Small molecule recognition of homopurine nucleic acid structures

• Main Author: Persil Cetinkol, Ozgul
• Published: Georgia Institute of Technology 2009
• Subjects: Physical characterization; Nucleic acids; Small molecule binding; Assembly; Intercalation; Biomolecules; Supramolecular chemistry; Purines
• Online Access: http://hdl.handle.net/1853/29739

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.