A Caltech Library Service

1:1 Motif for DNA Recognition by β-Alanine Linked Polyamides


Urbach, Adam Robert (2002) 1:1 Motif for DNA Recognition by β-Alanine Linked Polyamides. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/V6FD-YQ78.


Polyamides composed of N-methylpyrrole (Py), N-methylimidazole (Im), and 3-hydroxypyrrole (Hp) amino acids linked by beta-alanine (beta) bind in the minor groove of DNA in 1:1 and 2:1 ligand:DNA complexes. Although the energetics and structure of the 2:1 motif have been explored extensively, there is remarkably less understood about 1:1 recognition beyond the initial studies on netropsin and distamycin. Laemmli and coworkers used beta-linked polyamides, which bind in a 1:1 motif, to effect phenotypic changes in Drosophila melanogaster. The thesis work described here investigates Laemmli's 1:1 motif in order to further understand and exploit this novel mode of DNA recognition.

y selectively replacing Py residues with beta it was found that the Im-beta-Im subunit is important for high-affinity binding in 1:1 and 2:1 modes. This study also demonstrates that a single ligand can target very different DNA sequences based on 1:1 or 2:1 binding. This ambiguity of sequence targeting based on stoichiometry was addressed. It was discovered that hairpin and 1:1 binding modes, which are dependent on ligand conformation, are controlled by changing the linker between polyamide subunits.

The possibility of developing a 1:1 recognition code was explored by selectively mutating polyamide residues and DNA base pairs and comparing the association constants for the resulting complexes. It was found that Im residues tolerate all four Watson-Crick base pairs; Py and beta residues are specific for A?T and T?A base pairs; and Hp specifies a single base pair, A?T, in the sequence context 5'-AAAGAGAAGAG-3'. Attempts to improve upon this recognition code using novel heterocyclic amino acids, such as furan, thiophene, thiazole, and hydroxythiophene, are presented. The sequence-dependence of ligand orientation and the effect of ligand size on binding affinity were also explored.

The NMR structure of a 1:1 polyamide:DNA complex was determined. It reveals B-form DNA with a narrow minor groove and large negative propeller twist, which are shown to be stabilized by bifurcated hydrogen bonds between polyamide NH groups and purine N3 and pyrimidine O2 atoms. The first direct evidence is provided for hydrogen bond formation between Im-N3 and guanine NH2 in the 1:1 motif, thus confirming the original lexitropsin model.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:beta-alanine; DNA recognition; minor groove; NMR structure; polyamide
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Readhead, Anthony C. S. (advisor)
  • Dervan, Peter B. (advisor)
Thesis Committee:
  • Grubbs, Robert H. (chair)
  • Readhead, Anthony C. S.
  • Dervan, Peter B.
  • Roberts, Richard W.
  • Mayo, Stephen L.
Defense Date:17 May 2002
Non-Caltech Author Email:aurbach (AT)
Record Number:CaltechETD:etd-05202002-104244
Persistent URL:
Urbach, Adam Robert0000-0003-3426-4760
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1884
Deposited By: Imported from ETD-db
Deposited On:28 May 2002
Last Modified:14 Jan 2022 01:21

Thesis Files

PDF (Complete Thesis) - Final Version
See Usage Policy.

PDF (1_Title_Ab_TOC.pdf) - Final Version
See Usage Policy.

PDF (2_Introduction.pdf) - Final Version
See Usage Policy.

PDF (3_Results_and_Discussion.pdf) - Final Version
See Usage Policy.

PDF (4_Conclusions.pdf) - Final Version
See Usage Policy.

PDF (5_Experimental.pdf) - Final Version
See Usage Policy.

PDF (6_References.pdf) - Final Version
See Usage Policy.

PDF (7_Appendix.pdf) - Final Version
See Usage Policy.


Repository Staff Only: item control page