Autonomous Multistep Organic Synthesis in a Single Isothermal Solution Mediated by a DNA Walker

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 may 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 multistep products generated by this primitive ribosome mimetic are programmed by the sequence of the DNA track, are unrelated to the structure of DNA, and are formed with speeds and overall yields significantly greater than those previously achieved by multistep DNA-templated small-molecule synthesis.

[1]  Z. Gartner,et al.  The generality of DNA-templated synthesis as a basis for evolving non-natural small molecules. , 2001, Journal of the American Chemical Society.

[2]  T. Steitz,et al.  The structural basis of ribosome activity in peptide bond synthesis. , 2000, Science.

[3]  Erik Winfree,et al.  Molecular robots guided by prescriptive landscapes , 2010, Nature.

[4]  N. Seeman From genes to machines: DNA nanomechanical devices. , 2005, Trends in biochemical sciences.

[5]  David R. Liu,et al.  Ordered multistep synthesis in a single solution directed by DNA templates. , 2005, Angewandte Chemie.

[6]  A. Turberfield,et al.  A free-running DNA motor powered by a nicking enzyme. , 2005, Angewandte Chemie.

[7]  P. Schultz,et al.  A general and efficient route for chemical aminoacylation of transfer RNAs , 1991 .

[8]  J. Reif,et al.  A unidirectional DNA walker that moves autonomously along a track. , 2004, Angewandte Chemie.

[9]  Andreas Plückthun,et al.  Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target , 2007, Nature Methods.

[10]  P. Yin,et al.  A DNAzyme that walks processively and autonomously along a one-dimensional track. , 2005, Angewandte Chemie.

[11]  David R. Liu,et al.  Effects of template sequence and secondary structure on DNA-templated reactivity. , 2008, Journal of the American Chemical Society.

[12]  N. Seeman,et al.  A Proximity-Based Programmable DNA Nanoscale Assembly Line , 2010, Nature.

[13]  M. Fischbach,et al.  Total Biosynthesis: in vitro Reconstitution of Polyketide and Nonribosomal Peptide Pathways , 2008 .

[14]  David R. Liu,et al.  Multistep small-molecule synthesis programmed by DNA templates. , 2002, Journal of the American Chemical Society.

[15]  J. Åqvist,et al.  Mechanism of peptide bond synthesis on the ribosome. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[16]  A. Plückthun,et al.  In vitro selection and evolution of functional proteins by using ribosome display. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Ruojie Sha,et al.  A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.

[18]  Hao Yan,et al.  Addressable molecular tweezers for DNA-templated coupling reactions. , 2006, Nano letters.

[19]  M. Oss,et al.  Electrospray ionization efficiency scale of organic compounds. , 2010, Analytical chemistry.

[20]  Christopher T Walsh,et al.  Polyketide and Nonribosomal Peptide Antibiotics: Modularity and Versatility , 2004, Science.

[21]  P. Britz‐McKibbin,et al.  Virtual quantification of metabolites by capillary electrophoresis-electrospray ionization-mass spectrometry: predicting ionization efficiency without chemical standards. , 2009, Analytical chemistry.

[22]  Chengde Mao,et al.  Reprogramming DNA-directed reactions on the basis of a DNA conformational change. , 2004, Journal of the American Chemical Society.

[23]  A. Turberfield,et al.  DNA nanomachines. , 2007, Nature nanotechnology.

[24]  G. F. Joyce,et al.  A general purpose RNA-cleaving DNA enzyme. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[25]  I. Leito,et al.  Towards the electrospray ionization mass spectrometry ionization efficiency scale of organic compounds. , 2008, Rapid communications in mass spectrometry : RCM.

[26]  David R. Liu,et al.  Translation of DNA into a library of 13,000 synthetic small-molecule macrocycles suitable for in vitro selection. , 2008, Journal of the American Chemical Society.

[27]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[28]  Itamar Willner,et al.  DNA-based machines. , 2006, Organic & biomolecular chemistry.

[29]  David R. Liu,et al.  DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules. , 2004, Angewandte Chemie.

[30]  Wael Mamdouh,et al.  Single-molecule chemical reactions on DNA origami. , 2010, Nature nanotechnology.

[31]  F. Simmel,et al.  DNA-based nanodevices , 2007 .