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Designing Zinc Finger Proteins for Applications in Synthetic Biology

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Systems and Synthetic Biology

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Abstract

Transcription factors capable of regulating the expression repertoire of a cell possessing specific recognition patterns dominating their interaction with its respective DNA, that can be exploited to achieve targeted genome engineering, happens to be the cynosure of most studies encompassing DNA-protein interaction. The mostly widely studied transcription factors are zinc finger proteins that bind to its target DNA via few cardinal residues on its alpha–helix, comprising each finger of the protein. Exploiting the binding specificity and affinity of the interaction between the zinc fingers and the respective DNA can help to generate engineered zinc fingers for therapeutic purposes involving genome targeting. Exploring the structure-function relationships of the existing zinc finger-DNA complexes can aid in predicting the probable zinc fingers that could bind to any target DNA. This chapter describes the interaction of the zinc finger with its respective DNA, its prospective manipulation and application in the field of engineering the genome, various prediction tools dealing with either machine learning or physicochemical parameters for designing customized zinc fingers for any target DNA.

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Acknowledgement

The work on zinc finger proteins in the laboratory of DS is supported by grants from Lady Tata Memorial Trust, DuPont and Department of Biotechnology (DBT), Govt. of India, under the IYBA & National Bioscience Award schemes. SD is a recipient of DST INSPIRE Fellowship for her doctoral studies in the laboratory of DS.

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Authors and Affiliations

  1. Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, 110016, New Delhi, India

    Shayoni Dutta & Durai Sundar

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  1. Shayoni Dutta
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  2. Durai Sundar
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Correspondence to Durai Sundar .

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Editors and Affiliations

  1. Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, India

    Vikram Singh

  2. Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Budh Nagar, India

    Pawan K. Dhar

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Dutta, S., Sundar, D. (2015). Designing Zinc Finger Proteins for Applications in Synthetic Biology. In: Singh, V., Dhar, P. (eds) Systems and Synthetic Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9514-2_15

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