A stable antiparallel cytosine-thymine base pair occurring only at the end of a duplex

S.A.M. Vanhommerig, M.H.P. Genderen, van, H.M. Buck

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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 (H° and G° 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.
Original languageEnglish
Pages (from-to)1087-1094
JournalBiopolymers
Volume31
Issue number9
DOIs
Publication statusPublished - 1991

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