Reaction discovery enabled by DNA-templated synthesis and in vitro selection

Abstract

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.

Figure 1

Key elements of a new approach to reaction discovery. a, Two pools of DNA-linked organic functional groups that associate each of n × m substrate combinations with a unique DNA sequence. b, A general one-pot selection and analysis method for the detection of bond-forming reactions between DNA-linked substrates.

Figure 2

Results from reaction discovery selections and analysis. a, Pool A and pool B substrates used in this work. b, Qualitative results of reaction discovery selections after exposure to the reaction conditions listed below each array image. Spots that are significantly green suggest bond formation between the corresponding substrates (quantitative fluorescence ratios in Fig. 3 and the Supplementary Data are used for actual interpretations). The 840 reaction possibilities in these five experiments were evaluated by one researcher in two days. See Supplementary Methods for detailed reaction conditions.

Figure 3

Characterization in a DNA-templated format of array positives resulting from exposure to 500 µM Na₂PdCl₄ at 37 °C for 1 h, or at 25 °C for 20 min. Putative reactions were screened by PAGE and MALDI–TOF mass spectrometric analysis (Supplementary Information). Template architectures and reaction conditions were chosen to match those used in the selection rather than to maximize product yields. Product structures other than those proposed are possible. The green/red fluorescence ratio for the internal standard at 37 °C and 25 °C is 2.9 and 3.5, respectively. For A8 + B3, reactivity was not sufficient to obtain reliable product mass characterization.

Figure 4

Characterization of a new alkyne–alkene macrocyclization reaction in a non-DNA-templated format. The macrocyclic enone product (2) was characterized by ¹H-NMR, ¹³C-NMR, COSY, UV–visible spectrometry and high-resolution mass electrospray (Supplementary Information). We speculate that product formation proceeds through the following sequence: soft deprotonation of the alkyne to form a Pd(II)–alkynyl intermediate; insertion of the alkene into the Pd-alkyne bond; β-hydride elimination to form a conjugated enyne; Pd(II)-catalysed hydration of the alkyne to form an enol π-allyl Pd complex; enol tautomerization and π-allyl Pd protonation to generate the trans-enone.