Influence of montmorillonite on nucleotide oligomerization reactions: A molecular dynamics study

Damien C. Mathew, Zaida Luthey-Schulten

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21 Scopus citations

Abstract

We investigate a proposed origins of life scenario involving the clay montmorillonite and its catalytic role in forming oligonucleotides from activated mononucleotides. Clay and mineral surfaces are important for concentrating the reactants and for promoting nucleotide polymerization reactions. Using classical molecular dynamics methods we provide atomic details of reactant conformations prior to polynucleotide formation, lending insight into previously reported experimental observations of this phenomenon. The simulations clarify the catalytic role of metal ions, demonstrate that reactions leading to correct linkages take place primarily in the interlayer, and explain the observed sequence selectivity in the elongation of the chain. The study comparing reaction probabilities involving L- and D-chiral forms of the reactants has found enhancement of homochiral over heterochiral products when catalyzed by montmorillonite.

Original languageEnglish (US)
Pages (from-to)303-317
Number of pages15
JournalOrigins of Life and Evolution of Biospheres
Volume40
Issue number3
DOIs
StatePublished - Jun 2010

Bibliographical note

Funding Information:
Acknowledgements This work was funded by NSF-FIBR # SBCSF0526747. Some simulations were performed at the National Center for Supercomputing Applications and the Texas Advanced Computing Center through Teragrid LRAC# TG-MCA03S027 and through the U of I School of Chemical Sciences computational resource through NSF CRIF 05-41659. We wish to thank members of the Luthey–Schulten group for helpful discussions.

Keywords

  • Catalysis
  • Clay
  • Molecular dynamics
  • Polynucleotide
  • Prebiotic chemistry
  • RNA world

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