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Issue No.05 - Sept.-Oct. (2013 vol.10)
pp: 1340-1343
Christian Bach , Dept. of Biomed. Eng., Univ. of Bridgeport, Bridgeport, CT, USA
Prabir K. Patra , Dept. of Biomed. Eng., Univ. of Bridgeport, Bridgeport, CT, USA
Jani M. Pallis , Dept. of Mech. Eng., Univ. of Bridgeport, Bridgeport, CT, USA
William B. Sherman , Bard High Sch., Queens, NY, USA
Hassan Bajwa , Dept. of Electr. Eng., Univ. of Bridgeport, Bridgeport, CT, USA
ABSTRACT
For clinical applications, the biological functions of DNA-binding proteins require that they interact with their target binding site with high affinity and specificity. Advances in randomized production and target-oriented selection of engineered artificial DNA-binding domains incited a rapidly expanding field of designer transcription factors (TFs). Engineered transcription factors are used in zinc-finger nuclease (ZFN) technology that allows targeted genome editing. Zinc-finger-binding domains fabricated by modular assembly display an unexpectedly high failure rate having either a lack of activity as ZFNs in human cells or activity at "off-target"' binding sites on the human genome causing cell death. To address these shortcomings, we created new binding domains using a targeted modification strategy. We produced two SP1 mutants by exchanging amino acid residues in the alpha-helical region of the transcription factor SP1. We identified their best target binding sites and searched the NCBI HuRef genome for matches of the nine-base-pair consensus binding site of SP1 and the best binding sites of its mutants. Our research concludes that we can alter the binding preference of existing zinc-finger domains without altering its biological functionalities.
INDEX TERMS
Clinical diagnosis, Bioinformatics, Genomics, Proteins, DNA, Amino acids,zinc-finger nuclease, Computational genomics, cytotoxicity, transcription factor SP1
CITATION
Christian Bach, Prabir K. Patra, Jani M. Pallis, William B. Sherman, Hassan Bajwa, "Strategy for Naturelike Designer Transcription Factors with Reduced Toxicity", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 5, pp. 1340-1343, Sept.-Oct. 2013, doi:10.1109/TCBB.2013.107
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