The Impact of Nε-Acryloyllysine Piperazides on the Conformational Dynamics of Transglutaminase 2.

In addition to the classic functions of proteins, such as acting as a biocatalyst or binding partner, the conformational states of proteins and their remodeling upon stimulation need to be considered. A prominent example of a protein that undergoes comprehensive conformational remodeling is transglutaminase 2 (TGase 2), the distinct conformational states of which are closely related to particular functions. Its involvement in various pathophysiological processes, including fibrosis and cancer, motivates the development of theranostic agents, particularly based on inhibitors that are directed toward the transamidase activity. In this context, the ability of such inhibitors to control the conformational dynamics of TGase 2 emerges as an important parameter, and methods to assess this property are in great demand. Herein, we describe the application of the switchSENSE® principle to detect conformational changes caused by three irreversibly binding Nε-acryloyllysine piperazides, which are suitable radiotracer candidates of TGase 2. The switchSENSE® technique is based on DNA levers actuated by alternating electric fields. These levers are immobilized on gold electrodes with one end, and at the other end of the lever, the TGase 2 is covalently bound. A novel computational method is introduced for describing the resulting lever motion to quantify the extent of stimulated conformational TGase 2 changes. Moreover, as a complementary biophysical method, native polyacrylamide gel electrophoresis was performed under similar conditions to validate the results. Both methods prove the occurrence of an irreversible shift in the conformational equilibrium of TGase 2, caused by the binding of the three studied Nε-acryloyllysine piperazides.

Magnesium-Dependent Electrical Actuation and Stability of DNA Origami Rods.

Dynamic methods of biosensing based on electrical actuation of surface-tethered nanolevers require the use of levers whose movement in ionic liquids is well controllable and stable. In particular, mechanical integrity of the nanolevers in a wide range of ionic strengths will enable to meet the chemical conditions of a large variety of applications where the specific binding of biomolecular analytes is analyzed. Herein, we study the electrically induced switching behavior of different rodlike DNA origami nanolevers and compare to the actuation of simply double-stranded DNA nanolevers. Our measurements reveal a significantly stronger response of the DNA origami to switching of electrode potential, leading to a smaller potential change necessary to actuate the origami and subsequently to a long-term stable movement. Dynamic measurements in buffer solutions with different Mg2+ contents show that the levers do not disintegrate even at very low ion concentrations and constant switching stress and thus provide stable actuation performance. The latter will pave the way for many new applications without largely restricting application-specific environments.

Electrical Actuation of a DNA Origami Nanolever on an Electrode.

Development of electrically powered DNA origami nanomachines requires effective means to actuate moving origami parts by externally applied electric fields. We demonstrate how origami nanolevers on an electrode can be manipulated (switched) at high frequency by alternating voltages. Orientation switching is long-time stable and can be induced by applying low voltages of 200 mV. The mechanical response time of a 100 nm long origami lever to an applied voltage step is less than 100 µs, allowing dynamic control of the induced motion. Moreover, through voltage assisted capture, origamis can be immobilized from folding solution without purification, even in the presence of excess staple strands. The results establish a way for interfacing and controlling DNA origamis with standard electronics, and enable their use as moving parts in electro-mechanical nanodevices.

Tunable Fluorescence of a Semiconducting Polythiophene Positioned on DNA Origami.

A novel approach for the integration of π-conjugated polymers (CPs) into DNA-based nanostructures is presented. Using the controlled Kumada catalyst-transfer polycondensation, well-defined thiophene-based polymers with controllable molecular weight, specific end groups, and water-soluble oligoethylene glycol-based side chains were synthesized. The end groups were used for the easy but highly efficient click chemistry-based attachment of end-functionalized oligodeoxynucleotides (ODNs) with predesigned sequences. As demonstrated by surface plasmon resonance spectroscopy, the prepared block copolymers (BCPs), P3(EO)3T-b-ODN, comprising different ODN lengths and specific or repetitive sequences, undergo specific hybridization with complementary, thiol-functionalized ODNs immobilized on a gold surface. Furthermore, the site-specific attachment of the BCPs to DNA origami structures is studied. We demonstrate that a nanoscale object, that is, a single BCP with a single ODN handle, can be directed and bound to the DNA origami with reasonable yield, site-specificity, and high spatial density. On the basis of these results, we are able to demonstrate for the first time that optical properties of CP molecules densely immobilized on DNA origami can be locally fine-tuned by controlling the attractive π-π-stacking interactions between the CPs. In particular, we show that the fluorescence of the immobilized CP molecules can be significantly enhanced by surfactant-induced breakup of π-π-stacking interactions between the CP's backbones. Such molecular control over the emission intensity of the CPs can be valuable for the construction of sophisticated switchable nanophotonic devices and nanoscale biosensors.

Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures.

