Wen Zhang1,2,3, Seohyun Chris Kim1,4, Chun Pong Tam1,4, Victor S Lelyveld1,2, Saikat Bala5, John C Chaput5, Jack W Szostak1,2,4. 1. Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA. 2. Department of Genetics, Harvard Medical School, Boston, MA 02114, USA. 3. Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. 4. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. 5. Department of Chemistry and of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA.
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.
The prebiotic synthesis of n class="Chemical">ribonucleotides is likely to have been accompanpan>ied by the synpan>thesis of noncanpan>onical pan> class="Gene">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.
Authors: Irina Anosova; Ewa A Kowal; Nicholas J Sisco; Sujay Sau; Jen-Yu Liao; Saikat Bala; Eriks Rozners; Martin Egli; John C Chaput; Wade D Van Horn Journal: Chembiochem Date: 2016-07-29 Impact factor: 3.164
Authors: Constantin Giurgiu; Ziyuan Fang; Harry R M Aitken; Seohyun Chris Kim; Lydia Pazienza; Shriyaa Mittal; Jack W Szostak Journal: Angew Chem Int Ed Engl Date: 2021-09-14 Impact factor: 16.823