Current approaches to reaction discovery focus on one particular transformation. Typically, researchers choose substrates based on their predicted ability to serve as precursors for the target structure, then evaluate reaction conditions for their ability to effect product formation. This approach is ideal for addressing specific reactivity problems, but its focused nature might leave many areas of chemical reactivity unexplored. Here we report a reaction discovery approach that uses DNA-templated organic synthesis and in vitro selection to simultaneously evaluate many combinations of different substrates for bond-forming reactions in a single solution. Watson-Crick base pairing controls the effective molarities of substrates tethered to DNA strands; bond-forming substrate combinations are then revealed using in vitro selection for bond formation, PCR amplification and DNA microarray analysis. Using this approach, we discovered an efficient and mild carbon-carbon bond-forming reaction that generates an enone from an alkyne and alkene using an inorganic palladium catalyst. Although this approach is restricted to conditions and catalysts that are at least partially compatible with DNA, we expect that its versatility and efficiency will enable the discovery of additional reactions between a wide range of substrates.

Abstract:We have developed and applied an approach to reaction discovery that takes advantage of DNA encoding, DNA-programmed assembly of substrate pairs, in vitro selection, and PCR amplification, yet does not require reaction conditions that support DNA hybridization. This system allows the simultaneous evaluation of >200 potential bond-forming combinations of substrates in a single experiment and can be applied in a range of solvent and temperature conditions. In an initial application, we applied this system to explore Au(III)-mediated chemistry and uncovered a simple, mild method for the selective Markovnikovtype hydroarylation of vinyl arenes and trisubstituted olefins with indoles.

The amination of ketoacids to amino acids by pyridoxamine is greatly accelerated when the pyridoxamine is covalently linked to polyethylenimine carrying N-methyl and N-lauryl groups. Michaelis-Menten kinetics is seen with all substrates, from which the effect of the lauryl groups and the methyl groups can be determined with respect to the strength of binding of the substrate and the rate constant k2 within the complex. The polyamine catalyzes the reaction using acid and base groups, the lauryl groups increase k2 by producing a nonpolar medium in which the reaction occurs, and the lauryl groups promote binding of hydrophobic substrates. The result is that the amination of indolepyruvic acid to produce tryptophan is accelerated by 240000-fold.

DNA-templated organic synthesis (DTS) [1a] enables new modes of controlling chemical reactivity [1b-d] and allows evolutionary principles to be applied to the discovery of synthetic small molecules, [1e,f] synthetic polymers, [1g] and new chemical reactions.[1h] 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 [2] and others [3][4][5][6] 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 1 A).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 1 B): 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 [7] 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 [7] 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 40 mM EDC and 25 mM N-hydrosuccinimide (NHS) to result in a final solvent composition of 95 % acetonitrile and 5 % water. Under these conditions, the E1, E10, and W5 architectures all generated amide products efficiently (88, 82, and 70 % yield, respectively), as charac...