New designed DNA light switch Ruthenium complexes as DNA photocleavers and Topoisomerase I inhibitors

Two ruthenium complexes containing a new ligand phipz (phipz = 2‐(1,10‐phenanthroline)‐1H‐imidazo[4,5‐b]phenazine) were designed and synthesized. These complexes were found to inhibit the DNA supercoiled relaxation mediated by topoisomerase I (topo I), cleave DNA under irradiation and bind to calf thymus DNA through intercalative mode. Furthermore, complex 2 shows higher photocleavage activity, topo I inhibition activity and DNA affinity than complex 1 . Additionally, introduction of phenazine unit may be the reason that two complexes exhibit DNA ‘light switch’ behavior. The present work shows that two complexes might be potential as new DNA ‘light switches’, DNA photocleavers and topo I inhibitors.     

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.     

Graphene and its derivatives: switching ON and OFF

As the thinnest material ever known in the universe, graphene has been attracting tremendous amount of attention in both materials science and condensed-matter physics since its successful isolation a few years ago. This one-atom-thick two-dimensional pseudo-infinite nano-crystal consists of sp(2)-hybridized aromatic carbon atoms covalently packed into a continuous hexagonal lattice. Graphene exhibits a range of unique properties, viz., high three-dimensional aspect ratio and large specific surface area, superior mechanical stiffness and flexibility, remarkable optical transmittance, extraordinary thermal response and excellent electronic transport properties, promising its applications in the next generation electronics. To switch graphene and its derivatives between ON and OFF states in nanoelectronic memory devices, various techniques have been developed to manipulate the carbon atomic sheets via introducing the valence-conduction bandgap and to enhance their processability. In this article, we review the utilization of electrically, thermally and chemically modified graphene and its polymer-functionalized derivatives for switching and information storage applications. The challenges posed on the development of novel graphene materials and further enhancements of the device switching performance have also been discussed.     

Chemical investigation of light induced DNA bipyrimidine damage and repair

In all organisms, genetic information is stored in DNA and RNA. Both of these macromolecules are damaged by many exogenous and endogenous events, with UV irradiation being one of the major sources of damage. The major photolesions formed are the cyclobutane pyrimidine dimers (CPD), pyrimidine-pyrimidone-(6-4)-photoproducts, Dewar valence isomers and, for dehydrated spore DNA, 5-(α-thyminyl)-5,6-dihydrothymine (SP). In order to be able to investigate how nature's repair and tolerance mechanisms protect the integrity of genetic information, oligonucleotides containing sequence and site-specific UV lesions are essential. This tutorial review provides an overview of synthetic procedures by which these oligonucleotides can be generated, either through phosphoramidite chemistry or direct irradiation of DNA. Moreover, a brief summary on their usage in analysing repair and tolerance processes as well as their biological effects is provided.     

Chemical and light triggering of peptide networks under partial thermodynamic control

The kinetics of novel dynamic libraries that operate via reversible replication is described. In these systems, selective product formation is governed by peptides autocatalytic efficiency and by differences in their unfolding stability. We suggest ways to significantly alter the network behavior by chemical inputs (templates) or physical triggers (light).     

Reversible ON/OFF nanoswitch for organocatalysis: mimicking the locking and unlocking operation of CaMKII

Flip a switch: a nanoswitch uses chemical inputs to turn an organocatalytic Knoevenagel reaction on and off (see scheme: R=reactant, P=product). To stop catalysis the chemical input (pink and green) wraps around the inhibitory segment of the nanoswitch to effect release or unlocking of the switch. The process can run reversibly over three cycles without loss of activity.     

Spectroscopy of Ru(II) polypyridyl complexes used as intercalators in DNA: Towards a theoretical study of the light switch effect

The absorption spectroscopy of [Ru(phen)₂dppz]²⁺ and [Ru(tap)₂dppz]²⁺ (phen = 1,10-phenanthroline, tap = 1,4,5,8-tetraazaphenanthrene; dppz = dipyridophenazine) complexes used as molecular light switches by intercalation in DNA has been analysed by means of Time-Dependent Density Functional Theory (TD-DFT). The electronic ground state structures have been optimized at the DFT (B3LYP) level of theory. The absorption spectra are characterized by a high density of excited states between 500 nm and 250 nm. The absorption spectroscopy of [Ru (phen)₂dppz]²⁺ in vacuum is characterized by metal-to-ligand-charge-transfer (MLCT) transitions corresponding to charge transfer from Ru(II) either to the phen ligands or to the dppz ligand with a strong MLCT () absorption at 411 nm. In contrast, the main feature of the lowest part of the vacuum theoretical spectrum of [Ru(tap)₂dppz]²⁺ between 522 nm and 400 nm is the presence of various excited states such as MLCT (), ligand-to-ligand-charge-transfer LLCT () or intra-ligand IL () states. When taking into account solvent corrections within the polarizable continuum model (PCM) approach (H₂O, CH₃CN) the absorption spectrum of [Ru(tap)₂dppz]²⁺ is dominated by a strong absorption at 388 nm (CH₃CN) or 390 nm (H₂O) assigned to a ¹IL () corresponding to a charge transfer from the outside end of the dppz ligand to the site of coordination to Ru(II). These differences in the absorption spectra of the two Ru(II) complexes have dramatic effects on the mechanism of deactivation of these molecules after irradiation at about 400 nm. In particular, the electronic deficiency at the outside end of the dppz ligand created by absorption to the ¹IL state will favour electron transfer from the guanine to the Ru(II) complex when it is intercalated in DNA.     

