Robotic hierarchical mixing for the production of combinatorial libraries of proteins and small molecules

We present a method to automatically plan a robotic process to mix individual combinations of reactants in individual reaction vessels (vials or wells in a multiwell plate), mixing any number of reactants in any desired stoichiometry, and ordering the mixing steps according to an arbitrarily complex treelike assembly protocol. This process enables the combinatorial generation of complete or partial product libraries in individual reaction vessels from intermediates formed in the presence of different sets of reactants. It can produce either libraries of chimeric genes constructed by ligation of fragments from different parent genes or libraries of chemical compounds constructed by convergent synthesis. Given concentrations of the input reactants and desired amounts or volumes of the products, our algorithm, RoboMix, computes the required reactant volumes and the resulting product concentrations, along with volumes and concentrations for all intermediate combinations. It outputs a sequence of robotic liquid transfer steps that ensures that each combination is correctly mixed even when individualized stoichiometries are employed and with any fractional yield for a product. It can also account for waste in robotic liquid handling and residual volume needed to ensure accurate aspiration. We demonstrate the effectiveness of the method in a test mixing dyes with different UV-vis absorption spectra, verifying the desired combinations spectroscopically.