Recognition of all four Watson-Crick base pairs in the minor groove of DNA by synthetic ligands

Citation

White, Sarah (1999) Recognition of all four Watson-Crick base pairs in the minor groove of DNA by synthetic ligands. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/wxsr-8x37. https://resolver.caltech.edu/CaltechETD:etd-05052006-141420

Abstract

The design of synthetic ligands that read the information stored in the DNA double helix has been a long standing goal at the interface of chemistry and biology. Cell-permeable small molecules which target predetermined DNA sequences offer a potential approach for the regulation of gene-expression. Oligodeoxynucleotides that recognize the major groove of double-helical DNA via triple-helix formation bind to a broad range of sequences with high affinity and specificity. Although oligonucleotides and their analogs have been shown to interfere with gene expression, the triple helix approach is limited to purine tracks and suffers from poor cellular uptake. The subsequent development of pairing rules for minor groove binding polyamides containing pyrrole (Py) and imidazole (Im) amino acids offers a second code to control sequence specificity. An Im/Py pair distinguishes G•C from C•G and both of these from A•T/T•A base pairs. A Py/Py pair specifies A,T from G,C but does not distinguish A•T from T•A. In order to break this degeneracy, a new aromatic amino acid, 3-hydroxypyrrole (Hp), has been added to the repertoire to test for pairings which discriminate A•T from T•A. We find that replacement of a single hydrogen atom with a hydroxy group in a Hp/Py pairing regulates affinity and specificity by an order of magnitude. By incorporation of a third amino acid, hydroxypyrrole-imidazole-pyrrole polyamides form four ring-pairings (Im/Py, Py/Im, Hp/Py, and Py/Hp) which distinguish all four Watson-Crick base pairs in the minor groove of DNA.

Thesis Files