Nucleic Acids Research Advance Access published online on September 18, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl607
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Molecular Biology |
A peptide with alternating lysines can act as a highly specific Z-DNA binding domain
1 Department of Biology, Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, MA 02139, USA 2 Department of Chemistry, Sungkyunkwan University 300 Chunchundong, Jangangu, Suwon, Kyunggido 440-746, Korea 3 College of Pharmacy, Sungkyunkwan University 300 Chunchundong, Jangangu, Suwon, Kyunggido 440-746, Korea 4 Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University 300 Chunchundong, Jangangu, Suwon, Kyunggido 440-746, Korea
*To whom correspondence should be addressed. Tel: +1 617 253 4710; Fax: +1 61 258 8299; Email: kytsing{at}mit.edu
Received May 18, 2006. Revised August 1, 2006. Accepted August 2, 2006.
Many nucleic acid binding proteins use short peptide sequences to provide specificity in recognizing their targets, which may be either a specific sequence or a conformation. Peptides containing alternating lysine have been shown to bind to poly(dG–d5meC) in the Z conformation, and stabilize the higher energy form [H. Takeuchi, N. Hanamura, H. Hayasaka and I. Harada (1991) FEBS Lett., 279, 253–255 and H. Takeuchi, N. Hanamura and I. Harada (1994) J. Mol. Biol., 236, 610–617.]. Here we report the construction of a Z-DNA specific binding protein, with the peptide KGKGKGK as a functional domain and a leucine zipper as a dimerization domain. The resultant protein, KGZIP, induces the Z conformation in poly(dG–d5meC) and binds to Z-DNA stabilized by bromination with high affinity and specificity. The binding of KGZIP is sufficient to convert poly(dG–d5meC) from the B to the Z form, as shown by circular dichroism. The sequence KGKGKGK is found in many proteins, although no functional role has been established. KGZIP also has potential for engineering other Z-DNA specific proteins for future studies of Z-DNA in vitro and in vivo.