Synthetic biology projects in vitro.

Advances in the in vitro synthesis and evolution of DNA, RNA, and polypeptides are accelerating the construction of biopolymers, pathways, and organisms with novel functions. Known functions are being integrated and debugged with the aim of synthesizing life-like systems. The goals are knowledge, tools, smart materials, and therapies.

[1]  Fredrik Dahl,et al.  Circle-to-circle amplification for precise and sensitive DNA analysis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[2]  F. Studier,et al.  Pausing and termination by bacteriophage T7 RNA polymerase. , 1998, Journal of molecular biology.

[3]  W. Dower,et al.  In vitro selection as a powerful tool for the applied evolution of proteins and peptides. , 2002, Current opinion in chemical biology.

[4]  D. Bartel,et al.  Synthesizing life , 2001, Nature.

[5]  Masaru Tomita,et al.  E-CELL: software environment for whole-cell simulation , 1999, Bioinform..

[6]  O. White,et al.  Global transposon mutagenesis and a minimal Mycoplasma genome. , 1999, Science.

[7]  P. Luisi,et al.  Toward the engineering of minimal living cells , 2002, The Anatomical record.

[8]  Tsutomu Suzuki,et al.  Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. , 2006, Molecular cell.

[9]  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.

[10]  Probing Protein Structure and Function with an Expanded Genetic Code , 1995 .

[11]  Richard W Roberts,et al.  mRNA display: ligand discovery, interaction analysis and beyond. , 2003, Trends in biochemical sciences.

[12]  George M Church,et al.  Towards synthesis of a minimal cell , 2006, Molecular systems biology.

[13]  Ronald R. Breaker,et al.  Natural and engineered nucleic acids as tools to explore biology , 2004, Nature.

[14]  Rebecca L. Rawis.  'Synthetic Biology' Makes Its Debut , 2000 .

[15]  Dan Ferber,et al.  Synthetic biology. Microbes made to order. , 2004, Science.

[16]  G. Björk.  Biosynthesis and Function of Modified Nucleosides , 1995 .

[17]  G. Church,et al.  Accurate multiplex gene synthesis from programmable DNA microchips , 2004, Nature.

[18]  R. Green,et al.  Osmolytes stimulate the reconstitution of functional 50S ribosomes from in vitro transcripts of Escherichia coli 23S rRNA. , 2002, RNA.

[19]  R. Tsien,et al.  Evolution of new nonantibody proteins via iterative somatic hypermutation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Aziz El Hage,et al.  The chaperonin GroEL and other heat-shock proteins, besides DnaK, participate in ribosome biogenesis in Escherichia coli , 2001, Molecular Genetics and Genomics.

[21]  D. Dressman,et al.  Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Peter G Schultz,et al.  An Expanded Eukaryotic Genetic Code , 2003, Science.

[23]  Sarah J Kodumal,et al.  Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[24]  W. Dower,et al.  An in vitro polysome display system for identifying ligands from very large peptide libraries. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M P Orsi,et al.  On Synthetic Life , 2001, The Linacre quarterly.

[26]  B A Pfeifer,et al.  Biosynthesis of Complex Polyketides in a Metabolically Engineered Strain of E. coli , 2001, Science.

[27]  R. Quatrano.  Genomics , 1998, Plant Cell.

[28]  Zemer Gitai,et al.  The New Bacterial Cell Biology: Moving Parts and Subcellular Architecture , 2005, Cell.

[29]  Onnop Srivannavit,et al.  Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. , 2004, Nucleic acids research.

[30]  David R. Liu,et al.  DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles , 2004, Science.

[31]  Dan S. Tawfik,et al.  In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. , 2004, Analytical biochemistry.

[32]  D. Pieper,et al.  Engineering bacteria for bioremediation. , 2000, Current opinion in biotechnology.

[33]  Dan Ferber,et al.  Microbes Made to Order , 2004, Science.

[34]  S. Blacklow,et al.  Programming peptidomimetic syntheses by translating genetic codes designed de novo , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Peter G Schultz,et al.  An expanded genetic code with a functional quadruplet codon. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Franco Cerrina,et al.  Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis. , 2004, Nucleic acids research.

[37]  C. Hutchison,et al.  Essential genes of a minimal bacterium. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[38]  M. Yarus,et al.  A membrane transporter for tryptophan composed of RNA. , 2004, RNA.

[39]  C. Merryman,et al.  Transformation of aminoacyl tRNAs for the in vitro selection of "drug-like" molecules. , 2004, Chemistry & biology.

[40]  D. Mills,et al.  An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[41]  S. Hecht,et al.  Enhanced D-amino acid incorporation into protein by modified ribosomes. , 2003, Journal of the American Chemical Society.

[42]  Dan S. Tawfik,et al.  Man-made enzymes--from design to in vitro compartmentalisation. , 2000, Current opinion in biotechnology.

[43]  Hiroshi Murakami,et al.  A highly flexible tRNA acylation method for non-natural polypeptide synthesis , 2006, Nature Methods.

[44]  L. Gold,et al.  Aptamers as therapeutic and diagnostic agents. , 2000, Journal of biotechnology.

[45]  V. Vaida,et al.  Organic Aerosols and the Origin of Life: An Hypothesis , 2004, Origins of life and evolution of the biosphere.

[46]  Vincent Noireaux,et al.  A vesicle bioreactor as a step toward an artificial cell assembly. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[47]  G. Kim,et al.  Life without a cell membrane: regeneration of protoplasts from disintegrated cells of the marine green alga Bryopsis plumosa. , 2001, Journal of cell science.

[48]  Yu Wang.  A total synthesis of yeast alanine transfer RNA , 1984 .

[49]  P. Silver,et al.  Cells by design , 2004 .

[50]  F. Blattner,et al.  Emergent Properties of Reduced-Genome Escherichia coli , 2006, Science.

[51]  Peter G. Schultz,et al.  A New Strategy for the Synthesis of Glycoproteins , 2004, Science.

[52]  S. Blacklow,et al.  Pure translation display. , 2004, Analytical biochemistry.

[53]  M. Elowitz,et al.  Combinatorial Synthesis of Genetic Networks , 2002, Science.

[54]  M. Cho,et al.  Policy forum: genetics. Ethical considerations in synthesizing a minimal genome. , 1999, Science.

[55]  D. Bartel,et al.  Synthesizing life : Paths to unforeseeable science & technology , 2001 .

[56]  Carl Zimmer,et al.  Tinker, Tailor: Can Venter Stitch Together a Genome From Scratch? , 2003, Science.

[57]  N. Brot,et al.  The mRNA-directed synthesis of the α-peptide of β-galactosidase, ribosomal proteins L12 and L10, and elongation factor Tu, using purified translational factors , 1978 .

[58]  J Craig Venter,et al.  Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[59]  Richard Robinson.  Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks , 2005, PLoS biology.

[60]  P. Harbury,et al.  DNA Display II. Genetic Manipulation of Combinatorial Chemistry Libraries for Small-Molecule Evolution , 2004, PLoS biology.

[61]  Peter A Carr,et al.  Protein-mediated error correction for de novo DNA synthesis. , 2004, Nucleic acids research.

[62]  A. Paul,et al.  Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template , 2002, Science.

[63]  L. Orgel.  Unnatural selection in chemical systems. , 1995, Accounts of chemical research.

[64]  Arthur L. Caplan,et al.  Policy forum: genetics. Ethical considerations in synthesizing a minimal genome. , 1999, Science.