The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis
Open accessAbstract
The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than the original source of DNA. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard to the parent genome. Yet design and construction of synthetic genes, especially those coding for large proteins, can be a slow, difficult and confusing process. We have written a computer program that automates the design of oligonucleotides for gene synthesis. Our program requires simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation. With the help of this program and a two-step PCR method, we have successfully constructed numerous synthetic genes, ranging from 139 to 1042 bp. The approach presented here simplifies the production of proteins from a wide variety of organisms for genomics-based studies.
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Vetterling, W. T., Teukolsky, S. A., Press, W. H., & Flannery, B. P. (1988) · Cited by 7,701
Press, W. H., Teukolsky, S. L. A., Flannery, B. P., & Vetterling, W. T. (1990) · Infoscience (Ecole Polytechnique Fédérale de Lausanne) · Cited by 6,980
[6] Use of T7 RNA polymerase to direct expression of cloned genes
William Studier, F., Rosenberg, A. H., Dunn, J. J., & Dubendorff, J. W. (1990) · Methods in Enzymology · doi:10.1016/0076-6879(90)85008-c · Cited by 6,562
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
SantaLucia, J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.4.1460 · Cited by 2,793
‘Touchdown’ PCR to circumvent spurious priming during gene amplification
Don, R. H., Cox, P. T., Wainwright, B. J., Baker, K., & Mattick, J. S. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.14.4008 · Cited by 2,586
A peptide antibiotic from human skin
Harder, J., Bartels, J., Christophers, E., & Schröder, J.-M. (1997) · Nature · doi:10.1038/43088 · Cited by 1,363
Isolation and Characterization of Human μ-Defensin-3, a Novel Human Inducible Peptide Antibiotic
Harder, J., Bartels, J., Christophers, E., & Schröder, J.-M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m008557200 · Cited by 1,311
Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability
SantaLucia, Allawi, H. T., & Seneviratne, P. A. (1996) · Biochemistry · doi:10.1021/bi951907q · Cited by 831
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides
Stemmer, W. P. C., Crameri, A., Ha, K. D., Brennan, T. M., & Heyneker, H. L. (1995) · Gene · doi:10.1016/0378-1119(95)00511-4 · Cited by 728
PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases
Cline, J. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.18.3546 · Cited by 718
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Miller, J. C., Tan, S., Qiao, G., Barlow, K. A., Wang, J., Xia, D. F., Meng, X., Paschon, D. E., Leung, E., Hinkley, S. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1755 · Cited by 2,098
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
Cao, L., Goreshnik, I., Coventry, B., Case, J. B., Miller, L., Kozodoy, L., Chen, R. E., Carter, L., Walls, A. C., Park, Y.-J., et al. (2020) · Science · doi:10.1126/science.abd9909 · Cited by 742
Design of protein-binding proteins from the target structure alone
Cao, L., Coventry, B., Goreshnik, I., Huang, B., Sheffler, W., Park, J. S., Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., et al. (2022) · Nature · doi:10.1038/s41586-022-04654-9 · Cited by 577
Global analysis of protein folding using massively parallel design, synthesis, and testing
Rocklin, G. J., Chidyausiku, T. M., Goreshnik, I., Ford, A., Houliston, S., Lemak, A., Carter, L., Ravichandran, R., Mulligan, V. K., Chevalier, A., et al. (2017) · Science · doi:10.1126/science.aan0693 · Cited by 501
Massively parallel de novo protein design for targeted therapeutics
Chevalier, A., Silva, D.-A., Rocklin, G. J., Hicks, D. R., Vergara, R., Murapa, P., Bernard, S. M., Zhang, L., Lam, K.-H., Yao, G., et al. (2017) · Nature · doi:10.1038/nature23912 · Cited by 453
Metadata
- Authors
- Hoover, D. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-05-15
- Volume
- 30
- Issue
- 10
- Pages
- 43e-43
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2136364313
- Cited by
- 522
- References
- 26
- FWCI
- 3.13
- Type
- journal article
- Language
- en
- Open access
- bronze
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