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Targeting DNA Repeat Sequences with Py-Im Polyamides

Citation

Kang, JeenJoo Sophia (2015) Targeting DNA Repeat Sequences with Py-Im Polyamides. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z93R0QSQ. http://resolver.caltech.edu/CaltechTHESIS:04052015-200117829

Abstract

Hairpin pyrrole-imdazole polyamides are cell-permeable, sequence-programmable oligomers that bind in the minor groove of DNA. This thesis describes studies of Py-Im polyamides targeted to biologically important DNA repeat sequences for the purpose of modulating disease states. Design of a hairpin polyamide that binds the CG dyad, a site of DNA methylation that can become dysregulated in cancer, is described. We report the synthesis of a DNA methylation antagonist, its sequence specificity and affinity informed by Bind-n-Seq and iteratively designed, which improves inhibitory activity in a cell-free assay by 1000-fold to low nanomolar IC50. Additionally, a hairpin polyamide targeted to the telomeric sequence is found to trigger a slow necrotic-type cell death with the release of inflammatory molecules in a model of B cell lymphoma. The effects of the polyamide are unique in this class of oligomers; its effects are characterized and a functional assay of phagocytosis by macrophages is described. Additionally, hairpin polyamides targeted to pathologically expanded CTG•CAG triplet repeat DNA sequences, the molecular cause of myotonic dystrophy type 1, are synthesized and assessed for toxicity. Lastly, ChIP-seq of Hypoxia-Inducible Factor is performed under hypoxia-induced conditions. The study results show that ChIP-seq can be employed to understand the genome-wide perturbation of Hypoxia-Inducible Factor occupancy by a Py-Im polyamide.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:DNA ligand; Py-Im polyamides; repeat sequences; immunogenicity; DNA methylation
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:
  • Grubbs, Robert H. (chair)
  • Hsieh-Wilson, Linda C.
  • Heath, James R.
  • Dervan, Peter B.
Defense Date:27 March 2015
Record Number:CaltechTHESIS:04052015-200117829
Persistent URL:http://resolver.caltech.edu/CaltechTHESIS:04052015-200117829
DOI:10.7907/Z93R0QSQ
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/ja500211zDOIArticle adapted for ch. 2
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8812
Collection:CaltechTHESIS
Deposited By: JeenJoo Kang
Deposited On:28 May 2015 23:05
Last Modified:02 Oct 2017 19:22

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PDF (JSK_Thesis_Ch4-DM1) - Final Version
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