Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding.

TitleAssembly of an antiparallel homo-adenine DNA duplex by small-molecule binding.
Publication TypeJournal Article
Year of Publication2004
AuthorsPersil, O, Santai, CT, Jain, SS, Hud, NV
JournalJ Am Chem Soc
Date Published2004 Jul 21
KeywordsAdenine, Berberine Alkaloids, Binding Sites, Circular Dichroism, DNA, Microscopy, Atomic Force, Molecular Structure, Nucleic Acid Conformation, Proflavine, Temperature

Molecules that reversibly bind DNA and trigger the formation of non-Watson-Crick secondary structures would be useful in the design of dynamic DNA nanostructures and as potential leads for new therapeutic agents. We demonstrate that coralyne, a small crescent-shaped molecule, promotes the formation of a duplex secondary structure from homo-adenine oligonucleotides. AFM studies reveal that the staggered alignment of homo-adenine oligonucleotides upon coralyne binding produces polymers of micrometers in length, but only 2 nm in height. A DNA duplex was also studied that contained eight A.A mismatches between two flanking 7-bp Watson-Crick helices. CD spectra confirm that the multiple A.A mismatches of this duplex bind coralyne in manner similar to that of homo-adenine oligonucleotides. Furthermore, the melting temperature of this hybrid duplex increases by 13 degrees C upon coralyne binding. These observations illustrate that the helical structure of the homo-adenine-coralyne duplex is compatible with the B-form DNA helix.

Alternate JournalJ. Am. Chem. Soc.
PubMed ID15250704
Grant ListGM62873 / GM / NIGMS NIH HHS / United States