Sequence-specific synthesis with artificial molecular machines

Abstract

Sequence-specific synthesis is essential to life. In nature, information-rich polymers such as polynucleotides, polypeptides and polysaccharides are responsible for virtually all vital processes. As opposed to nature’s optimised approach towards sequence control employing sophisticated molecular machines such as ribosomes and nucleotide polymerases, the synthetic chemist’s toolbox for the generation of highly ordered monomeric sequences is limited in scope. In this thesis, the realisation of the first artificial small-molecule machines capable of synthesising peptides, translating information that is encoded in a molecular strand, is described. The chemical structure of such machines is based on a rotaxane architecture: a molecular ring threaded onto a molecular axle. The ring carries a reactive arm, a thiolate group that iteratively removes amino acids from the strand that block the path of the macrocycle. The acyl monomers are transferred to a peptide-elongation site through native chemical ligation, thereby translating the information encoded in the track into a growing peptide strand. The synthesis is demonstrated with ~1018 molecular machines acting in parallel; this process generates milligram quantities of a peptide with a single sequence as confirmed by tandem mass spectrometry. Chapter I describes previous strategies that have been employed to realise sequence specific synthesis and gives an overview about relevant literature in the field. Chapter II describes the concept, previous work and model studies which lay the ground work for the more advanced machines. The first generation design of a molecular machine based on transacylation catalysis as well as the second generation design based on native chemical ligation are discussed. The successful operation of a single-barrier rotaxane capable of elongating its reactive arm by a single amide bond formation and subsequent self-immolation is described. Chapter III describes the first small-molecule molecular machine capable of sequence-specific assembly of a tripeptide. The sequence-integrity of the operation product is determined by tandem mass spectrometry and comparison with an authentic sample. Chapter IV describes a novel synthetic approach towards highly complex molecular machines. Using this rotaxane elongation strategy, a molecular machine with four aminoacyl monomers on the strand is reported. The successful operation afforded the expected product resulting from four amide bond forming events without any detectable sequence scrambling.