| Abstract
| - We have recently described an engineered zinc finger protein (Gq1) that binds with highspecificity to the intramolecular G-quadruplex formed by the human telomeric sequence 5‘-(GGTTAG)5-3‘, and that inhibits the activity of the enzyme telomerase in vitro. Here we report site-directed mutagenesis,biophysical, and molecular modeling studies that provide new insights into quadruplex recognition by thezinc finger scaffold. We show that any one finger of Gq1 can be replaced with the corresponding fingerof Zif268, without significant loss of quadruplex affinity or quadruplex versus duplex discrimination.Replacement of two fingers, with one being finger 2, of Gq1 by Zif268 results in significant impairmentof quadruplex recognition and loss of discrimination. Molecular modeling suggests that the zinc fingersof Gq1 can bind to the human parallel-stranded quadruplex structure in a stable arrangement, whereasZif268−quadruplex models show significantly weaker binding energy. Modeling also suggests that animportant role of the key protein finger residues in the Gq1−quadruplex complex is to maintain Gq1 inan optimum conformation for quadruplex recognition.
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