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| Status |
Public on Jul 05, 2024 |
| Title |
Computational design of sequence-specific DNA-binding proteins |
| Platform organism |
Homo sapiens |
| Sample organism |
synthetic construct |
| Experiment type |
Other
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| Summary |
Sequence-specific DNA-binding proteins (DBPs) play critical roles in biology and biotechnology, and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications. While there has been some success in reprogramming naturally occurring DBPs using selection methods, the computational design of new DBPs that recognize arbitrary target sites remains an outstanding challenge. We describe a computational method for the design of small DBPs that recognize specific target sequences through interactions with bases in the major groove.
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| Overall design |
Universal protein-binding microarray (PBM) experiments were performed for small, recombinant, DNA-binding protein designs 1, 3, 5, 6, 9, 35, & 48. Briefly, universal PBMs involved binding of his-tagged proteins to double-stranded 15K Agilent microarrays containing a DNA library designed to cover all possible 9-bp sequences, with every 7-mer occurring in at least 16 different spots on the array. This design allows comprehensive and unbiased characterization of the binding specificity of transcription factors for all possible 7-bp sequences.
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| Contributor(s) |
Gordan R, Boivin O |
| Citation missing |
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| |
| Submission date |
Jul 10, 2023 |
| Last update date |
Jul 05, 2024 |
| Contact name |
Raluca Gordan |
| E-mail(s) |
raluca.gordan@duke.edu
|
| Organization name |
Duke University
|
| Department |
Center for Genomic and Computational Biology
|
| Street address |
101 Science Dr, CIEMAS 2179
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platforms (1) |
| GPL23935 |
Universal PBM 4x44k (Bulyk lab design) |
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| Samples (12)
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| GSM7593072 |
DBP1 at 300uM concentration replicate 1 |
| GSM7593073 |
DBP3 at 75uM concentration replicate 1 |
| GSM7593074 |
DBP5 at 300uM concentration replicate 1 |
| GSM7593075 |
DBP6 at 200uM concentration replicate 1 |
| GSM7593076 |
DBP9 at 75uM concentration replicate 1 |
| GSM7593077 |
DBP35 at 100uM concentration replicate 1 |
| GSM7593078 |
DBP48 at 75uM concentration replicate 1 |
| GSM7593079 |
DBP1 at 300uM concentration replicate 2 |
| GSM7593080 |
DBP3 at 75uM concentration replicate 2 |
| GSM7593081 |
DBP6 at 200uM concentration replicate 2 |
| GSM7593082 |
DBP9 at 75uM concentration replicate 2 |
| GSM7593083 |
DBP35 at 100uM concentration replicate 2 |
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| Relations |
| BioProject |
PRJNA993300 |
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