Synthesis of 5-/8-Halogenated or Ethynylated Lipophilic Nucleobases as Potential Synthetic Intermediates for Supramolec­ular Chemistry

Synthesis of Fluorescent C-C Bonded Triazole-Purine Conjugates

A design toward C-C bonded 2,6-bis(1H-1,2,3-triazol-4-yl)-9H-purine and 2-piperidinyl-6-(1H-1,2,3-triazol-4-yl)-9H-purine derivatives was established using the combination of Mitsunobu, Sonogashira, copper (I) catalyzed azide-alkyne cycloaddition, and SNAr reactions. 11 examples of 2,6-bistriazolylpurine and 14 examples of 2-piperidinyl-6-triazolylpurine intermediates were obtained, in 38-86% and 41-89% yields, respectively. Obtained triazole-purine conjugates expressed good fluorescent properties which were studied in the solution and in the thin layer film for the first time. Quantum yields reached up to 49% in DMSO for bistriazolylpurines and up to 81% in DCM and up to 95% in DMSO for monotriazolylpurines. Performed biological studies in mouse embryo fibroblast, human keratinocyte, and transgenic adenocarcinoma of the mouse prostate cell lines showed that most of obtained triazole-purine conjugates are not cytotoxic. The 50% cytotoxic concentration of the tested derivatives was in the range from 59.6 to 1528.7 µM.

Pd-Catalyzed Ring-Opening/Arylation/Cyclization of 2-Aminothiazole Derivatives Provides Modular Access to Isocytosine Analogues

We report a Pd-catalyzed ring-opening/arylation/cyclization reaction sequence between 2-aminothiazoles and aryl (pseudo)halides that provides modular access to isocytosine analogues. The scope of the reaction is broad with respect to both coupling partners and a robustness test demonstrated the functional group tolerance of the methodology. Visual kinetic analysis revealed that the product may inhibit catalyst turnover for some substrates.

The Role of Peripheral Amide Groups as Hydrogen-Bonding Directors in the Tubular Self-Assembly of Dinucleobase Monomers

Nanotubes are a fascinating kind of self-assembled structure which have a wide interest and potential in supramolecular chemistry. We demonstrated that nanotubes of defined dimensions can be produced from dinucleobase monomers through two decoupled hierarchical cooperative processes: cyclotetramerization and supramolecular polymerization. Here we analyze the role of peripheral amide groups, which can form an array of hydrogen bonds along the tube axis, on this self-assembly process. A combination of 1 H NMR and CD spectroscopy techniques allowed us to analyze quantitatively the thermodynamics of each of these two processes separately. We found out that the presence of these amide directors is essential to guide the polymerization event and that their nature and number have a strong influence, not only on the stabilization of the stacks of macrocycles, but also on the supramolecular polymerization mechanism.

Construction of hydrogen bonding and coordination networks based on ethynylpyridine-appended nucleobases

A series of ethynylpyridine-appended nucleobases have been designed, synthesized, characterized and employed for the formation of crystalline molecular networks by hydrogen/coordination bonding.

Crystalline supramolecular organic frameworks via hydrogen-bonding between nucleobases

We describe here the first crystalline hydrogen-bonded organic framework made from complementary guanine and cytosine nucleobases.

Synthesis of Phosphoramidite Monomers Equipped with Complementary Bases for Solid-Phase DNA Oligomerization

We describe the preparation of two monomers that bear complementary nucleobases at the edges (guanine-2'-deoxycytidine and 2-aminoadenine-2'-deoxyuridine) and that are conveniently protected and activated for solid-phase automated DNA synthesis. We report the optimized synthetic routes leading to the four nucleobase derivatives involved, their cross-coupling reactions into dinucleobase-containing monomers, and their oligomerization in the DNA synthesizer.

Guidelines for the assembly of hydrogen-bonded macrocycles

This article highlights selected examples on the synthesis of hydrogen-bonded macrocycles from ditopic molecules and analyze the main factors, often interrelated, that influence the equilibrium between ring and chain species.

