Self-Assembly of Functionalized Lipophilic Guanosines into Cation-Free Stacked Guanine-Quartets.
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ABSTRACT:
SUBMITTER: Campitiello M
PROVIDER: S-EPMC8389894 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Guanine-quadruplex, consisting of several stacked guanine-quartets (GQs), has emerged as an important category of novel molecular targets with applications from nanoelectronic devices to anticancer drugs. Incorporation of metal cations into a GQ structure is utilized to form stable G-quadruplexes, while formation of a cation-free GQ network has been challenging. Here we report the room temperature (RT) molecular self-assembly of extended pristine GQ networks on an Au(111) surface. An implanted molybdenum atom within the Au(111) surface is used to nucleate and stabilize the cation-free GQ network. Additionally, decoration of the Au(111) surface with 7-armchair graphene nanoribbons (7-AGNRs) enhances the GQ domain size by suppressing the influence of the disordered phase nucleated from Au step edges. Scanning tunneling microscopy/spectroscopy (STM/STS) and density functional theory (DFT) calculations confirm the formation of GQ networks and unravel the nucleation and growth mechanism. Our work, utilizing a hetero-atom doped substrate, provides a facile approach to enhance the stability and domain size of the GQ self-assembly, which would be applicable for other molecular structures.
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Project description:Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine-guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).
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Project description:We have previously reported that 8-phenyl-2'-deoxyguanosine derivatives (8PhGs) are able to extract metal cations from an aqueous phase into an organic phase. Herein we report on the ability of 8PhGs to transport metal cations across a bulk lipophilic liquid membrane. The experiments were performed using lithium, sodium, potassium, and strontium picrate salts with the parent lipophilic Gi, two isomeric 8PhG derivatives, cis-dicyclohexano-18-crown-6 (CD18C6) and [2•2•2] cryptand as reference compounds. The relative amounts of the picrate salts were measured by UV spectroscopy in both, the source phase and the receiving phase over a period of 24 h. The results show that the transport efficiency of the self-assembled ionophores formed by 8PhGs is either similar or superior to that of CD18C6, and in all but one case higher than the parent compound Gi. The varying efficiencies between the derivatives can be attributed to the stability (kinetic and thermodynamic) and the different molecularities of the supramolecules formed by these 8PhGs. The ease of the synthesis of 8PhGs, their anion independent assembly and the fact that the transport efficiency can be modulated as a function of the structure of the 8PhGs bode well for the use of such compounds in the development of novel antimicrobial agents and cation sensing devices.
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Project description:Self-assembly characterizes the fundamental basis toward realizing the formation of highly ordered hierarchical heterostructures. A systematic approach toward the supramolecular self-assembly of free-standing guanine nucleobases and the role of graphene as a substrate in directing the monolayer assembly are investigated using the molecular dynamics simulation. We find that the free-standing bases in gas phase aggregate into clusters dominated by intermolecular H-bonds, whereas in solvent, substantial screening of intermolecular interactions results in π-stacked configurations. Interestingly, graphene facilitates the monolayer assembly of the bases mediated through the base-substrate π-π stacking. The bases assemble in a highly compact network in gas phase, whereas in solvent, a high degree of immobilization is attributed to the disruption of intermolecular interactions. Graphene-induced stabilization/aggregation of free-standing guanine bases appears as one of the prerequisites governing molecular ordering and assembly at the solid/liquid interface. The results demonstrate an interplay between intermolecular and π-stacking interactions, central to the molecular recognition, aggregation dynamics, and patterned growth of functional molecules on two-dimensional nanomaterials.
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Project description:Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Although biology relies on such schemes, they have not been available in materials science. Here, we demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activates the next droplet in the sequence, akin to living polymerization. Our strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.Natural complex systems are often constructed by sequential assembly but this is not readily available for synthetic systems. Here, the authors program the sequential self-assembly of DNA functionalized emulsions by altering the DNA grafted strands.
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Project description:We study the assembly of magnetite nanoparticles in water-based ferrofluids in wetting layers close to silicon substrates with different functionalization without and with an out-of-plane magnetic field. For particles of nominal sizes 5, 15, and 25 nm, we extract density profiles from neutron reflectivity measurements. We show that self-assembly is only promoted by a magnetic field if a seed layer is formed at the silicon substrate. Such a layer can be formed by chemisorption of activated N-hydroxysuccinimide ester-coated nanoparticles at a (3-aminopropyl)triethoxysilane functionalized surface. Less dense packing is reported for physisorption of the same particles at a piranha-treated (strongly hydrophilic) silicon wafer, and no wetting layer is found for a self-assembled monolayer of octadecyltrichlorosilane (strongly hydrophobic) at the interface. We show that once the seed layer is formed and under an out-of-plane magnetic field further wetting layers assemble. These layers become denser with time, larger magnetic fields, higher particle concentrations, and larger moment of the nanoparticles.
