Abstract
Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology, and synthetic biology. We developed an error-correcting recursive construction procedure that attempts to address this challenge. Making DNA molecules from synthetic oligonucleotides using the procedure described here surpasses existing methods for de novo DNA synthesis in speed, precision, and amenability to automation. It provides for the first time a unified DNA construction platform for combining synthetic and natural DNA fragments, for constructing designer DNA libraries, and for making the faultless long synthetic DNA building blocks needed for de novo genome construction.
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References
John Von Neumann, R. S. P. (1952) Lectures on probabilistic logics and the synthesis of reliable organisms from unreliable components, California Institute of Technology, Pasadena.
Drexler, K. E. (1992) Nanosystems: molecular machinery, manufacturing, and computation, Wiley, New York.
Merkle, R. C. (1997) Convergent assembly, Nanotechnology 8, 18–22.
Forster, A. C., and Church, G. M. (2006) Towards synthesis of a minimal cell, Mol Syst Biol 2, 45.
Carr, P. A., Park, J. S., Lee, Y. J., Yu, T., Zhang, S., and Jacobson, J. M. (2004) Protein-mediated error correction for de novo DNA synthesis, Nucleic Acids Res 32, e162.
Tian, J., Gong, H., Sheng, N., Zhou, X., Gulari, E., Gao, X., and Church, G. (2004) Accurate multiplex gene synthesis from programmable DNA microchips, Nature 432, 1050–1054.
Stemmer, W. P., Crameri, A., Ha, K. D., Brennan, T. M., and Heyneker, H. L. (1995) Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides, Gene 164, 49–53.
Au, L. C., Yang, F. Y., Yang, W. J., Lo, S. H., and Kao, C. F. (1998) Gene synthesis by a LCR-based approach: high-level production of leptin-L54 using synthetic gene in Escherichia coli, Biochem Biophys Res Commun 248, 200–203.
Xiong, A. S., Yao, Q. H., Peng, R. H., Li, X., Fan, H. Q., Cheng, Z. M., and Li, Y. (2004) A simple, rapid, high-fidelity and cost–effective PCR-based two-step DNA synthesis method for long gene sequences, Nucleic Acids Res 32, e98.
Gao, X., Yo, P., Keith, A., Ragan, T. J., and Harris, T. K. (2003) Thermodynamically balanced inside-out (TBIO) PCR-based gene synthesis: a novel method of primer design for high-fidelity assembly of longer gene sequences, Nucleic Acids Res 31, e143.
Smith, H. O., Hutchison, C. A., 3rd, Pfannkoch, C., and Venter, J. C. (2003) Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides, Proc Natl Acad Sci USA 100, 15440–15445.
Rogers, H. (1967) Theory of recursive functions and effective computability, McGraw-Hill, New York.
Mandelbrot, B. B. (1982) The Fractals Book, Observatory 102, 151–151.
Chomsky, N. (1964) Syntactic structures, Mouton, The Hague.
Hopcroft, J. E., and Ullman, J. D. (1979) Introduction to automata theory, languages, and computation, Addison-Wesley, Reading, Mass.
Aho, A. V., Hopcroft, J. E., and Ullman, J. D. (1983) Data structures and algorithms, Addison-Wesley, Reading, Mass.; London.
SLONING, BIOTECHNOLOGY, and GMBH. (2006) DE NOVO ENZYMATIC PRODUCTION OF NUCLEIC ACID MOLECULES.
Knight, T. (2003) Idempotent Vector Design for Standard Assembly of Biobricks, MIT Synthetic Biology Working Group.
Heinemann, M., and Panke, S. (2006) Synthetic biology – putting engineering into biology, Bioinformatics 22, 2790–2799.
Ryu, D. D., and Nam, D. H. (2000) Recent progress in biomolecular engineering, Biotechnol Prog 16, 2–16.
Caruthers, M. H. (1985) Gene synthesis machines: DNA chemistry and its uses, Science 230, 281–285.
Hutchison, C. A., 3rd, Phillips, S., Edgell, M. H., Gillam, S., Jahnke, P., and Smith, M. (1978) Mutagenesis at a specific position in a DNA sequence, J Biol Chem 253, 6551–6560.
Alsuwaiyel, M. H. (1999) Algorithms: design techniques and analysis, World Scientific, Singapore; New Jersey.
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Linshiz, G., Yehezkel, T.B., Shapiro, E. (2012). Recursive Construction of Perfect DNA Molecules and Libraries from Imperfect Oligonucleotides. In: Peccoud, J. (eds) Gene Synthesis. Methods in Molecular Biology, vol 852. Humana Press. https://doi.org/10.1007/978-1-61779-564-0_12
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DOI: https://doi.org/10.1007/978-1-61779-564-0_12
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