Insights into the Structure and Energy of DNA Nanoassemblies

Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.     

Chloride‐Selective Electrodes Based on “Two‐Wall” Aryl‐Extended Calix[4]Pyrroles: Combining Hydrogen Bonds and Anion–π Interactions to Achieve Optimum Performance

The performance of chloride‐selective electrodes based on “two‐wall” aryl‐extended calix[4]pyrroles and multiwall carbon nanotubes is presented. The calix[4]pyrrole receptors bear two phenyl groups at opposite meso‐positions. When the meso‐phenyl groups are decorated with strong electron‐withdrawing substituents, attractive anion–π interactions may exist between the receptor’s aromatic walls and the sandwiched anion. These anion–π interactions are shown to significantly affect the selectivity of the electrodes. Calix[4]pyrrole, bearing a p‐nitro withdrawing group on each of the meso‐phenyl rings, afforded sensors that display anti‐Hofmeister behavior against the lipophilic salicylate and nitrate anions. Based on the experimental data, a series of principles that help in predicting the suitability of synthetic receptors for use as anion‐specific ionophores is discussed. Finally, the sensors deliver excellent results in the direct detection of chloride in bodily fluids.     

Excited-State Dynamics of Thienoguanosine,an Isomorphic Highly Fluorescent Analogue of Guanosine

Thienoguanosine (^thG) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, ^thG exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto–amino tautomers. We herein investigate the photophysics of ^thG in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5–20.5 and 7–13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of ^thG, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.     

On-Surface Synthesis and Characterization of Acene-Based Nanoribbons Incorporating Four-Membered Rings

A bottom up method for the synthesis of unique tetracene-based nanoribbons, which incorporate cyclobutadiene moieties as linkers between the acene segments, is reported. These structures were achieved through the formal [2+2] cycloaddition reaction of ortho-functionalized tetracene precursor monomers. The formation mechanism and the electronic and magnetic properties of these nanoribbons were comprehensively studied by means of a multitechnique approach. Ultra-high vacuum scanning tunneling microscopy showed the occurrence of metal-coordinated nanostructures at room temperature and their evolution into nanoribbons through formal [2+2] cycloaddition at 475 K. Frequency-shift non-contact atomic force microscopy images clearly proved the presence of bridging cyclobutadiene moieties upon covalent coupling of activated tetracene molecules. Insight into the electronic and vibrational properties of the so-formed ribbons was obtained by scanning tunneling microscopy, Raman spectroscopy, and theoretical calculations. Magnetic properties were addressed from a computational point of view, allowing us to propose promising candidates to magnetic acene-based ribbons incorporating four-membered rings. The reported findings will increase the understanding and availability of new graphene-based nanoribbons with high potential in future spintronics.     

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S⁻)=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G^.+-P(S⁻)=S. The ionization potential of G-P(S⁻)=S was calculated to be slightly lower than that of guanine in 5′-dGMP. Subsequent thermally activated hole transfer from G^.+ to P(S⁻)=S led to dithiyl radical (P-2S^.) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S^. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S⁻)=S concentrations showed a bimolecular conversion of P-2S^. to the σ²-σ*¹-bonded dimer anion radical [-P-2S 2S-P-]⁻ [ΔG (150 K, DFT)=−7.2 kcal mol⁻¹]. However, [-P-2S 2S-P-]⁻ formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=−1.4 kcal mol⁻¹]. Neither P-2S^. nor [-P-2S 2S-P-]⁻ oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.     

Between Aromatic and Quinoid Structure: A Symmetrical UV to Vis/NIR Benzothiadiazole Redox Switch

Reversibly switching the light absorption of organic molecules by redox processes is of interest for applications in sensors, light harvesting, smart materials, and medical diagnostics. This work presents a symmetrical benzothiadiazole (BTD) derivative with a high fluorescence quantum yield in solution and in the crystalline state and shows by spectroelectrochemical analysis that reversible switching of UV absorption in the neutral state, to broadband Vis/NIR absorption in the 1st oxidized state, to sharp band Vis absorption in the 2nd oxidized state, is possible. For the one-electron oxidized species, formation of a delocalized radical is confirmed by electron paramagnetic resonance spectroelectrochemistry. Furthermore, our results reveal an increasing quinoidal distortion upon the 1st and 2nd oxidation, which can be used as the leitmotif for the development of BTD based redox switches.     

Luminescent Graphene-Based Materials via Europium Complexation on Dipyridylpyridazine-Functionalized Graphene Sheets

Graphene-based materials exhibit outstanding physical properties and so are potentially applicable in a great variety of fields. Unlike their corresponding oxides, graphite and graphene are not prone to functionalization. Diels–Alder reactions are among the scarce reactions that they can occur without disrupting their conjugated sp² systems. Herein, the reaction between graphite and 3,6-di(2-pyridyl)-1,2,4,5-tetrazine under different conditions affords several graphene-based materials consisting of dipyridylpyridazine-functionalized few-layer graphene, multilayer graphene and graphite, the sheets of which act as ligands for the grafting of a europium complex. These three materials show strong red emission under 365 nm UV radiation. Their emitting particles can be visualized by confocal microscopy. The rich coordination chemistry of dipyridylpyridazine ligands has potential novel properties for similarly functionalized graphene-based materials grafted with other metal complexes.     

Minimizing Side Product Formation in Alkyne Functionalization of Ruthenium Complexes by Introduction of Protecting Groups

The synthesis of alkyne functionalized bipyridine ruthenium complexes are reported. The improved synthetic approach through application of stable protecting groups prevents formation of possible side products while facilitating purification. By applying copper-catalysed azide-alkyne cycloaddition reactions (CuAAC) pyrene units with flexible alkyl linkers are introduced at the periphery of the complex, opening up various applications including surface immobilization and DNA intercalation. All complexes are characterized structurally as well as photophysically, especially regarding the influence of the introduced alkyne and triazolyl substituents on their photophysical behavior.     

Marine Exopolysaccharide Complexed With Scandium Aimed as Theranostic Agents

(1) Background: Exopolysaccharide (EPS) derivatives, produced by Alteromonas infernus bacterium, showed anti-metastatic properties. They may represent a new class of ligands to be combined with theranostic radionuclides, such as ⁴⁷Sc/⁴⁴Sc. The goal of this work was to investigate the feasibility of such coupling. (2) Methods: EPSs, as well as heparin used as a drug reference, were characterized in terms of molar mass and dispersity using Asymmetrical Flow Field-Flow Fractionation coupled to Multi-Angle Light Scattering (AF4-MALS). The intrinsic viscosity of EPSs at different ionic strengths were measured in order to establish the conformation. To determine the stability constants of Sc with EPS and heparin, a Free-ion selective radiotracer extraction (FISRE) method has been used. (3) Results: AF4-MALS showed that radical depolymerization produces monodisperse EPSs, suitable for therapeutic use. EPS conformation exhibited a lower hydrodynamic volume for the highest ionic strengths. The resulting random-coiled conformation could affect the complexation with metal for high concentration. The LogK of Sc-EPS complexes have been determined and showing that they are comparable to the Sc-Hep. (4) Conclusions: EPSs are very promising to be coupled with the theranostic pair of scandium for Nuclear Medicine.