EFFECTS OF INTERNAL NONBONDED BASES AND A G.U BASE PAIR ON THE STABILITY OF A SHORT RIBONUCLEIC-ACID HELIX

Proton nuclear magnetic resonance has been used to examine the effect of both noncomplementary and G-U oppositions in the duplexes formed by the synthetic pentaribonucleotides [formula omitted] The lack of any sigmoidal behavior in the chemical shift vs. temperature plots of the base protons in the individual pentaribonucleotides indicates that duplexes with noncomplementary base oppositions of the type were recorded over the range of 70-10 °C. The chemical shift vs. temperature plot of the purine aromatic protons displayed sigmoidal curves. This demonstrated both duplex formation and the presence of a G-U base pair. The average Tm of the duplex was found to be 23.4 ± 2.0 °C. This is similar to that of the duplex formed by CpApUpG (24.0 ± 1.0 °C) but less than the Tm of the following duplexes: [formula omitted] and is a region of local instability within the double helix. This 1H NMR study is the first to investigate both the formation and relative stability of an internal G-U base pair neighboring regular Watson-Crick base pairs. © 1979, American Chemical Society. All rights reserved.