RESUMO
We demonstrate that a recombinase ribozyme achieves multiple functions in the same reaction network: self-reproduction, iterative elongation and circularization of other RNAs, leading to synthesis of diverse products predicted by a kinetic model. This shows that key mechanisms can be integrated and controlled toward Darwinian evolution in RNA reaction networks.
Assuntos
RNA Bacteriano/genética , RNA Catalítico/genética , RNA/genética , Azoarcus/enzimologia , Biocatálise , Fenômenos Genéticos , Sequenciamento de Nucleotídeos em Larga Escala , Sequências Repetidas Invertidas , Cinética , RNA/química , RNA Bacteriano/química , RNA Catalítico/química , Recombinases/química , Recombinases/genéticaRESUMO
To exert its role of a functional polymer, DNA relies on a molecular self-assembly process that is driven by the interactions of only four units placed in a defined order. Extending the structural diversity of recognition motifs in DNA, to and beyond analogues of the nucleobases, will open doors to self-assembled materials with advanced programmable properties. DNA-inspired systems are becoming useful for numerous applications unachievable by the nucleic acids in their native composition. Potential applications of rationally designed oligo- and polyphosphodiesters reside in the areas of drug delivery, diagnostic signalling and imaging, in systems for efficient energy transfer or the precise ordering on the nanoscale. The field of DNA-inspired phosphodiesters highlights the general value and utility of precision in the composition of oligomers and polymers. In this tutorial review, we will summarize the approaches of directing the self-assembly of DNA-inspired, sequence-specific polyphosphodiesters into soft materials with unique properties. These data expose the so far underexploited potential of DNA-derived systems in solving some of the key issues in various technological areas, such as advanced biomaterials, morphologically defined soft matter or the controlled polymer folding and assembly. Moreover, precise positioning of structurally diverse molecules within a polymer chain creates unmatched opportunities for encoding information on the molecular level and transmitting it further to the microscopic and even macroscopic level via noncovalent interactions.
Assuntos
DNA/química , Polímeros/química , Azidas/química , Lipossomos/química , Compostos Organofosforados/química , Polímeros/síntese químicaRESUMO
Established less than a decade ago, the fascinating field of two-dimensional (2D) soft materials is advancing continuously towards widespread recognition. After demonstrating the feasibility of obtaining nano-thin supramolecular sheets and morphologically related tubular objects, considerable efforts are being undertaken to explore the functional potential of soft nanosheets. Self-assembly is a major tool for the controlled formation of nanometre-sized 2D objects. In this account, we share our current understanding of the structural requirements to direct the self-assembly of water-soluble, negatively charged oligomers in 2D. The discussion covers some promising areas of utilization such as the reporting of weak mechanical perturbations, the assembly of light-harvesting antennae, the transfer of excitation energy and the polymerization of pre-organized assemblies. The systems presented in this work illustrate the potential of 2D supramolecular materials as complementary systems to their covalent counterparts.
RESUMO
A 1,2,4-triazole motif is present in numerous commercialized and investigational bioactive molecules. Despite its importance for medicinal chemistry, there is a lack of convenient combinatorial approaches toward this molecular core. Herein, we present a synthetic strategy suitable for the quick preparation of a library of structurally diverse 1,2,4-triazoles in a one-pot setting. The key steps include the formation of thioureas followed by S-alkylation using 1,3-propane sultone and consecutive ring closure leading to the desired 1,2,4-triazoles. Parallel synthesis yields thousands of 1,2,4-triazoles in a cost- and time-efficient manner from commercially available chemicals.
Assuntos
Bibliotecas de Moléculas Pequenas/síntese química , Triazóis/síntese química , Alquilação , Estrutura Molecular , Temperatura , Tiofenos/química , Tioureia/síntese química , Fatores de TempoRESUMO
The preparation of hybrid materials from supramolecular polymers through the sol-gel process is presented. Supramolecular polymers are assembled from phosphodiester-linked pyrene oligomers and act as water-soluble one- or two-dimensional templates for silicification. The fibrillary and planar morphologies of the assemblies, as well as the excitonic interactions between the chromophores, remain unaffected by the silicification process.
RESUMO
The synthesis, characterization and functionalization of DNA-grafted supramolecular polymers are described. Cargo loading of the helical supramolecular assemblies with gold nanoparticles is demonstrated.
Assuntos
DNA/química , Polímeros/química , Sítios de Ligação , Ouro/química , Substâncias Macromoleculares/química , Nanopartículas Metálicas/química , Tamanho da Partícula , TemperaturaRESUMO
The pathway diversity of the self-assembly of amphiphilic DNA-pyrene conjugates is described. The hydrophobic pyrene units drive the self-assembly of the anionic oligomers in an aqueous environment into ribbon-shaped, DNA-grafted supramolecular polymers. Isothermal mixing of two types of sorted ribbons, each of which contains only one of two kinds of complementary oligonucleotides, results in the formation of tight networks. Thermal disassembly of these kinetically trapped networks and subsequent reassembly of the liberated components leads to mixed supramolecular polymers, which now contain both types of oligonucleotides. The scrambling of the oligonucleotides prevents the interaction between ribbons and, thus, network formation. The results show that a high local density of DNA strands in linear arrays favors hybridization among sorted polymers, whereas hybridization among mixed arrays is prevented. The lack of DNA hybridization among mixed ribbons is ascribed to the electrostatic repulsion between identical, hence noncomplementary, oligonucleotides. The findings highlight the importance of kinetically trapped states on the structural and functional properties of supramolecular polymers containing orthogonal self-assembly motifs.
