Copying Life: Synthesis of an Enzymatically Active Mirror-Image DNA-Ligase Made of D-Amino Acids.

Our objective is the creation of a mirror-image synthetic biology: that is, to mimic, entirely independent of Nature, a biological system and to re-create it from artificial component parts. Utilizing enantiomeric L-nucleotides and D-amino acids rather than the natural components, we use chemical synthesis toward a basic, self-replicating mirror-image biological system. Here, we report the synthesis of a functional DNA-ligase in the D-enantiomeric conformation, which is an exact mirror-image of the natural enzyme, exhibiting DNA ligation activity on chirally inverted nucleic acids in L-conformation, but not acting on natural substrates and with natural co-factors. Starting from the known structure of the Paramecium bursaria chlorella virus 1 DNA-ligase and the homologous but shorter DNA-ligase of Haemophilus influenza, we designed and synthesized chemically peptides, which could then be assembled into a full-length molecule yielding a functional protein. The structure and the activity of the mirror-image ligase were characterized, documenting its enantiospecific functionality.

[1]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[2]  Lorenz M. Mayr,et al.  Identification of d-Peptide Ligands Through Mirror-Image Phage Display , 1996, Science.

[3]  J. Hoheisel,et al.  Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform , 2006, Nucleic acids research.

[4]  J. Berg,et al.  A comparison of the immunogenicity of a pair of enantiomeric proteins , 1993, Proteins.

[5]  Todd O Yeates,et al.  Racemic protein crystallography. , 2012, Annual review of biophysics.

[6]  M. Burkart,et al.  Explorations of catalytic domains in non-ribosomal peptide synthetase enzymology. , 2012, Natural product reports.

[7]  Y. Sugiura,et al.  Biomolecular mirror-image recognition: reciprocal chiral-specific DNA binding of synthetic enantiomers of zinc finger domain from GAGA factor. , 2006, Chirality.

[8]  S. Kent,et al.  In Situ Neutralization in Boc-chemistry Solid Phase Peptide Synthesis , 2007, International Journal of Peptide Research and Therapeutics.

[9]  R. Payne,et al.  Native chemical ligation in protein synthesis and semi-synthesis. , 2018, Chemical Society reviews.

[10]  J. Hoheisel,et al.  Personalised proteome analysis by means of protein microarrays made from individual patient samples , 2017, Scientific Reports.

[11]  A. Brik,et al.  Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins. , 2016, Nature chemistry.

[12]  Lei Liu,et al.  A synthetic molecular system capable of mirror-image genetic replication and transcription. , 2016, Nature chemistry.

[13]  K. Rose,et al.  Covalent capture: a new tool for the purification of synthetic and recombinant polypeptides. , 2001, Chemistry & biology.

[14]  C. Lima,et al.  Structural basis for nick recognition by a minimal pluripotent DNA ligase , 2007, Nature Structural &Molecular Biology.

[15]  Torsten Schwede,et al.  The SWISS-MODEL Repository and associated resources , 2008, Nucleic Acids Res..

[16]  Ting F. Zhu,et al.  Total chemical synthesis of a thermostable enzyme capable of polymerase chain reaction , 2017, Cell Discovery.

[17]  George M Church,et al.  Synthetic biology projects in vitro. , 2006, Genome research.

[18]  Gerald F. Joyce,et al.  A Cross-chiral RNA Polymerase Ribozyme , 2014, Nature.

[19]  P. Dawson,et al.  Synthesis of native proteins by chemical ligation. , 2000, Annual review of biochemistry.

[20]  Michael C Jewett,et al.  Molecular Systems Biology Peer Review Process File in Vitro Integration of Ribosomal Rna Synthesis, Ribosome Assembly, and Translation Transaction Report , 2022 .

[21]  M. Klein,et al.  Comparative immunological properties of enantiomeric peptides , 1996, Letters in Peptide Science.

[22]  J. Tam,et al.  Thiazolidine formation as a general and site-specific conjugation method for synthetic peptides and proteins. , 1996, Analytical biochemistry.

[23]  S. Kent,et al.  Insights into the mechanism and catalysis of the native chemical ligation reaction. , 2006, Journal of the American Chemical Society.

[24]  Nanfeng Zheng,et al.  L-DNA molecular beacon: a safe, stable, and accurate intracellular nano-thermometer for temperature sensing in living cells. , 2012, Journal of the American Chemical Society.

[25]  Dipali G. Sashital,et al.  A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli , 2014, eLife.

[26]  S. Kent,et al.  Total chemical synthesis of a D-enzyme: the enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected]. , 1992, Science.

[27]  Xuechen Li,et al.  Advances in Native Chemical Ligation-Desulfurization: A Powerful Strategy for Peptide and Protein Synthesis. , 2018, Chemistry.

[28]  T. Muir,et al.  Synthesis of proteins by native chemical ligation. , 1994, Science.

[29]  S. Kent Total chemical synthesis of proteins. , 2009, Chemical Society reviews.

[30]  Zaida Luthey-Schulten,et al.  Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly. , 2015, Biophysical journal.

[31]  M. Sternberg,et al.  Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.

[32]  Native Chemical Ligation Combined with Desulfurization and Deselenization: A General Strategy for Chemical Protein Synthesis , 2011 .

[33]  S. Kent,et al.  A one-pot total synthesis of crambin. , 2004, Angewandte Chemie.

[34]  R. Payne,et al.  Rapid and efficient protein synthesis through expansion of the native chemical ligation concept , 2018 .

[35]  John B. O. Mitchell,et al.  D‐amino acid residues in peptides and proteins , 2003, Proteins.

[36]  P. Dawson,et al.  An efficient Fmoc-SPPS approach for the generation of thioester peptide precursors for use in native chemical ligation. , 2008, Angewandte Chemie.

[37]  Hao Yan,et al.  Mirror image DNA nanostructures for chiral supramolecular assemblies. , 2009, Nano letters.

[38]  M. Laskowski,et al.  Left-handed comments. , 1992, Science.

[39]  S. Sidhu,et al.  A Potent d-Protein Antagonist of VEGF-A is Nonimmunogenic, Metabolically Stable, and Longer-Circulating in Vivo. , 2016, ACS chemical biology.

[40]  Philip E. Dawson,et al.  Modulation of Reactivity in Native Chemical Ligation through the Use of Thiol Additives , 1997 .

[41]  S. Hecht,et al.  Construction of modified ribosomes for incorporation of D-amino acids into proteins. , 2006, Biochemistry.

[42]  Matthew T. Weinstock,et al.  Synthesis and folding of a mirror-image enzyme reveals ambidextrous chaperone activity , 2014, Proceedings of the National Academy of Sciences.

[43]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[44]  S. Klußmann,et al.  A thermostable d-polymerase for mirror-image PCR , 2017, Nucleic acids research.

[45]  G. F. Joyce,et al.  An L-RNA Aptamer that Binds and Inhibits RNase. , 2015, Chemistry & biology.