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Project description:A block copolymer with discotic liquid crystalline behavior was synthesized using Grignard metathesis polymerization (GRIM) and initiators for continuous activator regeneration atom transfer radical polymerization (ICAR-ATRP). A novel discotic liquid crystalline mesogen, 6-(pyren-1-yloxy)hexyl methacrylate (PyMA), comprises a block that is attached to regioregular poly(3-hexylthiophene) (rr-P3HT) generated by GRIM and subjected to end-group modification. Due to the continuous regeneration of Cu+ in the reaction mixture in ICAR-ATRP compared to conventional methods, the synthesis was successfully performed with less catalyst. The purity and yield of the final product are increased by eliminating rigorous post-synthesis purification. Stacked pyrene units have contributed to the enhanced long-range π-π interactions and aligning of the P3HT block as observed in thin-film X-ray diffraction (XRD). Furthermore, field-effect mobilities in the order of 10-2 cm2 V-1 s-1 in bottom-gate, top-contact organic field-effect transistors (OFETs) suggest an enhancement in charge transport due to the discotic electron-rich pyrene units that help mitigate the insulating effect of the methacrylate backbone. The formation of uniform microdomains of P3HT-b-poly(PyMA) observed with tapping mode atomic force microscopy (TMAFM) on the channel regions of OFETs indicates the unique packing of the block copolymer in comparison to pristine P3HT. Thermotropic properties of the novel discotic mesogen in the presence and absence of P3HT were observed with both the poly(3-hexylthiophene)-b-poly(6-(pyren-1-yloxy)hexyl methacrylate) (P3HT-b-poly(PyMA)) block copolymer and poly(6-(pyren-1-yloxy)hexyl methacrylate) (poly(PyMA)) homopolymer using polarized optical microscopy (POM) and differential scanning calorimetry (DSC).
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Project description:Structural variations of the well-known guanine quartet (G4) motif in nucleic acid structures, namely substitution of two guanine bases (G) by two adenine (A) nucleobases in mutual trans positions, are discussed and studied by density functional theory (DFT) methods. This work was initiated by three findings, namely (1) that GA mismatches are compatible with complementary pairing patterns in duplex-DNA structures and can, in principle, be extended to quartet structures, (2) that GA pairs can come in several variations, including with a N1 protonated adeninium moiety (AH), and (3) that cross-linking of the major donor sites of purine nucleobases (N1 and N7) by transition metal ions of linear coordination geometries produces planar purine quartets, as demonstrated by some of us in the past. Here, possible structures of mixed AGAG quartets both in the presence of protons and alkali metal ions are discussed, and in particular, the existence of a putative four-purine, two-metal motif.
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Project description:Histamine functionalized poly(allyl glycidyl ether)-b-poly(ethylene glycol)-b-poly(allyl glycidyl ether) (PAGE-PEO-PAGE) triblock copolymers represent a new class of physically cross-linked, pH-responsive hydrogels with significant potential for biomedical applications. These telechelic triblock copolymers exhibited abrupt and reversible hydrogelation above pH 7.0 due to a hudrophilic/hydrophobic transition of the histamine units to form a network of hydrophobic domains bridged by a hydrophilic PEO matrix. These hydrophobic domains displayed improved ordering upon increasing pH and self-assembled into a body centered cubic lattice at pH 8.0, while at lower concentrations formed well-defined micelles. Significantly, all materials were found to be non-toxic when evaluated on three different cell lines and suggests a range of medical and biomedical applications.
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Project description:The fabrication of nanomaterials involves self-ordering processes of functional molecules on inorganic surfaces. To obtain specific molecular arrangements, a common strategy is to equip molecules with functional groups. However, focusing on the functional groups alone does not provide a comprehensive picture. Especially at interfaces, processes that govern self-ordering are complex and involve various physical and chemical effects, often leading to unexpected structures, as we showcase here on the example of a homologous series of quinones on Ag(111). Naively, one could expect that such quinones, which all bear the same functionalization, form similar motifs. In salient contrast, our joint theoretical and experimental study shows that profoundly different structures are formed. Using a machine-learning-based structure search algorithm, we find that this is due to a shift of the balance of three antagonizing driving forces: adsorbate-substrate interactions governing adsorption sites, adsorbate-adsorbate interactions favoring close packing, and steric hindrance inhibiting certain otherwise energetically beneficial molecular arrangements. The theoretical structures show excellent agreement with our experimental characterizations of the organic/inorganic interfaces, both for the unit cell sizes and the orientations of the molecules within. The nonintuitive interplay of similarly important interaction mechanisms will continue to be a challenging aspect for the design of functional interfaces. With a detailed examination of all driving forces, we are, however, still able to devise a design principle for self-assembly of functionalized molecules.
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