1. Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization
- Author
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Jack W. Szostak, Victor S. Lelyveld, Seohyun Chris Kim, Wen Zhang, Saikat Bala, John C. Chaput, and Chun Pong Tam
- Subjects
Models, Molecular ,Ribonucleotide ,AcademicSubjects/SCI00010 ,Stereochemistry ,Origin of Life ,Molecular Conformation ,Biology ,010402 general chemistry ,01 natural sciences ,Primer extension ,Polymerization ,Structure-Activity Relationship ,chemistry.chemical_compound ,Chemical Biology and Nucleic Acid Chemistry ,Genetic ,Models ,Information and Computing Sciences ,Genetics ,Nucleotide ,chemistry.chemical_classification ,Molecular Structure ,010405 organic chemistry ,Oligonucleotide ,Molecular ,RNA ,Templates, Genetic ,Biological Sciences ,0104 chemical sciences ,Monomer ,chemistry ,Templates ,Primer (molecular biology) ,Tetroses ,Environmental Sciences ,Developmental Biology - 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.
- Published
- 2020