Synthesis, Optoelectronic Properties, Self-Association, and Base Pairing of Nucleobase-Functionalized Oligothiophenes

Device-relevant π-conjugated oligothiophenes with the canonical nucleobases directly embedded into the π-framework have been designed, synthesized, and characterized. These oligomers offer the ability to tune optoelectronic properties via the intimate merging of the nucleobase molecular electronic structure with base-pairing fidelity. Analysis of their optical and electronic properties in a hydrogen-bond-disrupting solvent (DMF) indicates that the nucleobase identity influences the intrinsic electronic properties of the semiconductors. These differences are supported by DFT calculations which demonstrate that the HOMO/LUMO orbitals are distributed differently for each compound. The solubility and competition between self-association and base pairing in a hydrogen-bond-supporting solvent (chloroform) was studied to better understand the oligomer behavior under conditions relevant for downstream solution processing into thin-film devices. These solution studies reveal that in each case base-pairing is preferred to self-aggregation; the relatively weak heteroassociation of 1A-1U (35 ± 5 M^-1) should be amenable to facile solution processing and successive hydrogen bond formation in the solid state, while the strong heteroassociation between 1G and 1C (>10⁴ M^-1) should enable assemblies to be preformed in solution. These results are expected to enable the synthesis of more complex π-conjugated architectures and facilitate their extension to optoelectronic devices.

Well-defined, persistent, chiral phthalocyanine nanoclusters via G-quadruplex assembly

Octameric near-IR dye nanoclusters are produced by complexation of potassium cations with a phthalocyanine-guanosine conjugate. The combination of hydrogen-bonding, K(+) coordination, π-π stacking and steric interactions between the chiral side groups is responsible for defining a specific helical chromophore arrangement in the clusters, which display high stability and maintain their supramolecular identity onto substrates.

Synthesis of Lipophilic Guanine N-9 Derivatives: Membrane Anchoring of Nucleobases Tailored to Fatty Acid Vesicles

Covalent or noncovalent surface functionalization of soft-matter structures is an important tool for tailoring their function and stability. Functionalized surfaces and nanoparticles have found numerous applications in drug delivery and diagnostics, and new functionalization chemistry is continuously being developed in the discipline of bottom-up systems chemistry. The association of polar functional molecules, e.g., molecular recognition agents, with soft-matter structures can be achieved by derivatization with alkyl chains, allowing noncovalent anchoring into amphiphilic membranes. We report the synthesis of five new guanine-N9 derivatives bearing alkyl chains with different attachment chemistries, exploiting a synthesis pathway that allows a flexible choice of hydrophobic anchor moiety. In this study, these guanine derivatives were functionalized with C₁₀ chains for insertion into decanoic acid bilayer structures, in which both alkyl chain length and attachment chemistry determined their interaction with the membrane. Incubation of these guanine conjugates, as solids, with a decanoic acid vesicle suspension, showed that ether- and triazole-linked C₁₀ anchors yielded an increased partitioning of the guanine derivative into the membranous phase compared to directly N-9-linked saturated alkyl anchors. Decanoic acid vesicle membranes could be loaded with up to 5.5 mol % guanine derivative, a 6-fold increase over previous limits. Thus, anchor chemistries exhibiting favorable interactions with a bilayer's hydrophilic surface can significantly increase the degree of structure functionalization.

Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer

Resonance energy transfer is used here to study the association and self-sorting events between lipophilic nucleosides in apolar aromatic solvents.

TET1-Mediated Oxidation of 5-Formylcytosine (5fC) to 5-Carboxycytosine (5caC) in RNA

It was recently revealed that 5-methylcytosine (5mC) in mRNA, similar to its behavior in DNA, can be oxidized to produce 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC), implying the potential regulatory roles of this post-transcriptional RNA modification. In this study, we demonstrate the in vitro oxidation of 5fC to 5-carboxycytidine (5caC) by the catalytic domain of mammalian ten-eleven translocation enzyme (TET1) in different RNA contexts. We observed that this oxidation process has very low sequence dependence and can take place in single-stranded, double-stranded, or hairpin forms of RNA sequences, although the overall conversion yields are low.