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Allosteric Inhibition of Zinc Finger Proteins by DNA Binding Polyamides


Nguyen Hackley, Doan Hanh (2002) Allosteric Inhibition of Zinc Finger Proteins by DNA Binding Polyamides. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/NJ2K-H827.


Small molecules that can bind selectively to any predetermined DNA sequence in the human genome could potentially be powerful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) are small molecules that bind DNA according to a set of "pairing rules" with affinities and specificities similar to many naturally occurring DNA binding proteins. The study of DNA binding polyamides is further expanded by the development of new monomer pairings and new synthetic methods which allow access to polyamides with varying truncated tails. A new pairing of N-methylpyrazole with N-methylpyrrole increased specificity substantially without loss in affinity. This result indicates that other ring positions, besides the 3-position, can also greatly impact DNA recognition properties. Polyamides having truncated tails are shown to bind DNA with greater generality at the tail positions while maintaining high affinity, and may allow the targeting of a larger number of biologically relevant DNA sequences. Small molecules that bind DNA may offer a general approach to the chemical down- or up-regulation of gene expression by the inhibition or recruitment of transcription factors, respectively. Polyamide-peptide conjugates were synthesized and evaluated for their ability to activate transcription. A greater than 30-fold enhancement over basal levels was observed and activation could be correlated to DNA occupancy levels. Cys_2His_2 zinc finger proteins are the most common DNA binding motif in higher eukaryotes. We have elucidated an allosteric mechanism for the inhibition of zinc finger proteins, binding purely in the major groove, by Py/Im polyamides. The inhibition of this large class of proteins greatly enlarges the applicability of these minor groove ligands for gene regulation.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Chemistry
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Dervan, Peter B.
Thesis Committee:
  • Dervan, Peter B. (chair)
  • Gray, Harry B.
  • Roberts, Richard W.
  • Mayo, Stephen L.
Defense Date:2 April 2002
Record Number:CaltechTHESIS:04262012-135843100
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:6979
Deposited By: Tony Diaz
Deposited On:30 Apr 2012 21:08
Last Modified:20 Dec 2019 19:20

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