Small molecule recognition of homopurine
nucleic acid structures
Small molecule recognition of homopurine nucleic acid structures
Persil Cetinkol, Ozgul
Hud, Nicholas V.
The thesis topic entitled above involves the use of small molecules as a general means to drive nucleic acid assembly and structural transitions. We have shown that coralyne, a crescent-shaped small molecule, can assemble homo-adenine DNA and RNA sequences into anti-parallel duplexes at neutral pH, a structure containing putative purine-purine (A*A) base pairs that is otherwise unstable. The importance of the structure of the small molecule in the recognition and stabilization of A*A base pairing has been established by experimental evidence. We further provide structural evidence for the putative A*A base pairing that is stabilized by coralyne and molecules of similar size and shape. Our hypothesis that planar molecules that are slightly too large to intercalate Watson-Crick base pairs might intercalate the larger purine-purine base pairs has led to the design of a new class of small molecules that tightly bind purine-purine duplexes with excellent selectively. We have demonstrated that azacyanines can exhibit strong and selective association with a human telomeric sequence that forms a unimolecular G-quadruplex in solution. The synthetic accessibility of azacyanines makes this class of molecules amenable to library preparation for high-throughput screening. Together, the findings reported in this thesis provide further evidence for the robust and versatile nature of selective small molecule recognition of nucleic acids, especially purine-purine duplexes.