title: Synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having stilbenedicarboxamide linkers.
abstract: The synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having A-tract base pair domains connected by rod-like stilbenedicarboxamide linkers are reported. The nicked dumbbells have one to eight dA-dT base pairs and are missing a sugar-phosphate bond either between the linker and a thymine nucleoside residue or between two thymine residues. Chemical ligation of all of the nicked dumbbells with cyanogen bromide affords the dumbbell conjugates in good yield, providing the smallest mini-dumbbells prepared to date. The dumbbells have exceptionally high thermal stability, whereas the nicked dumbbells are only marginally more stable than the hairpin structures on either side of the nick. The structures of the nicked dumbbells and dumbbells have been investigated using a combination of circular dichroism spectroscopy and molecular modeling. The base pair domains are found to adopt normal B'-DNA geometry and thus provide a helical ruler for studies of the distance and angular dependence of electronic interactions between the chromophore linkers.
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA.
authors.forename: Ligang
authors.initials: L
authors.lastname: Zhang
authors.forename: Hai
authors.initials: H
authors.lastname: Long
authors.forename: George C
authors.initials: GC
authors.lastname: Schatz
authors.forename: Frederick D
authors.initials: FD
authors.lastname: Lewis
mesh_terms: D000225:Adenine / Q000737:chemistry; D020029:Base Pairing; D002942:Circular Dichroism; D003432:Cross-Linking Reagents / Q000737:chemistry*; D003488:Cyanogen Bromide / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D013056:Spectrophotometry, Ultraviolet; D013267:Stilbenes / Q000737:chemistry*; D013403:Sugar Phosphates / Q000737:chemistry; D013696:Temperature; D013941:Thymine / Q000737:chemistry
chemical_list: D003432:Cross-Linking Reagents; D013267:Stilbenes; D013403:Sugar Phosphates; C066598:stilbenemide; D004247:DNA; D000225:Adenine; D003488:Cyanogen Bromide; D013941:Thymine