DNA nanostructures are promising construction materials to bridge the gap between self-assembly of functional molecules and conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac dielectrophoresis. The dielectrophoretic behavior was investigated employing fluorescence microscopy. For the pristine origami, a significant dielectrophoretic response was found to take place in the megahertz range, whereas, due to the higher polarizability of the metallic nanoparticles, the nanoparticle/DNA hybrid structures required a lower electrical field strength and frequency for a comparable trapping at the edges of the electrode structure. The nanoparticle conjugation additionally resulted in a remarkable alteration of the DNA structure arrangement. The growth of linear, chain-like structures in between electrodes at applied frequencies in the megahertz range was observed. The long-range chain formation is caused by a local, gold nanoparticle-induced field concentration along the DNA nanostructures, which in turn, creates dielectrophoretic forces that enable the observed self-alignment of the hybrid structures.

Exceptional adsorption-induced cluster and network deformation in the flexible metal-organic framework DUT-8(Ni) observed by in situ X-ray diffraction and EXAFS.

The "gate opening" mechanism in the highly flexible MOF Ni2(2,6-ndc)2dabco (DUT-8(Ni), DUT = Dresden University of Technology) with unprecedented unit cell volume change was elucidated in detail using combined single crystal X-ray diffraction, in situ XRD and EXAFS techniques. The analysis of the crystal structures of closed pore (cp) and large pore (lp) phases reveals a drastic and unique unit cell volume expansion of up to 254%, caused by adsorption of gases, surpassing other gas-pressure switchable MOFs significantly. To a certain extent, the structural deformation is specific for the guest molecule triggering the transformation due to subtle differences in adsorption enthalpy, shape, and kinetic diameter of the guest. Combined adsorption and powder diffraction experiments using nitrogen (77 K), carbon dioxide (195 K), and n-butane (272.5 K) as a probe molecules reveal a one-step structural transformation from cp to lp. In contrast, adsorption of ethane (185 K) or ethylene (169 K) results in a two-step transformation with the formation of intermediate phases. In situ EXAFS during nitrogen adsorption was used for the first time to monitor the local coordination geometry of the metal atoms during the structural transformation in flexible MOFs revealing a unique local deformation of the nickel-based paddle-wheel node.

Conformation-controlled sorption properties and breathing of the aliphatic Al-MOF [Al(OH)(CDC)].

The Al-MOF CAU-13 ([Al(OH)(trans-CDC)]; trans-H2CDC = trans-1,4-cyclohexanedicarboxylic acid) is structurally related to the MIL-53 compounds that are well-known for their "breathing" behavior, i.e., the framework flexibility upon external stimuli such as the presence of adsorbate molecules. The adsorption properties of CAU-13 were investigated in detail. The sorption isotherms of N2, H2, CH4, CO, CO2, and water were recorded, and the adsorption enthalpies for the gases were determined by microcalorimetry. The structural changes upon adsorption of CO2 were followed with in situ synchrotron powder X-ray diffraction (PXRD). The patterns were analyzed by parametric unit cell refinement, and the preferential arrangement of the CO2 molecules was modeled by density functional theory calculations. The adsorption and separation of mixtures of o-, m-, and p-xylene from mesitylene showed a preferred adsorption of o-xylene. The structures of o/m/p-xylene-loaded CAU-13 were determined from PXRD data. The adsorption of xylene isomers induces a larger pore opening than that in the thermal activation of CAU-13. In the crystal structure of the activated sample CAU-13(empty pore), half of the linkers adopt the a,a confirmation and the other half the e,e conformation, and the presence of a,a-CDC(2-) ions hampers the structural flexibility of CAU-13. However, after the adsorption of xylene, all linkers are present in the e,e conformation, allowing for a wider pore opening by this new type of "breathing".

Imine-linked polymer-derived nitrogen-doped microporous carbons with excellent CO2 capture properties.

A series of nitrogen-doped microporous carbons (NCs) was successfully prepared by direct pyrolysis of high-surface-area microporous imine-linked polymer (ILP, 744 m(2)/g) which was formed using commercial starting materials based on the Schiff base condensation under catalyst-free conditions. These NCs have moderate specific surface areas of up to 366 m(2)/g, pore volumes of 0.43 cm(3)/g, narrow micropore size distributions, and a high density of nitrogen functional groups (5.58-8.74%). The resulting NCs are highly suitable for CO2 capture adsorbents because of their microporous textural properties and large amount of Lewis basic sites. At 1 bar, NC-800 prepared by the pyrolysis of ILP at 800 °C showed the highest CO2 uptakes of 1.95 and 2.65 mmol/g at 25 and 0 °C, respectively. The calculated adsorption capacity for CO2 per m(2) (µmol of CO2/m(2)) of NC-800 is 7.41 µmol of CO2/m(2) at 1 bar and 25 °C, the highest ever reported for porous carbon adsorbents. The isosteric heats of CO2 adsorption (Qst) for these NCs are as high as 49 kJ/mol at low CO2 surface coverage, and still ~25 kJ/mol even at high CO2 uptake (2.0 mmol/g), respectively. Furthermore, these NCs also exhibit high stability, excellent adsorption selectivity for CO2 over N2, and easy regeneration and reuse without any evident loss of CO2 adsorption capacity.