Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides

Nature Methods

Volumn 10, Issue 7, 2013, Pages 647-652

  Ducani, Cosimo ^a   Kaul, Corinna ^a   Moche, Martin ^a   Shih, William M ^b,c,d   Högberg, Björn ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b HARVARD UNIVERSITY   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; SINGLE STRANDED DNA;

ARTICLE; BACTERIUM COLONY; CRYSTAL STRUCTURE; DNA STRUCTURE; DNA TEMPLATE; ENZYME SYNTHESIS; ESCHERICHIA COLI; GENE AMPLIFICATION; IN VITRO STUDY; MONOCLONAL STOICHIOMETRY; NONHUMAN; PHAGEMID; PRIORITY JOURNAL; PROTEIN FOLDING; STOICHIOMETRY;

DNA RESTRICTION-MODIFICATION ENZYMES; DNA, BACTERIAL; ESCHERICHIA COLI; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SYNTHETIC BIOLOGY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 84879695721     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2503     Document Type: Article

References (36)

1. Merrifield, R.B. Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. J. Am. Chem. Soc. 85, 2149-2154 (1963).
2. The International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
3. Badi, N. & Lutz, J.F. Sequence control in polymer synthesis. Chem. Soc. Rev. 38, 3383-3390 (2009).
4. Oberacher, H., Niederstätter, H. & Parson, W. Characterization of synthetic nucleic acids by electrospray ionization quadrupole time-of-flight mass spectrometry. J. Mass Spectrom. 40, 932-945 (2005).
5. Semenyuk, A. et al. Cartridge-based high-throughput purification of oligonucleotides for reliable oligonucleotide arrays. Anal. Biochem. 356, 132-141 (2006).
6. Zhang, D.Y., Turberfield, A.J., Yurke, B. & Winfree, E. Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318, 1121-1125 (2007).
7. Yin, P., Choi, H.M.T., Calvert, C.R. & Pierce, N.A. Programming biomolecular self-assembly pathways. Nature 451, 318-322 (2008).
8. Zhang, D.Y. & Seelig, G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103-113 (2011).
9. Tian, J. et al. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432, 1050-1054 (2004).
10. Antson, D.O., Isaksson, A., Landegren, U. & Nilsson, M. PCR-generated padlock probes detect single nucleotide variation in genomic DNA. Nucleic Acids Res. 28, E58 (2000).
11. Kosuri, S. et al. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat. Biotechnol. 28, 1295-1299 (2010).
12. Sha, R. et al. Self-assembled DNA crystals: the impact on resolution of 5'-phosphates and the DNA source. Nano Lett. 13, 793-797 (2013).
13. Lohmann, J.S., Stougaard, M. & Koch, J. A new enzymatic route for production of long 5'-phosphorylated oligonucleotides using suicide cassettes and rolling circle DNA synthesis. BMC Biotechnol. 7, 49 (2007).
14. Stemmer, W.P.C., Crameri, A., Ha, K.D., Brennan, T.M. & Heyneker, H.L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164, 49-53 (1995).
15. Zheng, J. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74-77 (2009).
16. Rothemund, P.W.K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302 (2006).
17. Douglas, S.M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414-418 (2009).
18. Högberg, B., Liedl, T. & Shih, W.M. Folding DNA origami from a double-stranded source of scaffold. J. Am. Chem. Soc. 131, 9154-9155 (2009).
19. Andersen, E.S. et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73-76 (2009).
20. Douglas, S.M., Chou, J.J. & Shih, W.M. DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc. Natl. Acad. Sci. USA 104, 6644-6648 (2007).
21. Douglas, S.M., Bachelet, I. & Church, G.M. A logic-gated nanorobot for targeted transport of molecular payloads. Science 335, 831-834 (2012).
22. Zhao, Y.-X. et al. DNA origami delivery system for cancer therapy with tunable release properties. ACS Nano 6, 8684-8691 (2012).
23. Jiang, Q. et al. DNA origami as a carrier for circumvention of drug resistance. J. Am. Chem. Soc. 134, 13396-13403 (2012).
24. Dietz, H., Douglas, S. & Shih, W.M. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725 (2009).
25. Patil, S.D., Rhodes, D.G. & Burgess, D.J. DNA-based therapeutics and DNA delivery systems: a comprehensive review. AAPS J. 7, E61-E77 (2005).
26. Rosi, N.L. et al. Oligonucleotide-modified gold nanoparticles for intracellular gene regulation. Science 312, 1027-1030 (2006).
27. Esteban, J.A., Salas, M. & Blanco, L. Fidelity of phi29 DNA Polymerase. J. Biol. Chem. 268, 2719-2726 (1993).
28. Schaaper, R.M. Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J. Biol. Chem. 268, 23762-23765 (1993).
29. Lee, H. et al. Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery. Nat. Nanotechnol. 7, 389-393 (2012).
30. Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623-626 (2012).
31. Castro, C.E. et al. A primer to scaffolded DNA origami. Nat. Methods 8, 221-229 (2011).
32. Douglas, S.M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001-5006 (2009).
33. Mueller, U. et al. Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin. J. Synchrotron Radiat. 19, 442-449 (2012).
34. Grosse-Kunstleve, R.W., Echols, N. & Adams, P.D. Fuzzy space group symbols: H3 and H32. Computational Crystallography Newsletter 2, 12-14 (2011).
35. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763 (1994).
36. Bricogne, G. et al. BUSTER version 2.11.2. (Global Phasing Ltd., 2011).