DNA-templated synthesis in organic solvents.

DNA-templated organic synthesis (DTS) enables new modes of controlling chemical reactivity and allows evolutionary principles to be applied to the discovery of synthetic small molecules, synthetic polymers, and new chemical reactions. The structures that can be accessed in a DNA-templated format thus far have been limited to those that can be generated in aqueous solvents. Here we report efficient and sequence-specific DTS in a variety of organic solvents with low or minimal water content. These methods expand the scope of DTS by providing access to reagents that are insoluble in water as well as reactions in which the participation of water inhibits product formation. Previous studies by Okahata and others suggest that quaternary ammonium salts can associate with DNA phosphates to form complexes that are soluble in organic solvents. We hypothesized that short (10–30 bp) DNA duplexes formed in aqueous solution and then transferred to an organic solvent containing low concentrations (mM) of quaternary ammonium salts might retain their double-stranded structure and mediate DNA-templated organic synthesis. Although we found that DNA-templated chemistry could indeed take place efficiently and sequence-specifically in organic solvents in the presence of alkyl ammonium salts (see Supporting Information), we further speculated that at the extremely low concentrations required for DTS (nM), alkyl ammonium salts might not be necessary for the solubilization of duplexes preformed in aqueous solution (Figure 1A). To evaluate the ability of preformed duplexes to support DTS in primarily organic solvents, we first investigated three known DNA-templated chemistries in four distinct contexts (Figure 1B): i) in a simple end-of-helix architecture with juxtaposed reactants (E1), ii) in a long-distance end-of-helix architecture with ten intervening nucleotides between the hybridized reactants (E10), iii) in the “omega” architecture with a five-base loop (W5), and iv) with reactants linked to noncomplementary (mismatched) oligonucleotides. Products were characterized both by denaturing PAGE analysis and by MALDI mass spectrometry (see Table 1 and Supporting Information for details). DNA-templated amine acylation mediated by 1-(3-dimethylaminopropyl)-3-ethyl carbodiimide (EDC) and N-hydroxysulfosuccinimide (sNHS) has been well characterized in aqueous solution and is known to take place efficiently even when reactive groups are separated by many intervening nucleotides. To carry out DNA-templated amine acylation in organic solvent, template and reagent oligonucleotides (Table 1) were prehybridized in a small volume of aqueous 70 mM NaCl. Amine acylation was initiated by the addition of organic solvent containing