The strength of the template effect attracting nucleotides to naked DNA.
Bottom Line: Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not.For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical.Our results thus provide a quantitative basis for enzyme-free copying.
Affiliation: Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.Show MeSH
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Mentions: With the binding constants in hand, we asked to what extent the reaction site of primer extension was occupied by the cognate nucleotide at a given concentration. Figure 8 shows calculated occupancies for different nucleotides and binding scenarios. When the reaction site is occupied, the primer terminus is protected from side reactions (38). An extension site occupied by the correctly paired monomer is also blocked from untemplated misincorporations. Untemplated reactions are common, and over-extension of primers, beyond the length of the template, are frequently observed (37,44). Finally, in the bound state, the activated nucleotide will be at least partially protected from side reactions with other nucleotides (unspecific polymerization, pyrophosphate formation, etc.) (61) and, being sterically less accessible, less prone to hydrolyze.
Affiliation: Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.