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Marlatt SA, Kong Y, Cammett TJ, Korbel G, Noonan JP, DiMaio D. Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering. Protein Eng Des Sel 2011; 24:311-20. [PMID: 21149273 PMCID: PMC3038463 DOI: 10.1093/protein/gzq112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 10/29/2010] [Accepted: 11/14/2010] [Indexed: 11/12/2022] Open
Abstract
Genetic selection from libraries expressing proteins with randomized amino acid segments is a powerful approach to identify proteins with novel biological activities. Here, we assessed the utility of deep DNA sequencing to characterize the composition, diversity, size and stability of such randomized libraries. We used 454 pyrosequencing to sequence a retroviral library expressing small proteins with randomized transmembrane domains. Despite the potential for unintended random mutagenesis during its construction, the overall hydrophobic composition and diversity of the proteins encoded by the sequenced library conformed well to its design. In addition, our sequencing results allowed us to calculate a more accurate estimate of the number of different proteins encoded by the library and suggested that the traditional methods for estimating the size of randomized libraries may overestimate their true size. Our results further demonstrated that no significant genetic bottlenecks exist in the methods used to express complex retrovirus libraries in mammalian cells and recover library sequences from these cells. These findings suggest that deep sequencing can be used to determine the quality and content of other libraries with randomized segments and to follow individual sequences during selection.
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Affiliation(s)
- Sara A. Marlatt
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 300 George Street, 8th Floor, New Haven, CT 06511-6624, USA
- Keck Biotechnology Resource Laboratory, Yale University, 300 George Street, Box 201, New Haven, CT 06511, USA
| | - Tobin J. Cammett
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Present address: Alexion Pharmaceuticals, 352 Knotter Drive, Cheshire, CT 06410, USA
| | - Gregory Korbel
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Present address: The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Yale Comprehensive Cancer Center, PO Box 208028, New Haven, CT 06520-8028, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 300 George Street, 8th Floor, New Haven, CT 06511-6624, USA
- Department of Therapeutic Radiology, Yale School of Medicine, PO Box 208040, New Haven, CT 06520-8040, USA
- Yale Comprehensive Cancer Center, PO Box 208028, New Haven, CT 06520-8028, USA
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