Skip to main content

Design and Synthesis of Artificial Zinc Finger Proteins

  • Protocol

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 352))

Abstract

Of the DNA-binding motifs, the (Cys)2(His)2-type zinc finger motif has great potential for manipulation. The zinc finger motif offers an attractive framework for the design of novel DNA-binding proteins. Specially, a structure-based design strategy is valuable for the creation of new artificial zinc finger proteins that have novel DNA-binding properties, namely, long-DNA recognition, DNA bending, and AT-rich sequence recognition. Herein, new strategies for the design of multi-zinc finger proteins for the recognition of a target DNA sequence, a DNA-bending zinc finger protein, a (His)4-type zinc finger protein, and an AT-recognizing zinc finger protein are described based on recent experimental results.

This is a preview of subscription content, log in via an institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Nagaoka, M. and Sugiura, Y. (2000) Artificial zinc finger peptides: creation, DNA recognition, and gene regulation. J. Inorg. Biochem. 82, 57–63.

    Article  PubMed  CAS  Google Scholar 

  2. Imanishi, M., Hori, Y., Nagaoka, M., and Sugiura, Y. (2001) Design of novel zinc finger proteins: towards artificial control of specific gene expression. Eur. J. Pharm. Sci. 13, 91–97.

    Article  PubMed  CAS  Google Scholar 

  3. Pabo, C. O., Peisach, E., and Grant, R. A. (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 70, 313–340.

    Article  PubMed  CAS  Google Scholar 

  4. Pavletich, N. P. and Pabo, C. O. (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252, 809–816.

    Article  PubMed  CAS  Google Scholar 

  5. Pavletich, N. P. and Pabo, C. O. (1993) Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science 261, 1701–1707.

    Article  PubMed  CAS  Google Scholar 

  6. Kim, C. A. and Berg, J. M. (1996) A 2.2 Å resolution crystal structure of a designed zinc finger protein bound to DNA. Nat. Struct. Biol. 3, 940–945.

    Article  PubMed  CAS  Google Scholar 

  7. Nolte, R. T., Conlin, R. M., Harrison, S. C., and Brown, R. S. (1998) Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. Proc. Natl. Acad. Sci. USA 95, 2938–2943.

    Article  PubMed  CAS  Google Scholar 

  8. Wütrich, K. (1986) NMR of Proteins and Nuleic Acids. Wiley Interscience, New York, NY.

    Google Scholar 

  9. Kuwahara, J. and Coleman, J. E. (1990) Role of the zinc(II) ions in the structure of the three-finger DNA binding domain of the Sp1 transcription factor. Biochemistry 29, 8627–8631.

    Article  PubMed  CAS  Google Scholar 

  10. Kamiuchi, T., Abe, E., Imanishi, M., Kaji, T., Nagaoka, M., and Sugiura, Y. (1998) Artificial nine zinc-finger peptide with 30-base-pair binding sites. Biochemistry 37, 13,827–13,834.

    Article  PubMed  CAS  Google Scholar 

  11. Imanishi, M., Hori, Y., Nagaoka, M., and Sugiura, Y. (2000) DNA-bending finger: artificial design of 6-zinc finger peptides with polyglycine linker and induction of DNA bending. Biochemistry 39, 4383–4390.

    Article  PubMed  CAS  Google Scholar 

  12. Hori, Y., Suzuki, K., Okuno, Y., Nagaoka, M., Futaki, S., and Sugiura, Y. (2000) Artificial zinc finger peptide containing a novel His4 domain. J. Am. Chem. Soc. 122, 7648–7653.

    Article  CAS  Google Scholar 

  13. Nagaoka, M., Doi, Y., Kuwahara, J., and Sugiura, Y. (2002) Novel strategy for the design of a new zinc finger: creation of a zinc finger for the AT-rich sequence by α-helix substitution. J. Am. Chem. Soc. 124, 6526–6527.

    Article  PubMed  CAS  Google Scholar 

  14. Imanishi, M. and Sugiura, Y. (2002) Artificial DNA-bending six-zinc finger peptides with different charged linkers: Distinct kinetic properties of DNA binding. Biochemistry 41, 1328–1334.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Humana Press Inc.

About this protocol

Cite this protocol

Nomura, W., Sugiura, Y. (2007). Design and Synthesis of Artificial Zinc Finger Proteins. In: Arndt, K.M., Müller, K.M. (eds) Protein Engineering Protocols. Methods in Molecular Biology™, vol 352. Humana Press. https://doi.org/10.1385/1-59745-187-8:83

Download citation

  • DOI: https://doi.org/10.1385/1-59745-187-8:83

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-072-4

  • Online ISBN: 978-1-59745-187-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics