A peptide with alternating lysines can act as a highly specific Z-DNA binding domain.
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.
Kim
Yang-Gyun
YG
Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Park
Hyun-Ju
HJ
Kim
Kyeong Kyu
KK
Lowenhaupt
Ky
K
Rich
Alexander
A
D000595:Amino Acid Sequence; D000818:Animals; D050976:Basic-Leucine Zipper Transcription Factors / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D001667:Binding, Competitive; D002942:Circular Dichroism; D004247:DNA / Q000032:analysis; D043542:DNA, Z-Form / Q000737:chemistry / Q000378:metabolism*; D015257:DNA-Cytosine Methylases / Q000737:chemistry; D003854:Deoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D006801:Humans; D016350:Leucine Zippers; D008239:Lysine / Q000737:chemistry*; D051379:Mice; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D015202:Protein Engineering; D017434:Protein Structure, Tertiary; D051381:Rats; D020349:Surface Plasmon Resonance
D050976:Basic-Leucine Zipper Transcription Factors; D043542:DNA, Z-Form; D003854:Deoxyribonucleotides; D010455:Peptides; C514592:poly(dG-d5meC); D004247:DNA; D015257:DNA-Cytosine Methylases; D008239:Lysine