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Programming protein patterns on DNA nanostructures with pyrrole-imidazole polyamides

Citation

Cohen, Justin Delgado (2009) Programming protein patterns on DNA nanostructures with pyrrole-imidazole polyamides. Dissertation (Ph.D.), California Institute of Technology. http://resolver.caltech.edu/CaltechETD:etd-11232008-171327

Abstract

Molecular recognition of DNA has important applications for gene regulation, molecular biology, and DNA nanotechnology. Pyrrole-imidazole polyamides are a unique class of molecules with the ability to bind to DNA in a programmable manner. These small molecule analogues of distamycin A can be programmed to target virtually any DNA sequence with high affinity and specificity. Originally characterized for their ability to bind to B-form DNA, polyamides are also able to target DNA in architectures such as the nucleosome core particle (NCP) and two-dimensional DNA nanostructures including DX-arrays and DNA origami. In addressing DNA nanostructures, polyamide-biotin conjugates can be used to create nanoscale molecular assemblies in a bottom-up approach to self-assembly. The ability to address unique sequences on a DNA nanostructure with different polyamides makes it possible to create unique arrangements of protein on a single 2-dimensional DNA template. Polyamides targeted to the NCP can be used for a variety of exciting applications including NCP-templated ligation reactions, gene regulation, and as tools for X-ray crystallography. The programmability of polyamides makes them an ideal tool for addressing a variety of DNA architectures for varying applications.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:DNA nanostructures; DNA origami; nucleosome core particle; polyamide; self-assembly
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)
  • Rees, Douglas C.
  • Winfree, Erik
  • Dervan, Peter B.
Defense Date:10 November 2008
Record Number:CaltechETD:etd-11232008-171327
Persistent URL:http://resolver.caltech.edu/CaltechETD:etd-11232008-171327
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:4645
Collection:CaltechTHESIS
Deposited By: Imported from ETD-db
Deposited On:23 Dec 2008
Last Modified:26 Dec 2012 03:10

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