title: Large stacking stability of a base pair-mimic nucleotide on the DNA duplex.
abstract: We synthesized novel adenosine derivatives tethering an aromatic hydrocarbon group by an amido linker. The single adenosine derivatives at 5' dangling end stabilized the DNA duplex of 5'-ATGCGCAT-3' more or equally than Watson-Crick base pair. When the number of the dangling residues increased from one to three, the duplex stability became larger by 1.8-3.6 kcal/mol. When the adenosine derivative was opposite to an abasic site in a DNA duplex, the destabilization by the abasic site was significantly reduced. These observations suggest that the adenosine derivatives developed in this study can stack with a DNA base pair by forming a base pair-mimic geometry.
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D018716:Molecular Mimicry; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004247:DNA