Light-Activated Assembly of DNA Origami into Dissipative Fibrils

Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif—protonated, self-complementary poly(adenine) sequences—can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.     

Conformational adaptation and selective adatom capturing of tetrapyridyl-porphyrin molecules on a copper (111) surface

We present a combined low-temperature scanning tunneling microscopy and near-edge X-ray adsorption fine structure study on the interaction of tetrapyridyl-porphyrin (TPyP) molecules with a Cu(111) surface. A novel approach using data from complementary experimental techniques and charge density calculations allows us to determine the adsorption geometry of TPyP on Cu(111). The molecules are centered on "bridge" sites of the substrate lattice and exhibit a strong deformation involving a saddle-shaped macrocycle distortion as well as considerable rotation and tilting of the meso-substituents. We propose a bonding mechanism based on the pyridyl-surface interaction, which mediates the molecular deformation upon adsorption. Accordingly, a functionalization by pyridyl groups opens up pathways to control the anchoring of large organic molecules on metal surfaces and tune their conformational state. Furthermore, we demonstrate that the affinity of the terminal groups for metal centers permits the selective capture of individual iron atoms at low temperature.     

Hydrogen peroxide decomposition by a non-heme iron(III) catalase mimic: a DFT study

Non-heme iron(III) complexes of 14-membered tetraaza macrocycles have previously been found to catalytically decompose hydrogen peroxide to water and molecular oxygen, like the native enzyme catalase. Here the mechanism of this reaction is theoretically investigated by DFT calculations at the (U)B3LYP/6-31G* level, with focus on the reactivity of the possible spin states of the FeIII complexes. The computations suggest that H2O2 decomposition follows a homolytic route with intermediate formation of an iron(IV) oxo radical cation species (L.+FeIV==O) that resembles Compound I of natural iron porphyrin systems. Along the whole catalytic cycle, no significant energetic differences were found for the reaction proceeding on the doublet (S=1/2) or on the quartet (S=3/2) hypersurface, with the single exception of the rate-determining O--O bond cleavage of the first associated hydrogen peroxide molecule, for which reaction via the doublet state is preferred. The sextet (S=5/2) state of the FeIII complexes appears to be unreactive in catalase-like reactions.     

Imidization and interdiffusion of poly(amic ethyl ester) precursors of PMDA/3,4′-ODA

Para-, meta-, and mixed isomeric poly(amic ethyl ester) precursors of the polyimide based on pyromellitic dianhydride (PMDA) and 3,4′-oxydianiline (3,4′-ODA) were synthesized. The intrinsic viscosity of each of the isomers was measured in an NMP solution and found to be less than corresponding isomers derived from PMDA and 4,4′-oxydianiline (4,4′-ODA) precursors with comparable molecular weight. The imidization and solvent retention were measured as a function of imidization temperatures, T_i using forward recoil spectrometry (FRES). For samples cast from a single solvent, either N-methyl pyrrolidone (NMP) or dimethyl sulfoxide (DMSO), no difference was observed in the temperature-dependent imidization behavior between the isomers. In all cases the imide fraction f increased as T_i increased, and reached a value of unity, i.e., full conversion at 400°C. At the same T_i, samples cast from DMSO showed a slightly higher f than samples cast from NMP. FRES and time of flight FRES (TOF-FRES) were used to measure the interdiffusion distance, w, of deuterium-labeled tracers into nondeuterated base layers of the polyimide of PMDA/3,4′-ODA treated at various T_i. The primary determinant of w for all isomers was T_i, and the particular isomer used as either the base or the tracer molecule did not seem to affect w. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 2247–2258, 1998     

Perfluoro‐Tagged Benzyloxycarbonyl Protecting Group and Its Application in Fluorous Biphasic Systems

The synthesis of a new perfluoro‐tagged benzyloxycarbonyl protecting group is reported, as well as its application in the parallel protection of amines. Isolation of the protected amines was performed by simple liquid‐liquid extraction between perfluorinated and organic solvents. Deprotection was achieved by standard hydrogenolysis. The novel protecting group was also applied to cyclization protocols leading to quinazoline‐2,4‐diones. These products were isolated by simple extraction procedures     

Triple Helices of Optimally Capped Duplex DNA (σ-DNA) with Homopyrimidine DNA and RNA at Neutral pH

An optimally capped duplex DNA (σ-DNA) was synthesized in which the cytosines in the homopyrimidine strand of σ-DNA 1 were replaced by 5-methylcytosine leading to σ-DNA 2 . Although only involving 13 base pairs, this modification resulted in very high melting temperatures above 90°. In addition, σ-DNA 2 was able to form triple helices with the corresponding homopyrimidine DNA or RNA even at neutral pH. This opens up the possibility to use σ-DNA in a triple-helix approach to modulate gene expressions on the level of the translation process.     

Anomalous discrete chiral symmetry in the Gross–Neveu model and loop gas simulations

We investigate the discrete chiral transformation of a Majorana fermion on a torus. Depending on the boundary conditions the integration measure can change sign. Taking this anomalous behavior into account we define a chiral order parameter as a ratio of partition functions with differing boundary conditions. Then the lattice realization of the Gross–Neveu model with Wilson fermions is simulated using the recent ‘worm’ technique on the loop gas or all-order hopping representation of the fermions. An algorithm is formulated that includes the Gross–Neveu interaction for N fermion species. The critical line m_c(g) is constructed for a range of couplings at N=6 and for N=2, the Thirring model, as examples.