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Caterpillar Track Complexes in Template-Directed Synthesis and Correlated Molecular Motion.

ABSTRACT: Small alterations to the structure of a star-shaped template totally change its mode of operation. The hexapyridyl template directs the conversion of a porphyrin dimer to the cyclic hexamer, but deleting one pyridine site changes the product to the cyclic decamer, while deleting two binding sites changes the product to the cyclic octamer. This surprising switch in selectivity is explained by the formation of 2:1 caterpillar track complexes, in which two template wheels bind inside the nanoring. Caterpillar track complexes can also be prepared by binding the hexapyridyl template inside the 8- and 10-porphyrin nanorings. NMR exchange spectroscopy (EXSY) experiments show that these complexes exhibit correlated motion, in which the conrotatory rotation of the two template wheels is coupled to rotation of the nanoring track. In the case of the 10-porphyrin system, the correlated motion can be locked by binding palladium(II) dichloride between the two templates.

SUBMITTER: Liu S

PROVIDER: S-EPMC4974918 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Caterpillar track complexes in template-directed synthesis and correlated molecular motion.

Project description:Small alterations to the structure of a star-shaped template totally change its mode of operation. The hexapyridyl template directs the conversion of a porphyrin dimer to the cyclic hexamer, but deleting one pyridine site changes the product to the cyclic decamer, while deleting two binding sites changes the product to the cyclic octamer. This surprising switch in selectivity is explained by the formation of 2:1 caterpillar track complexes, in which two template wheels bind inside the nanoring. Caterpillar track complexes can also be prepared by binding the hexapyridyl template inside the 8- and 10-porphyrin nanorings. NMR exchange spectroscopy (EXSY) experiments show that these complexes exhibit correlated motion, in which the conrotatory rotation of the two template wheels is coupled to rotation of the nanoring track. In the case of the 10-porphyrin system, the correlated motion can be locked by binding palladium(II) dichloride between the two templates.

| S-EPMC4471551 | biostudies-literature

Nonenzymatic template-directed RNA synthesis inside model protocells.

Project description:Efforts to recreate a prebiotically plausible protocell, in which RNA replication occurs within a fatty acid vesicle, have been stalled by the destabilizing effect of Mg(2+) on fatty acid membranes. Here we report that the presence of citrate protects fatty acid membranes from the disruptive effects of high Mg(2+) ion concentrations while allowing RNA copying to proceed, while also protecting single-stranded RNA from Mg(2+)-catalyzed degradation. This combination of properties has allowed us to demonstrate the chemical copying of RNA templates inside fatty acid vesicles, which in turn allows for an increase in copying efficiency by bathing the vesicles in a continuously refreshed solution of activated nucleotides.

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Template-Framework Interactions in Tetraethylammonium-Directed Zeolite Synthesis.

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Sequence information transfer using covalent template-directed synthesis.

Project description:Template-directed synthesis is the biological method for the assembly of oligomers of defined sequence, providing the molecular basis for replication and the process of evolution. To apply analogous processes to synthetic oligomeric molecules, methods are required for the transfer of sequence information from a template to a daughter strand. We show that covalent template-directed synthesis is a promising approach for the molecular replication of sequence information in synthetic oligomers. Two monomer building blocks were synthesized: a phenol monomer and a benzoic acid monomer, each bearing an alkyne and an azide for oligomerization via copper catalyzed azide alkyne cycloaddition (CuAAC) reactions. Stepwise synthesis was used to prepare oligomers, where information was encoded as the sequence of phenol (P) and benzoic acid (A) units. Ester base-pairing was used to attach monomers to a mixed sequence template, and CuAAC was used to zip up the backbone. Hydrolysis of the ester base-pairs gave back the starting template and the sequence complementary copy. When the AAP trimer was used as the template, the complementary sequence PPA was obtained as the major product, with a small amount of scrambling resulting in PAP as a side-product. This covalent base-pairing strategy represents a general approach that can be implemented in different formats for the replication of sequence information in synthetic oligomers.

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A prebiotic template-directed peptide synthesis based on amyloids.

Project description:The prebiotic replication of information-coding molecules is a central problem concerning life's origins. Here, we report that amyloids composed of short peptides can direct the sequence-selective, regioselective and stereoselective condensation of amino acids. The addition of activated DL-arginine and DL-phenylalanine to the peptide RFRFR-NH2 in the presence of the complementary template peptide Ac-FEFEFEFE-NH2 yields the isotactic product FRFRFRFR-NH2, 1 of 64 possible triple addition products, under conditions in which the absence of template yields only single and double additions of mixed stereochemistry. The templating mechanism appears to be general in that a different amyloid formed by (Orn)V(Orn)V(Orn)V(Orn)V-NH2 and Ac-VDVDVDVDV-NH2 is regioselective and stereoselective for N-terminal, L-amino-acid addition while the ornithine-valine peptide alone yields predominantly sidechain condensation products with little stereoselectivity. Furthermore, the templating reaction is stable over a wide range of pH (5.6-8.6), salt concentration (0-4 M NaCl), and temperature (25-90 °C), making the amyloid an attractive model for a prebiotic peptide replicating system.

