title: Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding.
abstract: 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.
authors.affiliation: School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
authors.forename: Ozgül
authors.initials: O
authors.lastname: Persil
authors.forename: Catherine T
authors.initials: CT
authors.lastname: Santai
authors.forename: Swapan S
authors.initials: SS
authors.lastname: Jain
authors.forename: Nicholas V
authors.initials: NV
authors.lastname: Hud
mesh_terms: D000225:Adenine / Q000737:chemistry*; D001600:Berberine Alkaloids / Q000737:chemistry*; D001665:Binding Sites; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D018625:Microscopy, Atomic Force; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011370:Proflavine / Q000737:chemistry; D013696:Temperature
chemical_list: D001600:Berberine Alkaloids; C000666:coralyne; D004247:DNA; D011370:Proflavine; D000225:Adenine