Nanorings and rods interconnected by self-assembly mimicking an artificial network of neurons

[EN] Molecular electronics based on structures ordered as neural networks emerges as the next evolutionary milestone in the construction of nanodevices with unprecedented applications. However, the straightforward formation of geometrically defined and interconnected nanostructures is crucial for the production of electronic circuitry nanoequivalents. Here we report on the molecularly fine-tuned self-assembly of tetrakis-Schiff base compounds into nanosized rings interconnected by unusually large nanorods providing a set of connections that mimic a biological network of neurons. The networks are produced through self-assembly resulting from the molecular conformation and noncovalent intermolecular interactions. These features can be easily generated on flat surfaces and in a polymeric matrix by casting from solution under ambient conditions. The structures can be used to guide the position of electron-transporting agents such as carbon nanotubes on a surface or in a polymer matrix to create electrically conducting networks that can find direct use in constructing nanoelectronic circuits.The research leading to these results has received funding from ICIQ, ICREA, the Spanish Ministerio de Economia y Competitividad (MINECO) through project CTQ2011-27385 and the European Community Seventh Framework Program (FP7-PEOPLE-ITN-2008, CONTACT consortium) under grant agreement number 238363. We acknowledge E. C. Escudero-Adan, M. Martinez-Belmonte and E. Martin from the X-ray department of ICIQ for crystallographic analysis, and M. Moncusi, N. Argany, R. Marimon, M. Stefanova and L. Vojkuvka from the Servei de Recursos Cientifics i Tecnics from Universitat Rovira i Virgili (Tarragona, Spain).Escarcega-Bobadilla, MV.; Zelada-Guillen, GA.; Pyrlin, SV.; Wegrzyn, M.; Ramos, MMD.; Giménez Torres, E.; Stewart, A.... (2013). Nanorings and rods interconnected by self-assembly mimicking an artificial network of neurons. Nature Communications. 4:2648-2648. https://doi.org/10.1038/ncomms3648S264826484Champness, N. R. Making the right connections. Nat. Chem. 4, 149–150 (2012).Hopfield, J. J. & Tank, D. W. Computing with neural circuits: A model. Science 233, 625–633 (1986).Andres, P. R. et al. Self-assembly of a two-dimensional superlattice of molecularly linked metal clusters. Science 273, 1690–1693 (1996).Eichen, Y., Braun, E., Sivan, U. & Ben-Yoseph, G. Self-assembly of nanoelectronic components and circuits using biological templates. Acta Polym. 49, 663–670 (1998).Kawakami, T. et al. Possibilities of molecule-based spintronics of DNA wires, sheets, and related materials. Int. J. Quantum Chem. 105, 655–671 (2005).Kashtan, N., Itzkovitz, S., Milo, R. & Alon, U. Topological generalizations of network motifs. Phys. Rev. E 70, 031909 (2004).Grill, L. et al. Nano-architectures by covalent assembly of molecular building blocks. Nat. Nanotech. 2, 687–691 (2007).Lafferentz, L. et al. Controlling on-surface polymerization by hierarchical and substrate-directed growth. Nat. Chem. 4, 215–220 (2012).Alivisatos, A. P. et al. From molecules to materials: current trends and future directions. Adv. Mater. 10, 1297–1336 (1998).Pauling, L. The principles determining the structure of complex ionic crystals. J. Am. Chem. Soc. 51, 1010–1026 (1929).Damasceno, P. F., Engel, M. & Glotzer, S. C. Predictive self-assembly of polyhedra into complex structures. Science 337, 453–457 (2012).De Graaf, J. & Manna, L. A roadmap for the assembly of polyhedral particles. Science 337, 417–418 (2012).Percec, V. et al. Controlling polymer shape through the self-assembly of dendritic side-groups. Nature 391, 161–164 (1998).Stupp, S. I. et al. Supramolecular materials: self-organized nanostructures. Science 276, 384–389 (1997).Mann, S. The chemistry of form. Angew. Chem. Int. Ed. 39, 3392–3406 (2000).Sakakibara, K., Hill, J. P. & Ariga, K. Thin-film-based nanoarchitectures for soft matter: controlled assemblies into two-dimensional worlds. Small 7, 1288–1308 (2011).Huang, Z. et al. Pulsating tubules from noncovalent macrocycles. Science 337, 1521–1526 (2012).Ackermann, D., Jester, S.-S. & Famulok, M. Design strategy for DNA rotaxanes with a mechanically reinforced PX100 axle. Angew. Chem. Int. Ed. 27, 6771–6775 (2012).Marx, J. L. Microtubules: versatile organelles. Science 181, 1236–1237 (1973).Heus, H. A. & Pardi, A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253, 191–194 (1991).Braun, E., Eichen, Y., Sivan, U. & Ben-Yoseph, G. DNA-templated assembly and electrode attachment of a conducting silver wire. Nature 391, 775–778 (1998).Zhang, S. Fabrication of novel biomaterials through molecular self-assembly. Nat. Biotechnol. 