title: Hydrogen bonding versus stacking stabilization by modified nucleobases incorporated in PNA.DNA duplexes.
abstract: The effects of incorporation of the modified nucleobases, 2,6-diaminopurine (D) (substituting for adenine) and 7-chloro-1,8-naphthyridin-2-(1H)-one (bicyclic thymine, bT) (substituting for thymine), that stabilize PNA.DNA duplex formation by increasing hydrogen bonding and/or base pair stacking interactions have been studied by thermal denaturation in terms of thermodynamics. Although the stabilizing effect of the bT base (in contrast to that of D base) is abolished upon addition of dimethyl formamide, thereby indicating that the stabilization is predominantly due to hydrophobic stacking forces, duplex stabilization was found to be enthalpic for both nucleobases. Increased stabilization (although not fully linearly) was observed with increasing numbers of modified bases, and single base sequence discrimination was only slightly compromised, but showed significant dependence on the sequence context.
authors.affiliation: Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Denmark.
authors.forename: Anjana
authors.initials: A
authors.lastname: Sen
authors.forename: Peter E
authors.initials: PE
authors.lastname: Nielsen
mesh_terms: D020029:Base Pairing / Q000187:drug effects; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004126:Dimethylformamide / Q000494:pharmacology; D006860:Hydrogen Bonding; D009691:Nucleic Acid Denaturation; D020135:Peptide Nucleic Acids / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013816:Thermodynamics; D013941:Thymine / Q000378:metabolism; D044366:Transition Temperature
chemical_list: D020135:Peptide Nucleic Acids; D004126:Dimethylformamide; D004247:DNA; D013941:Thymine