Targeting Repeat Sequences with DNA-Binding Small Molecules

• Main Author: Chevillet, John Richard
• Format: Others
• Language: en
• Published: 2002
• Online Access: https://thesis.library.caltech.edu/6806/1/Chevillet_jr_2002.pdf; Chevillet, John Richard (2002) Targeting Repeat Sequences with DNA-Binding Small Molecules. Master's thesis, California Institute of Technology. doi:10.7907/3YF2-Y771. https://resolver.caltech.edu/CaltechTHESIS:02022012-110126423 <https://resolver.caltech.edu/CaltechTHESIS:02022012-110126423>

Recognition of repeat sequences in DNA would have applications in molecular biology. One of the most biologically interesting repeat sequences is the telomeric repeat which composes the ends of eukaryotic chromosomes; in vertebrates 5'-TTAGGG-3'. This sequence has been used as a model to study how DNA-binding polyamide molecules composed of pyrrole (Py) and imidazole (Im) residues bind to repeating sequences. DNase I footprinting shows that the polyamide-fluorophore conjugate IrnImImPy-γ-PyPy((CH_2)_3N,N',N''trimethylbis hexamethylene)triamineOregonGreen488) PyPy-β-Me can bind the sequence 5'-AGGGTT-3' K_a = 1.8x10^8 M^(-1). Quantitative fluorescence titrations with varying patterns of telomeric repeat suggest that the molecule can tolerate another polyamide binding contiguously, but not two. Truncation of the tail of the conjugate to yield the molecule ImImImPy-γ-Py Py((CH_2)_3N,N',N''trimethylbis (hexamethylene)triamine-OregonGreen488) PyPy-Me allows the compound to bind three contiguous sites, suggesting that steric polyamide-polyamide interactions control binding in this manner.