21, 1171–1178 (2003).Cai, X. et al. Integrated compact optical vortex beam emitters. Science 338, 363–365 (2012).Clark, A. W. & Cooper, J. M. Nanogap ring antennae as plasmonically coupled SERRS substrates. Small 7, 119–125 (2011).Armani, A. M., Kulkarni, R. P., Fraser, S. E., Flagan, R. C. & Vahala, K. J. Label-free, single-molecule detection with optical microcavities. Science 317, 783–787 (2007).Frischmann, P. D., Guieu, S., Tabeshi, R. & MacLachlan, M. J. Columnar organization of head-to-tail self-assembled Pt4 rings. J. Am. Chem. Soc. 132, 7668–7675 (2010).Frischmann, P. D. et al. Capsule formation, carboxylate exchange, and DFT exploration of cadmium cluster metallocavitands: highly dynamic supramolecules. J. Am. Chem. Soc. 132, 3893–3908 (2010).Akine, S., Hotate, S. & Nabeshima, T. A molecular leverage for helicity control and helix Inversion. J. Am. Chem. Soc. 133, 13868–13871 (2011).Salassa, G. et al. Extremely strong self-assembly of a bimetallic salen complex visualized at the single-molecule level. J. Am. Chem. Soc. 134, 7186–7192 (2012).Escárcega-Bobadilla, M. V., Salassa, G., Martínez Belmonte, M., Escudero-Adán, E. C. & Kleij, A. W. Versatile switching in substrate topicity: supramolecular chirality induction in di- and trinuclear host complexes. Chem. Eur. J. 18, 6805–6810 (2012).Frischmann, P. D., Jiang, J., Hui, J. K.-H., Grzybowski, J. J. & MacLachlan, M. J. Reversible—irreversible approach to Schiff base macrocycles. Access to isomeric macrocycles with multiple salphen pockets. Org. Lett. 10, 1255–1258 (2008).Glaser, T. Rational design of single-molecule magnets: a supramolecular approach. Chem. Commun. 47, 116–130 (2011).Lee, E. C. et al. Understanding of assembly phenomena by aromatic−aromatic interactions: benzene dimer and the substituted systems. J. Phys. Chem. A 111, 3446–3457 (2007).Grybowski, B. A., Wilmer, C. E., Kim, J., Browne, K. P. & Bishop, K. J. M. Self-assembly: from crystals to cells. Soft Matter. 5, 1110–1128 (2009).Martínez Belmonte, M. et al. Self-assembly of Zn(salphen) complexes: steric regulation, stability studies and crystallographic analysis revealing an unexpected dimeric 3,3′-t-Bu-substituted Zn(salphen) complex. Dalton Trans. 39, 4541–4550 (2010).Salassa, G., Castilla, A. M. & Kleij, A. W. Cooperative self-assembly of a macrocyclic Schiff base complex. Dalton Trans. 40, 5236–5243 (2011).Hormoz, S. & Brenner, M. P. Design principles for self-assembly with short-range interactions. Proc. Natl Acad. Sci. 108, 5193–5198 (2011).Biemans, H. A. M. et al. Hexakis porphyrinato benzenes. A new class of porphyrin arrays. J. Am. Chem. Soc. 120, 11054–11060 (1998).Lensen, M. C. et al. Aided self-assembly of porphyrin nanoaggregates into ring-shaped architectures. Chem. Eur. J. 10, 831–839 (2004).Martin, A., Buguin, A. & Brochard-Wyart, F. Dewetting nucleation centers at soft interfaces. Langmuir. 17, 6553–6559 (2001).Schenning, A. P. H. J., Benneker, F. B. G., Geurts, H. P. M., Liu, X. Y. & Nolte, R. J. M. Porphyrin wheels. J. Am. Chem. Soc. 118, 8549–8552 (1996).Deegan, R. D. et al. Capillary flow as the cause of ring strains from dried liquid drops. Nature 389, 827–829 (1997).Scriven, L. E. & Sternling, C. V. The Marangoni effects. Nature 187, 186–188 (1960).Cai, Y. & Newby, B. Z. Marangoni flow-induced self-assembly of hexagonal and stripe-like nanoparticle patterns. J. Am. Chem. Soc. 130, 6076–6077 (2008).Whitesides, G. M. & Grzybowski, B. Self-assembly at all scales. Science 295, 2418–2421 (2002).Mann, S. Self-assembly and transformation of hybrid nano-objects and nanostructures under equilibrium and non-equilibrium conditions. Nat. Mater. 8, 781–792 (2009).Gröschnel, A. H. et al. Precise hierarchical self-assembly of multicompartment micelles. Nat. Commun. 3, 710 (2012).Adam, M., Dogic, Z., Keller, S. L. & Fraden, S. Entropically driven microphase transitions in mixtures of colloidal rods and spheres. Nature 393, 349–352 (1998).Ohara, P. C., Heath, J. R. & Gelbart, W. M. Self-assembly of submicrometer rings of particles from solutions of nanoparticles. Angew. Chem. Int. Ed. 36, 1077–1080 (1997).Xu, J., Xia, J. & Lin, Z. Evaporation-induced self-assembly of nanoparticles from a sphere-on-flat geometry. Angew. Chem. Int. Ed. 46, 1860–1863 (2007).Yosef, G. & Rabani, E. Self-assembly of nanoparticles into rings: A lattice-gas model. J. Phys. Chem. B 110, 20965–20972 (2006).Khanal, B. P. & Zubarev, E. R. Rings of nanorods. Angew. Chem. Int. Ed. 46, 2195–2198 (2007).Wang, Z. et al. One-step, self-assembly, alignment, and patterning of organic semiconductor nanowires by controlled evaporation of confined microfluids. Angew. Chem. Int. Ed. 50, 2811–2815 (2011).Hong, S. W. et al. Directed self-assembly of gradient concentric carbon nanotube rings. Adv. Func. Mater. 18, 2114–2122 (2008).Palma, M. et al. Controlled formation of carbon nanotube junctions via linker-induced assembly in aqueous solution. J. Am. Chem. Soc. 135, 8440–8443 (2013).Horcas, I. et al. WSXM: A software for scanning probe microscopy and a tool for nanotechnology. Rev. Sci. Instrum. 78, 013705 (2007).Soler, J. M. et al. The SIESTA method for ab initio order-n materials simulation. J. Phys. Cond. Matter 14, 2745–2779 (2002).Haynes, P. D., Mostof, A. A., Skylaris, C. & Payne, M. C. ONETEP: Linear-scaling density-functional theory with plane-waves. J. Phys. Conf. Ser. 26, 143–148 (2006).Valiev, M. et al. NWCHEM: A comprehensive and scalable open-source solution for large scale molecular simulations. Comp. Phys. Commun. 181, 1477–1489 (2010).Plimpton, S. Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117, 1–19 (1995)