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Template-directed synthesis of a genetic polymer in a model protocell.

Project description:Contemporary phospholipid-based cell membranes are formidable barriers to the uptake of polar and charged molecules ranging from metal ions to complex nutrients. Modern cells therefore require sophisticated protein channels and pumps to mediate the exchange of molecules with their environment. The strong barrier function of membranes has made it difficult to understand the origin of cellular life and has been thought to preclude a heterotrophic lifestyle for primitive cells. Although nucleotides can cross dimyristoyl phosphatidylcholine membranes through defects formed at the gel-to-liquid transition temperature, phospholipid membranes lack the dynamic properties required for membrane growth. Fatty acids and their corresponding alcohols and glycerol monoesters are attractive candidates for the components of protocell membranes because they are simple amphiphiles that form bilayer membrane vesicles that retain encapsulated oligonucleotides and are capable of growth and division. Here we show that such membranes allow the passage of charged molecules such as nucleotides, so that activated nucleotides added to the outside of a model protocell spontaneously cross the membrane and take part in efficient template copying in the protocell interior. The permeability properties of prebiotically plausible membranes suggest that primitive protocells could have acquired complex nutrients from their environment in the absence of any macromolecular transport machinery; that is, they could have been obligate heterotrophs.

| S-EPMC2743009 | biostudies-literature

Project description:In this review we highlight the recent efforts towards the development of molecular gears with an emphasis on building molecular gears in the solid state and the role that molecular gearing and correlated motions may play in the function of crystalline molecular machines. We discuss current molecular and crystal engineering strategies, challenges associated with engineering correlated motion in crystals, and outline experimental and theoretical tools to explore gearing dynamics while highlighting key advances made to date.

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Six-Coordinate Zinc Porphyrins for Template-Directed Synthesis of Spiro-Fused Nanorings.

Project description:Five-coordinate geometry is the standard binding mode of zinc porphyrins with pyridine ligands. Here we show that pseudo-octahedral six-coordinate zinc porphyrin complexes can also be formed in solution, by taking advantage of the chelate effect. UV-vis-NIR titrations indicate that the strength of this second coordination is ca. 6-8 kJ mol(-1). We have used the formation of six-coordinate zinc porphyrin complexes to achieve the template-directed synthesis of a 3D ?-conjugated spiro-fused array of 11 porphyrin units, covalently connected in a nontrivial topology. Time-resolved fluorescence anisotropy experiments show that electronic excitation delocalizes between the two perpendicular nanorings of this spiro-system within the experimental time-resolution of 270 fs.

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Nonenzymatic polymerase-like template-directed synthesis of acyclic L-threoninol nucleic acid.

Project description:Evolution of xeno nucleic acid (XNA) world essentially requires template-directed synthesis of XNA polymers. In this study, we demonstrate template-directed synthesis of an acyclic XNA, acyclic L-threoninol nucleic acid (L-aTNA), via chemical ligation mediated by N-cyanoimidazole. The ligation of an L-aTNA fragment on an L-aTNA template is significantly faster and occurs in considerably higher yield than DNA ligation. Both L-aTNA ligation on a DNA template and DNA ligation on an L-aTNA template are also observed. High efficiency ligation of trimer L-aTNA fragments to a template-bound primer is achieved. Furthermore, a pseudo primer extension reaction is demonstrated using a pool of random L-aTNA trimers as substrates. To the best of our knowledge, this is the first example of polymerase-like primer extension of XNA with all four nucleobases, generating phosphodiester bonding without any special modification. This technique paves the way for a genetic system of the L-aTNA world.

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Template-directed synthesis of linear porphyrin oligomers: classical, Vernier and mutual Vernier.

Project description:Three different types of template-directed syntheses of linear porphyrin oligomers are presented. In the classical approach the product has the same number of binding sites as the template, whereas in Vernier reactions the product has the lowest common multiple of the numbers of binding sites in the template and the building block. Mutual Vernier templating is like Vernier templating except that both strands of the Vernier complex undergo coupling simultaneously, so that it becomes impossible to say which is the 'template' and which is the 'building block'. The template-directed synthesis of monodisperse linear oligomers is more difficult than that of cyclic oligomers, because the products of linear templating have reactive ends. All three types of templating are demonstrated here, and used to prepare a nickel(ii) porphyrin dodecamer with 4-pyridyl substituents on all twelve porphyrin units. The stabilities and cooperativities of the double-strand complexes involved in these reactions were investigated by UV-vis-NIR titration. The four-rung ladder duplex has a stability constant of about 2 × 1018 M-1 in dichloromethane at 298 K.

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