A light-responsive RNA aptamer for an azobenzene derivative.

Regulation of complex biological networks has proven to be a key bottleneck in synthetic biology. Interactions between the structurally flexible RNA and various other molecules in the form of riboswitches have shown a high-regulation specificity and efficiency and synthetic riboswitches have filled the toolbox of devices in many synthetic biology applications. Here we report the development of a novel, small molecule binding RNA aptamer, whose binding is dependent on light-induced change of conformation of its small molecule ligand. As ligand we chose an azobenzene because of its reliable photoswitchability and modified it with chloramphenicol for a better interaction with RNA. The synthesis of the ligand 'azoCm' was followed by extensive biophysical analysis regarding its stability and photoswitchability. RNA aptamers were identified after several cycles of in vitro selection and then studied regarding their binding specificity and affinity toward the ligand. We show the successful development of an RNA aptamer that selectively binds to only the trans photoisomer of azoCm with a KD of 545 nM. As the aptamer cannot bind to the irradiated ligand (λ = 365 nm), a light-selective RNA binding system is provided. Further studies may now result in the engineering of a reliable, light-responsible riboswitch.

Light-Driven ATP Transmembrane Transport Controlled by DNA Nanomachines.

In nature, biological machines can perform sophisticated and subtle functions to maintain the metabolism of organisms. Inspired from these gorgeous works of nature, scientists have developed various artificial molecular motors and machines. However, selective transport of biomolecules across membrane has remained a great challenge. Here, we establish an ATP transport system by assembling photocontrolled DNA nanomachines into the artificial nanochannels. With alternant light irradiation, these ATP transport lines can selectively shepherd cargoes across the polymer membrane. These findings point to new opportunities for manipulating and improving the mass transportation and separation with light-controlled biomolecular motors, and can be used for other molecules and ions transmembrane transport powered by light.

Dependence of aptamer activity on opposed terminal extensions: improvement of light-regulation efficiency.

Aptamers that can be regulated with light allow precise control of protein activity in space and time and hence of biological function in general. In a previous study, we showed that the activity of the thrombin-binding aptamer HD1 can be turned off by irradiation using a light activatable 'caged' intramolecular antisense-domain. However, the activity of the presented aptamer in its ON state was only mediocre. Here we studied the nature of this loss in activity in detail and found that switching from 5'- to 3'-extensions affords aptamers that are even more potent than the unmodified HD1. In particular we arrived at derivatives that are now more active than the aptamer NU172 that is currently in phase 2 clinical trials as an anticoagulant. As a result, we present light-regulatable aptamers with a superior activity in their ON state and an almost digital ON/OFF behavior upon irradiation.

Phototoxic aptamers selectively enter and kill epithelial cancer cells.

The majority of cancers arise from malignant epithelial cells. We report the design of synthetic oligonucleotides (aptamers) that are only internalized by epithelial cancer cells and can be precisely activated by light to kill such cells. Specifically, phototoxic DNA aptamers were selected to bind to unique short O-glycan-peptide signatures on the surface of breast, colon, lung, ovarian and pancreatic cancer cells. These surface antigens are not present on normal epithelial cells but are internalized and routed through endosomal and Golgi compartments by cancer cells, thus providing a focused mechanism for their intracellular delivery. When modified at their 5' end with the photodynamic therapy agent chlorin e(6) and delivered to epithelial cancer cells, these aptamers exhibited a remarkable enhancement (>500-fold increase) in toxicity upon light activation, compared to the drug alone and were not cytotoxic towards cell types lacking such O-glycan-peptide markers. Our findings suggest that these synthetic oligonucleotide aptamers can serve as delivery vehicles in precisely routing cytotoxic cargoes to and into epithelial cancer cells.

Spatiotemporal patterning of photoresponsive DNA-based hydrogels to tune local cell responses.

Understanding the spatiotemporal effects of surface topographies and modulated stiffness and anisotropic stresses of hydrogels on cell growth remains a biophysical challenge. Here we introduce the photolithographic patterning or two-photon laser scanning confocal microscopy patterning of a series of o-nitrobenzylphosphate ester nucleic acid-based polyacrylamide hydrogel films generating periodically-spaced circular patterned domains surrounded by continuous hydrogel matrices. The patterning processes lead to guided modulated stiffness differences between the patterned domains and the surrounding hydrogel matrices, and to the selective functionalization of sub-regions of the films with nucleic acid anchoring tethers. HeLa cells are deposited on the circularly-shaped domains functionalized with the MUC-1 aptamers. Initiation of the hybridization chain reaction by nucleic acid tethers associated with the continuous hydrogel matrix results in stress-induced ordered orthogonal shape-changes on the patterned domains, leading to ordered shapes of cell aggregates bound to the patterns.

Regulation of singlet oxygen generation using single-walled carbon nanotubes.

We have designed a novel photodynamic therapy (PDT) agent using protein binding aptamer, photosensitizer, and single-walled carbon nanotube (SWNT). The PDT is based on covalently linking a photosensitizer with an aptamer then wrapping onto the surface of SWNTs, such that the photosensitizer can only be activated by light upon target binding. We have chosen the human alpha-thrombin aptamer and covalently linked it with Chlorin e6 (Ce6), which is a second generation photosensitizer. Our results showed that SWNTs are great quenchers to singlet oxygen generation (SOG). In the presence of its target, the binding of target thrombin will disturb the DNA interaction with the SWNTs and cause the DNA aptamer to fall off the SWNT surface, resulting in the restoration of SOG. This study validated the potential of our design as a novel PDT agent with regulation by target molecules, enhanced specificity, and efficacy of therapeutic function, which directs the development of photodynamic therapy to be safer and more selective.

