NMR Analysis of 5'-5' Phosphodiest Bonded rCUG

Abstract

<p>A mixture of two isomers of rCUG was separated by HPLC, 5'C3'-5'U3'-5'G3' (low Rf) and 3'C5'-5'U3'-5'G3' (high Rf). These were characterized by proton, carbon-13, and phosphorus-31 NMR and enzymatic methods. This allowed for the first detailed analysis of the effect of a 5'-5' phosphodiester bond upon the solution structure of a ribo - oligonucleotide trimer.</p> <p>The proton spectra of both isomers were assigned with the aid of COSY, NOE, RCT , and decoupling experiments. Variable temperature chemical shift plots and the use of first order coupling constants in various "Karplus-styled" equations allowed for the building of a solution structure model of the CUG high molecule that proved to adhere to Sundaralingam's "rigid" nucleotide concept (1973). The 5'-5' phosphodiester bond adopted a zig-zag right handed helical conformation with the terminal ribose oriented with the H-1' away from the center of base-stacking . This placed the C more distant from U and resulted in U/G base-stacking taking precedence over the dominant C/U base-stacking present in CUG low. The presence of the 5'-5' phosphodiester did not greatly effect the backbone structure of the adjacent 3'-5' linked phosphodiester bond.</p> <p>Both trimers were digested with Phy M to remove the G. Dimers with 2'/3' cyclic Us were obtained and compared with 3'-5' CpU.</p> <p>The presence of a 5'-5' phosphodiester bond allowed for a near complete assignment of the C-13 spectra of the two isomers. These spectra represent an addition to the small number of C-13 spectra available on ribo-oligonucleotide trimers.</p> <p>The P-31 spectrum of CUG low was unambiguously assigned by selective CW proton decoupling. The high isomer spectrum was interpreted on the basis of this assignment and revealed a substantial downfield movement in the chemical shift of the phosphorus involved in the 5'-5' bond.</p>