title: A stable antiparallel cytosine-thymine base pair occurring only at the end of a duplex.
abstract: Ultraviolet hyperchromicity experiments indicate that in DNA duplex formation, a C-T mismatch is destabilizing in the center of a duplex, but behaves as a stable base pair at the terminus of a duplex. The C-T base pair is thought to contain two hydrogen bonds, but has thermodynamic parameters (delta Ho and delta Go of dissociation) that are similar to a G-C base pair. AMBER molecular mechanics calculations were performed to study the possible structural properties of DNA duplexes with central and terminal C-T combinations. These calculations also indicate that a central C-T pair destabilizes a duplex, while terminal C-T forms a stable base pair. Hydrogen bonding between cytosine and thymine occurs only in the energy-minimized structures when the helix diameter decreases and the propeller twist angle between the bases increases. These changes are found to occur only at the end of a duplex in the calculations, which may explain the experimental results.
authors.affiliation: Laboratory of Organic Chemistry, Eindhoven University of Technology, The Netherlands.
authors.forename: S A
authors.initials: SA
authors.lastname: Vanhommerig
authors.forename: M H
authors.initials: MH
authors.lastname: van Genderen
authors.forename: H M
authors.initials: HM
authors.lastname: Buck
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D003198:Computer Simulation; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*; D014466:Ultraviolet Rays
chemical_list: D003596:Cytosine; D004247:DNA; D013941:Thymine