Aptamer-based fluorescence sensor for rapid detection of potassium ions in urine.

We unveil a new homogeneous assay-using OliGreen and an ATP-binding aptamer-for the highly selective and sensitive detection of potassium ions.

Surface engineering of macrophages with nucleic acid aptamers for the capture of circulating tumor cells.

In order to enhance the interactions between macrophages and cancer cells, thiol-terminated nucleic acid aptamers were immobilized on methacryloyl-functionalised carbohydrates of macrophages. The adhesion of cancer cells on the surface modified macrophages was significantly accelerated.

Investigation of low-energy proton effects on aptamer performance for astrobiological applications.

Biochips are promising instruments for the search for organic molecules in planetary environments. Nucleic acid aptamers are powerful affinity receptors known for their high affinity and specificity, and therefore are of great interest for space biochip development. A wide variety of aptamers have already been selected toward targets of astrobiological interest (from amino acids to microorganisms). We present a first study to test the resistance of these receptors to the constraints of the space environment. The emphasis is on the effect of cosmic rays on the molecular recognition properties of DNA aptamers. Experiments on beam-line facilities have been conducted with 2 MeV protons and fluences much higher than expected for a typical mission to Mars. Our results show that this irradiation process did not affect the performances of DNA aptamers as molecular recognition tools.

[Photoaptamer heterodimeric constructs as a new approach to enhance the efficiency of formation of photocrosslinking with a target protein].

Using two DNA aptamers selectively recognizing anion-binding exosites 1 and 2 of thrombin as a model, it has been demonstrated that their conjugation by a poly-(dT)-linker (ranging from 5 to 65 nt in length) to produce aptamer heterodimeric constructs results into affinity enhancement. The apparent dissociation constant (Kd(app)) measured at the optical biosensor Biacore-3000 for complexes of thrombin with the heterodimeric constructs reached minimum values (Kd(app) = 0.2-0.4 nM) which were approximately 30-fold less than for the complexes with the primary aptamers. A photoaptamer heterodimeric construct was designed connecting photoaptamer and aptamer sequences with the poly-(dT)-linker of 35 nt long. The photoaptamer used could form photo-induced cross-links with the exosite 2 of thrombin and the aptamer used could bind to the exosite 1. The measured value of Kd(app) for the photoaptamer construct was approximately 40-fold less than that for the primary photoaptamer (5.3 and 190 nM, respectively). Upon exposure to the UV radiation at 308 nm of the equimolar mixtures of thrombin with the photoaptamer construct, the equal yield of the crosslinked complexes was observed at concentrations which were lower by two orders of magnitude than in the case of the primary photoaptamer. It was found that concurrently with crosslinking to thrombin a photo-induced inactivation of the photoaptamer occurs presumably due to formation of the intermolecular crosslinking.

Nanomaterial-amplified "signal off/on" electrogenerated chemiluminescence aptasensors for the detection of thrombin.

Two electrogenerated chemiluminescence (ECL) aptasensors for the detection of thrombin were developed using the thrombin binding aptamer (TBA) taken as a molecular recognition element and nanomaterial as a carrier of the ECL capture/signal probe. In the "signal off" aptasensor, the thiolated capture probe (ss-DNA, 12-mer) was self-assembled on the gold nanoparticles (GNPs) which were self-assembled on the surface of gold electrode, and hybridized with six-base segment of the ss-DNA sequence (Tgt-aptamer, 21-mer) containing TBA-I (ss-DNA, 15-mer) tagged with ruthenium complex, producing a high ECL intensity. Introduction of the analyte thrombin triggered the dissociation of the Tgt-aptamer tagged with ruthenium complex from the aptasensors, led to significantly decrease in ECL intensity. The decreased ECL intensity was in proportion to the concentration of thrombin in a range from 2.7×10(-12) to 2.7×10(-9) M with a detection limit of 8×10(-13) M. In the "signal on" aptasensor, the thiolated TBA-I was self-assembled on the gold electrode for capturing thrombin onto the electrode and then the TBA-II (ss-DNA, 29-mer) labeled with single-walled carbon-nanotubes (SWNT)-ECL tag was bound with epitope of thrombin, producing a high ECL intensity. The increased ECL intensity was linearly with the concentration of thrombin from 1.0×10(-14) M to 1.0×10(-11) M with a detection limit of 3×10(-15) M. The present work demonstrates that using nanomaterial as a carrier for capture probe and signal probe is a promising way to amplify the ECL signal and to improve the sensitivity of the aptasensors.

Photo-controllable aptamer.

We have successfully developed a new method for photoregulation of G-quadruplex formation using cis-trans photoisomerization of the photochromic nucleobase (8FV)G. Our photo-controllable quadruplexes can be switched between a very stable quadruplex state and a non-structured state in a straightforward and reversible fashion. We also demonstrated reversibly control binding of a G-quadruplex aptamer to thrombin.

The use of light to investigate and modulate DNA and RNA conformations.

We report the use of light for two distinct kinds of investigation of the conformational changes of, respectively, DNA and RNA. First, 'Deoxyribosensors' are a class of DNA constructs that incorporate aptamers, and which report the binding of a ligand to the aptamer by attenuating the conformational/stacking relationship of two constituent DNA double helices within the sensor. Such attenuations can be monitored as electrical outputs via a light irradiation protocol. Second, RNA aptamers were selected for the specific binding of one but not the other isomer of different photochromic switch compounds. One such RNA aptamer, specific for binding the 'closed' isomer of a dihydropyrene compound, was used to create a highly effective, light-sensitive, RNA-cleaving ribozyme. Such ribozymes and riboswitches should find broad utility for the light-mediated control of gene expression within living cells and organisms.