Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker

Abstract

Multistep synthesis in the laboratory typically requires numerous reaction vessels, each containing a different set of reactants. In contrast, cells are capable of performing highly efficient and selective multistep biosynthesis under mild conditions with all reactants simultaneously present in solution. If the latter approach could be applied in the laboratory, it could improve the ease, speed and efficiency of multistep reaction sequences. Here, we show that a DNA mechanical device--a DNA walker moving along a DNA track--can be used to perform a series of amine acylation reactions in a single solution without any external intervention. The products of these reactions are programmed by the sequence of the DNA track, but they are not related to the structure of DNA. Moreover, they are formed with speeds and overall yields that are significantly greater than those previously achieved by multistep DNA-templated small-molecule synthesis.

Figure 1

Overview of the DNAsome system. (a) The system described in this work comprises six DNA or DNA-linked molecules. Three substrates (S1-S3) and an initiator (S0) can hybridize on a single-stranded DNA track (T). Each substrate has an amino acid NHS ester at its 5’ end and two ribonucleotides (green dot) in the middle of its DNA sequence. The DNA walker (W) contains a 3’ amine group and an RNA-cleaving DNAzyme (purple line) that can cleave the ribonucleotides in the substrates. (b) DNAsome-mediated multistep synthesis of a triamide product. All steps take place in a single solution under one set of reaction conditions without external intervention.

Figure 2

Analysis of reaction products generated by the DNAsome system. (a) Mass spectroscopy analysis of the three-step DNAsome-mediated reaction sequence. See the text for a detailed description of reaction conditions. (b) Mass spectrometry analysis of the experiment in (a) repeated using substrates lacking amino acid NHS esters. See the Supplementary Information for all expected and observed masses.

Figure 3

Mass spectroscopy analysis of reactions identical to the one shown in Figure 2a, but using different DNA tracks (a-c) or with no DNA track (d). The DNA tracks are as follows: (a) I-C1-C3-C2; (b) I-C2-C3-C1; (c) I-C3-C2-C1; (d) no DNA track. See the Supplementary Information for all expected and observed masses.