Assuntos
DNA/química , Interações Hidrofóbicas e Hidrofílicas , Cinética , Modelos Moleculares , Conformação de Ácido Nucleico , Pirenos/químicaRESUMO
DNA-grafted supramolecular polymers (SPs) allow the programmed organization of DNA in a highly regular, one-dimensional array. Oligonucleotides are arranged along the edges of pyrene-based helical polymers. Addition of complementary oligonucleotides triggers the assembly of individual nanoribbons resulting in the development of extended supramolecular networks. Network formation is enabled by cooperative coaxial stacking interactions of terminal GC base pairs. The process is accompanied by structural changes in the pyrene polymer core that can be followed spectroscopically. Network formation is reversible, and disassembly into individual ribbons is realized either via thermal denaturation or by addition of a DNA separator strand.
Assuntos
DNA/química , Substâncias Macromoleculares/química , Substâncias Macromoleculares/síntese química , Nanoestruturas/química , Polímeros/química , Pirenos/química , Pareamento de Bases , Estrutura Molecular , Polímeros/síntese químicaRESUMO
The self-assembly of an amphiphilic 2,7-linked pyrene trimer in an aqueous environment into two morphologically related forms is described. Supramolecular polymerization leads to the simultaneous formation of nanosheets and nanotubes.
RESUMO
The controlled arraying of DNA strands on adaptive polymeric platforms remains a challenge. Here, the noncovalent synthesis of DNA-grafted supramolecular polymers from short chimeric oligomers is presented. The oligomers are composed of an oligopyrenotide strand attached to the 5'-end of an oligodeoxynucleotide. The supramolecular polymerization of these oligomers in an aqueous medium leads to the formation of one-dimensional (1D) helical ribbon structures. Atomic force and transmission electron microscopy show rod-like polymers of several hundred nanometers in length. DNA-grafted polymers of the type described herein will serve as models for the development of structurally and functionally diverse supramolecular platforms with applications in materials science and diagnostics.
Assuntos
DNA/química , Polimerização , Polímeros/química , Pirenos/química , Sequência de Bases , Modelos Moleculares , Nanotecnologia , Conformação de Ácido Nucleico , Polímeros/síntese químicaRESUMO
Chiroptical properties of two-dimensional (2D) supramolecular assemblies (nanosheets) of achiral, charged pyrene trimers (Py3 ) are rendered chiral by asymmetric physical perturbations. Chiral stimuli in a cuvette can originate either from controlled temperature gradients or by very gentle stirring. The chiroptical activity strongly depends on the degree of supramolecular order of the nanosheets, which is easily controlled by the method of preparation. The high degree of structural order ensures strong cooperative effects within the aggregates, rendering them more susceptible to external stimuli. The samples prepared by using slow thermal annealing protocols are both CD and LD active (in stagnant and stirred solutions), whereas for isothermally aged samples chiroptical activity was in all cases undetectable. In the case of temperature gradients, the optical activity of 2D assemblies could be recorded for a stagnant solution due to migration of the aggregates from the hottest to the coldest regions of the system. However, a considerably stronger exciton coupling, coinciding with the J-band of the interacting pyrenes, is developed upon subtle vortexing (0.5â Hz, 30â rpm) of the aqueous solution of the nanosheets. The sign of the exciton coupling is inverted upon switching between clockwise and counter-clockwise rotation. The supramolecular chirality is evidenced by the appearance of CD activity. To exclude artefacts from proper CD spectra, the contribution from LD to the observed CD was determined. The data suggest that the aggregates experience asymmetrical deformation and alignment effects because of the presence of chiral flows.
RESUMO
Double stranded DNA hybrids containing up to four consecutive, face-to-face stacked porphyrins are described. Non-nucleosidic, 5,15-bisphenyl-substituted porphyrin building blocks were incorporated into complementary oligonucleotide strands. Upon hybridization multiple porphyrins are well accommodated inside the DNA scaffold without disturbing the overall B-DNA structure. The formation of double strands containing up to four free base porphyrins is enabled without compromising duplex stability. UV/vis, fluorescence, and CD spectroscopy demonstrate the formation of porphyrins H-aggregates inside the DNA double helix and provide evidence for the existence of strong excitonic coupling between interstrand stacked porphyrins. H-aggregation results in considerable fluorescence quenching. Most intense CD effects are observed in stacks containing four porphyrins. The findings demonstrate the value of DNA for the controlled formation of molecularly defined porphyrin aggregates.
Assuntos
DNA/química , Porfirinas/química , Dicroísmo Circular , Fluorescência , Modelos Moleculares , Conformação de Ácido Nucleico , Hibridização de Ácido NucleicoRESUMO
Reading the bands: Amphiphilic pyrene trimers self-assemble into two-dimensional, supramolecular polymers in aqueous medium. Folding and aggregation processes are accompanied by simultaneous development of J- and H-bands and significant changes in the fluorescence properties. The formation of sheet-like nano-structures is confirmed by AFM.