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The strength of the template effect attracting nucleotides to naked DNA.

Kervio E, Claasen B, Steiner UE, Richert C - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.

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Nucleotides and hairpins used for NMR titration. Loops are hexaethylene glycol linkers (HEG).
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Figure 2: Nucleotides and hairpins used for NMR titration. Loops are hexaethylene glycol linkers (HEG).

Mentions: Two experimental systems were used to measure the binding of nucleotides to templating bases (Figure 1). The first used NMR spectroscopy as monitoring technique and short hairpins as intramolecular models of primer–template duplexes (Figure 2). The overhang at the 5′-terminus of the hairpin provided the templating base to which deoxynucleoside monophosphates (dNMPs) 1a–t were allowed to bind. The stem of the hairpin oligonucleotides was chosen to be long enough to give a stable helix at room temperature, but short enough to allow for NMR without isotope enrichment. A hexaethylene glycol (HEG) linker loop (53) was chosen to provide stability without complicating assignment.


The strength of the template effect attracting nucleotides to naked DNA.

Kervio E, Claasen B, Steiner UE, Richert C - Nucleic Acids Res. (2014)

Nucleotides and hairpins used for NMR titration. Loops are hexaethylene glycol linkers (HEG).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4066754&req=5

Figure 2: Nucleotides and hairpins used for NMR titration. Loops are hexaethylene glycol linkers (HEG).
Mentions: Two experimental systems were used to measure the binding of nucleotides to templating bases (Figure 1). The first used NMR spectroscopy as monitoring technique and short hairpins as intramolecular models of primer–template duplexes (Figure 2). The overhang at the 5′-terminus of the hairpin provided the templating base to which deoxynucleoside monophosphates (dNMPs) 1a–t were allowed to bind. The stem of the hairpin oligonucleotides was chosen to be long enough to give a stable helix at room temperature, but short enough to allow for NMR without isotope enrichment. A hexaethylene glycol (HEG) linker loop (53) was chosen to provide stability without complicating assignment.

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.

View Article: PubMed Central - PubMed

Affiliation: Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.

Show MeSH
Related in: MedlinePlus