The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
Refactoring bacteriophage T7
Open accessAbstract
Natural biological systems are selected by evolution to continue to exist and evolve. Evolution likely gives rise to complicated systems that are difficult to understand and manipulate. Here, we redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. Our initial design goals were to physically separate and enable unique manipulation of primary genetic elements. Implicit in our design are the hypotheses that overlapping genetic elements are, in aggregate, nonessential for T7 viability and that our models for the functions encoded by elements are sufficient. To test our initial design, we replaced the left 11 515 base pairs (bp) of the 39 937 bp wild‐type genome with 12 179 bp of engineered DNA. The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention.
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Cites
Refactoring: Improving the Design of Existing Code
Fowler, M. (2002) · Lecture Notes in Computer Science · doi:10.1007/3-540-45672-4_31 · Cited by 5,591
Selective extraction of polyoma DNA from infected mouse cell cultures
Hirt, B. (1967) · Journal of Molecular Biology · doi:10.1016/0022-2836(67)90307-5 · Cited by 5,146
Analysis of bacteriophage T7 early RNAs and proteins on slab gels
Studier, F. W. (1973) · Journal of Molecular Biology · doi:10.1016/0022-2836(73)90003-x · Cited by 2,215
Refactoring improving the design of existing code
Saca, M. A. (2017) · 2017 IEEE 37th Central America and Panama Convention (CONCAPAN XXXVII) · doi:10.1109/concapan.2017.8278488 · Cited by 2,054
Ikemura, T. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90003-6 · Cited by 1,417
Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements
Dunn, J. J., Studier, F. W., & Gottesman, M. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80282-4 · Cited by 1,315
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides
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(2005) · Genetic Programming Series · doi:10.1007/b137549 · Cited by 693
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Foundations for engineering biology
Endy, D. (2005) · Nature · doi:10.1038/nature04342 · Cited by 1,511
Self-citationSynthetic biology: new engineering rules for an emerging discipline
Andrianantoandro, E., Basu, S., Karig, D. K., & Weiss, R. (2006) · Molecular Systems Biology · doi:10.1038/msb4100073 · Cited by 1,081
Dispersing biofilms with engineered enzymatic bacteriophage
Lu, T. K., & Collins, J. J. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704624104 · Cited by 895
Large-scale de novo DNA synthesis: technologies and applications
Kosuri, S., & Church, G. M. (2014) · Nature Methods · doi:10.1038/nmeth.2918 · Cited by 869
Self-citationEngineering BioBrick vectors from BioBrick parts
Shetty, R. P., Endy, D., & Knight, T. F. (2008) · Journal of Biological Engineering · doi:10.1186/1754-1611-2-5 · Cited by 760
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Metadata
- Authors
- Chan, L. Y., Kosuri, S., & Endy, D.
- Venue
- Molecular Systems Biology
- Published
- 2005-01
- Volume
- 1
- Issue
- 1
- Pages
- 2005.0018-2005.0018
- ISSN
- 1744-4292 (ISSN-L)
- OpenAlex
- W2149174733
- Cited by
- 357
- References
- 46
- FWCI
- 12.25
- Type
- journal article
- Language
- en
- Open access
- green
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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