Effects of template sequence and secondary structure on DNA-templated reactivity.

J Am Chem Soc
Authors
Keywords
Abstract

DNA-templated organic synthesis enables the translation, selection, and amplification of DNA sequences encoding synthetic small-molecule libraries. As the size of DNA-templated libraries increases, the possibility of forming intramolecularly base-paired structures within templates that impede templated reactions increases as well. To achieve uniform reactivity across many template sequences and to computationally predict and remove any problematic sequences from DNA-templated libraries, we have systematically examined the effects of template sequence and secondary structure on DNA-templated reactivity. By testing a series of template sequences computationally designed to contain different degrees of internal secondary structure, we observed that high levels of predicted secondary structure involving the reagent binding site within a DNA template interfere with reagent hybridization and impair reactivity, as expected. Unexpectedly, we also discovered that templates containing virtually no predicted internal secondary structure also exhibit poor reaction efficiencies. Further studies revealed that a modest degree of internal secondary structure is required to maximize effective molarities between reactants, possibly by compacting intervening template nucleotides that separate the hybridized reactants. Therefore, ideal sequences for DNA-templated synthesis lie between two undesirable extremes of too much or too little internal secondary structure. The relationship between effective molarity and intervening nucleic acid secondary structure described in this work may also apply to nucleic acid sequences in living systems that separate interacting biological molecules.

Year of Publication
2008
Journal
J Am Chem Soc
Volume
130
Issue
4
Pages
1392-401
Date Published
2008 Jan 30
ISSN
1520-5126
DOI
10.1021/ja076780u
PubMed ID
18179216
PubMed Central ID
PMC2533274
Links
Grant list
R01 GM065865 / GM / NIGMS NIH HHS / United States
R01 GM065865-04 / GM / NIGMS NIH HHS / United States
R01GM065865 / GM / NIGMS NIH HHS / United States