title: Temperature-sensitive protein-DNA dimerizers.
abstract: Programmable DNA-binding polyamides coupled to short peptides have led to the creation of synthetic artificial transcription factors. A hairpin polyamide-YPWM tetrapeptide conjugate facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. Such small molecules function as protein-DNA dimerizers that stabilize complexes at composite DNA binding sites. Here we investigate the role of the linker that connects the polyamide to the peptide. We find that a substantial degree of variability in the linker length is tolerated at lower temperatures. At physiological temperatures, the longest linker tested confers a "switch"-like property on the protein-DNA dimerizer, in that it abolishes the ability of the YPWM moiety to recruit the natural transcription factor to DNA. These observations provide design principles for future artificial transcription factors that can be externally regulated and can function in concert with the cellular regulatory circuitry.
authors.affiliation: Department of Biochemistry and the Genome Center, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Karl E
authors.initials: KE
authors.lastname: Hauschild
authors.forename: Renee E
authors.initials: RE
authors.lastname: Metzler
authors.forename: Hans-Dieter
authors.initials: HD
authors.lastname: Arndt
authors.forename: Rocco
authors.initials: R
authors.lastname: Moretti
authors.forename: Marni
authors.initials: M
authors.lastname: Raffaelle
authors.forename: Peter B
authors.initials: PB
authors.lastname: Dervan
authors.forename: Aseem Z
authors.initials: AZ
authors.lastname: Ansari
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism; D019281:Dimerization; D029721:Drosophila Proteins / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D015195:Drug Design; D019277:Entropy; D018398:Homeodomain Proteins / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D066298:In Vitro Techniques; D008958:Models, Molecular; D013696:Temperature; D013816:Thermodynamics; D014157:Transcription Factors / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D014157:Transcription Factors; C083405:exd protein, Drosophila; D004247:DNA