title: Strand displacement of double-stranded DNA by triplex-forming antiparallel purine-hairpins.
abstract: We characterize the binding affinity and the thermodynamics of hybridization of triplex-forming antiparallel purine-hairpins composed of two antiparallel purine domains linked by a loop directed toward single-stranded and double-stranded DNA (ssDNA, dsDNA). Gel retardation assays and melting experiments reveal that a 13-mer purine-hairpin binds specifically and with a K ( d ) of 8 x 10(8) M to polypyrimidine ssDNA to form a triple helical structure. Remarkably, we show that purine-hairpins also bind polypurine/polypyrimidine stretches included in a dsDNA of several hundred bp in length. Binding of purine-hairpins to dsDNA occurs by triplex formation with the polypyrimidine strand, causing displacement of the polypurine strand. Because triplex formation is restricted to polypurine/polypyrimidine stretches of dsDNA, we studied the triplex formation between purine-hairpins and polypyrimidine targets containing purine interruptions. We found that an 11-mer purine-hairpin with an adenine opposite to a guanine interruption in the polypyrimidine track binds to ssDNA and dsDNA, allowing expansion of the possible target sites and increase in the length of purine-hairpins. Thus, when using a 20-mer purine-hairpin targeting an interruption-containing polypyrimidine target, the binding affinity is increased compared to its 13-mer antiparallel purine-hairpin counterpart. Surprisingly, this increase is much more pronounced than that observed for a tail-clamp purine-hairpin extended up to 20 nt in the Watson-Crick domain only. Thus, triplexforming antiparallel purine-hairpins can be a potentially useful strategy for both single-strand and double-strand nucleic acid recognition.
authors.affiliation: Department of Biochemistry, School of Pharmacy, University of Barcelona, Barcelona, Spain.
authors.forename: Silvia
authors.initials: S
authors.lastname: Coma
authors.forename: Véronique
authors.initials: V
authors.lastname: Noé
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
authors.forename: Carlos J
authors.initials: CJ
authors.lastname: Ciudad
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D024202:Electrophoretic Mobility Shift Assay; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D011687:Purines / Q000737:chemistry*
chemical_list: D011687:Purines; D004247:DNA