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Nucleic Acids Research, Vol 26, Issue 2 554-557, Copyright © 1998 by Oxford University Press

ARTICLES

End effects in DNA recognition by zinc finger arrays

Y Choo
Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. choo@mrc-lmb.cam.ac.uk

The paradigmatic DNA binding domain from the transcription factor Zif268 contains three zinc finger modules in tandem repeat. When bound to their cognate DNA site the fingers read out the sequence of one DNA strand by making a linear series of successive base contacts. It is shown that the base-specific protein-DNA contacts made from the ends of the Zif268 three-finger array contribute less to the stability of the intermolecular complex than do structurally equivalent contacts from more central regions of the DNA binding domain. The effect is akin to the end fraying observed in duplex nucleic acid molecules.
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