scholarly journals Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization

2020 ◽  
Author(s):  
Wen Zhang ◽  
Seohyun Chris Kim ◽  
Chun Pong Tam ◽  
Victor S. Lelyveld ◽  
Saikat Bala ◽  
...  

ABSTRACTThe prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3’-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer ten-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.

2020 ◽  
Author(s):  
Wen Zhang ◽  
Seohyun Chris Kim ◽  
Chun Pong Tam ◽  
Victor S Lelyveld ◽  
Saikat Bala ◽  
...  

Abstract The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3′-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.


Soft Matter ◽  
2021 ◽  
Author(s):  
Jiawei Lu ◽  
Xiangyu Bu ◽  
Xinghua Zhang ◽  
Bing Liu

The shapes of colloidal particles are crucial to the self-assembled superstructures. Understanding the relationship between the shapes of building blocks and the resulting crystal structures is an important fundamental question....


2014 ◽  
Vol 18 (01n02) ◽  
pp. 115-122 ◽  
Author(s):  
Srinivas Banala ◽  
Klaus Wurst ◽  
Bernhard Kräutler

We report here the preparation (in "one-pot") of a tetra-β″-sulfoleno-meso-aryl-porphyrin in about 80% yield by using an optimized modification of Lindsey's variant of the Adler–Longo approach. The Zn ( II )-, Cu ( II )- and Ni ( II )-complexes of the symmetrical porphyrin were prepared and characterized spectroscopically. Crystal structures of the fluorescent Zn ( II )- and of the non-fluorescent Ni ( II )-tetra-β″-sulfoleno-meso-aryl-porphyrinates showed the highly substituted porphyrin ligands to be nearly perfectly planar. The Zn ( II )-complex of this porphyrin has been used as a thermal precursor of a reactive diene, and — formally — of lateral and diagonal bis-dienes, of a tris-diene and of a tetra-diene, which all underwent [4 + 2]-cycloaddition reactions in situ with a range of dienophiles. Thus, the tetra-β″-sulfoleno-meso-aryl-porphyrin and its metal complexes represent reactive building blocks, "programmed" for the syntheses of symmetrical and highly functionalized porphyrins.


2016 ◽  
Vol 72 (3) ◽  
pp. 268-293 ◽  
Author(s):  
Jean-Guillaume Eon

Topological properties of crystal structures may be analysed at different levels, depending on the representation and the topology that has been assigned to the crystal. Considered here is thecombinatorialorbond topologyof the structure, which is independent of its realization in space. Periodic nets representing one-dimensional complexes, or the associated graphs, characterize the skeleton of chemical bonds within the crystal. Since periodic nets can be faithfully represented by their labelled quotient graphs, it may be inferred that their topological features can be recovered by a direct analysis of the labelled quotient graph. Evidence is given for ring analysis and structure decomposition into building units and building networks. An algebraic treatment is developed for ring analysis and thoroughly applied to a description of coesite. Building units can be finite or infinite, corresponding to 1-, 2- or even 3-periodic subnets. The list of infinite units includes linear chains or sheets of corner- or edge-sharing polyhedra. Decomposing periodic nets into their building units relies on graph-theoretical methods classified assurgery techniques. The most relevant operations are edge subdivision, vertex identification, edge contraction and decoration. Instead, these operations can be performed on labelled quotient graphs, evidencing in almost a mechanical way the nature and connection mode of building units in the derived net. Various examples are discussed, ranging from finite building blocks to 3-periodic subnets. Among others, the structures of strontium oxychloride, spinel, lithiophilite and garnet are addressed.


2017 ◽  
Vol 17 (8) ◽  
pp. 4336-4346 ◽  
Author(s):  
Sara Fuertes ◽  
Andrés J. Chueca ◽  
Antonio Martín ◽  
Violeta Sicilia

2014 ◽  
Vol 43 (19) ◽  
pp. 7006-7019 ◽  
Author(s):  
Matteo Atzori ◽  
Flavia Artizzu ◽  
Elisa Sessini ◽  
Luciano Marchiò ◽  
Danilo Loche ◽  
...  

Here we report on new tris(haloanilato)metallate(iii) complexes with general formula [M(X2An)3]3−, their crystal structures, DFT calculations and magnetic properties.


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