Dual molecular light switches for pH and DNA based on a novel Ru(II) complex. A non-intercalating Ru(II) complex for DNA molecular light switch

A new Ru(II) complex of [Ru(phen)(2)(Hcdpq)](ClO(4))(2) {phen = 1,10-phenanthroline, Hcdpq = 2-carboxyldipyrido[3,2-f:2',3'-h]quinoxaline} was synthesized and characterized. The spectrophotometric pH and calf thymus DNA (ct-DNA) titrations showed that the complex acted as a dual molecular light switch for pH and ct-DNA with emission enhancement factors of 17 and 26, respectively. It was shown to be capable of distinguishing ct-DNA from yeast RNA with this binding selectivity being superior to two well-known DNA molecular light switches of [Ru(bpy)(2)(dppz)](2+) {bpy =2,2'-bipyridine, and dppz = dipyrido-[3,2-a:2',3'-c]phenazine}and ethidium bromide. The complex bond to ct-DNA probably in groove mode with a binding constant of (4.67 ± 0.06) × 10(3) M(-1) in 5 mM Tris-HCl, 50 mM NaCl (pH = 7.10) buffer solution, as evidenced by UV-visible absorption and luminescence titrations, the dependence of DNA binding constants on NaCl concentrations, DNA competitive binding with ethidium bromide, and emission lifetime and viscosity measurements. To get insight into the light-switch mechanism, theoretical calculations were also performed by applying density functional theory (DFT) and time-dependent DFT.     

Using light and a molecular switch to 'lock' and 'unlock' the Diels-Alder reaction

Light is used to 'gate' the Diels-Alder reaction using a photoresponsive dithienylfuran backbone and turn the reversibility of the Diels-Alder reaction 'off' and 'on' at 100 °C. These features make the reported system an excellent candidate for developing the next generation of self-healing polymers and photothermal drug delivery vehicles.     

Push-pull [2]pseudorotaxanes. Electronic control of threading by switching ON/OFF an intramolecular charge transfer

[reaction: see text] Addition of acid and base allows switching between two different structures in a push-pull bis(pyridinium)ethane axle, controlling its ability to form [2]pseudorotaxanes with a dibenzo-24-crown-8 ether wheel.     

Solution-Processable Unsymmetrical Triarylamines: Towards High Mobility and ON/OFF Ratio in Bottom-Gated OFETs

Self-assembly of organic small molecules into an ordered thin film has been the key strategy towards efficient charge transport for organic field-effect transistors (OFETs). Solution processing is a feasible and economic way to enhance pi–pi interaction. Herein, nitrile-substituted unsymmetrical triarylamines for OFET applications with high mobility are reported. The compounds were constructed by Suzuki cross-coupling reactions under inert conditions. The HOMO level of about 5.3 eV indicates good hole-transporting ability. OFETs were assembled in bottom-gate, top-contact architecture. Devices fabricated from a binary solvent system exhibited excellent p-channel characteristics, with impressively high charge-carrier mobility of up to 2.58 cm² V⁻¹ s⁻¹ and I_ON/OFF current ratios of 10⁶–10⁷. SEM and AFM analysis showed the efficient molecular self-assembly attained by the simple and effective solvent-engineering method. Theoretical insights obtained by DFT calculations supported by single-crystal structures showed that the crystalline nature and packing modes of these compounds ensure high mobility. The results prove that these compounds have great potential for use in numerous electronic applications, such as sensors and logic switches.     

Two-photon uncaging of bioactive compounds: Starter guide to an efficient IR light switch

Triggering physiological responses with a light switch has become a reality with the development of smart molecular probes such as photolabile protecting groups (PPGs), able to “uncage” biological ligands on demand. To make the light switch virtually harmless and confine the excitation to the single-cell level, the caged ligands can be released using two-photon (2P) absorption and 2P microscopy using red/infrared light. This exceptional level of precision however comes at the cost of a reduced photosensitivity and a poor compatibility of early PPGs with 2P excitation. This review aims to provide a tutorial guidebook to the design of 2P-sensitive PPGs suitable for optobiology by discussing challenges, strategies and progress in uncaging of bioactive compounds. To do so, we first recall the photo-physical principles governing 2P absorption, and the resulting ground rules in the design of efficient 2P absorbing organic dyes. We then detail how following these guidelines has led to tremendous progress in the development of a new generation of caged compounds, and the implications in the fields of biophotonics, from neurology to targeted therapy.     

Chemical control of electrode functionalization for detection of DNA hybridization by electrochemical impedance spectroscopy

We report sensitive label-free detection of DNA oligonucleotide sequences using ac impedance measurements. The surface attachment chemistry is critical, and using mixed self-assembled monolayers on a gold electrode results in much better performance than homogeneous self-assembled monolayers. Contrary to expectations, binding of the target sequence reduces rather than increases the charge transfer resistance. Similar behavior is observed on indium tin oxide electrodes, and we ascribe it to the hydrophilicity and rigidity of the DNA duplex that cause it to reside further from the electrode surface and facilitate the approach of negatively charged redox moieties to the interface.     

Design of OFF/ON fluorescent thiol probes based on coumarin fluorophore

This paper presents a series of first-and second-generation click-modified coumarin-based fluorescent probes for thiols.These molecules demonstrate high turn-on fluorescent response and good selectivity towards aromatic thiols over other relevant reactive sulfur species,reactive oxygen species and common nucleophiles.Moreover,probe 1a can detect thiols in the reduced rabbit plasma sample.Therefore,this approach provides a particularly impressive tool for detecting thiol in biological systems.