Crystal Structure Analysis Reveals Functional Flexibility in the Selenocysteine-Specific tRNA from Mouse

Selenocysteine tRNAs (tRNA(Sec)) exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec)-interacting factors are incompletely understood.We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec). tRNA(Sec) lacking the single-stranded 3'-acceptor end ((ΔGCCA)RNA(Sec)) yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCA)RNA(Sec) resembles the structure of human tRNA(Sec) determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec) used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Sec)in vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+)-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec).We provide the most highly resolved structure of a tRNA(Sec) molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec) support its interaction with proteins

A membrane-anchored aptamer sensor for probing IFNγ secretion by single cells

\u3cp\u3eInsight into the behavior of individual immune cells, in particular cytokine secretion, will contribute to a more fundamental understanding of the immune system. In this work, we have developed a cell membrane-anchored sensor for the detection of cytokines secreted by single cells using a combination of aptamer-based sensors and droplet microfluidics.\u3c/p\u3

Regioselective One-Step Synthesis and Topological Chirality of trans-3, trans-3,trans-3 and e,e,e [60]Fullerene-Cyclotriveratrylene Tris-adducts: Discussion on a Topological meso-Form

The C3-symmetrical [60]fullerene-cyclotriveratrylene (CTV) tris-adducts (±)-1 (with a trans-3,trans-3,trans-3 addition pattern) and (±)-2 (with ane,e,e addition pattern) were prepared in 11 and 9% yield, respectively, by the regio- and diastereoselective tether-directed Bingel reaction of C60with the tris-malonate-appended CTV derivative (±)-3 (Scheme). This is the first example for tris-adduct formation by a one-step tether-directedBingel addition. Interchromophoric interactions between the electron-rich CTV cap and the electron-attracting fullerene moiety have a profound effect on the electrochemical behavior of the C-sphere (Fig. 4 and Table 1). The fullerene-centered first reduction potentials in compounds (±)-1and (±)-2 are by 100 mV more negative than those of their corresponding tris[bis(ethoxycarbonyl)methano][60]fullerene analogs that lack the CTV cap. A particular interest in (±)-1 and (±)-2 arises from the topological chirality of these molecules. A complete topology study is presented, leading to the conclusion that the four possible classical stereoisomers of the e,e,e regioisomer are topologically different, and, therefore, there exist four different topological stereoisomers (Fig. 6). Interestingly, in the case of the trans-3,trans-3,trans-3 tris-adduct, there are four classical stereoisomers but only two topological stereoisomers (Fig. 7). An example of a target molecule representing a topologicalmeso-form is also presented (Fig. 8)

Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site