Conformational flexibility of the 3' acceptor end of transfer ribonucleic acid

Abstract
The intimate details of the conformational features and dynamics of the trinucleoside diphosphates CpCpA and ApCpC in aqueous solution were determined by the complete analysis of their PMR spectra. In addition to the right-handed stacked species in which the phosphodiester torsions conform to the gauche.sbd.gauche domains, sugar puckers 3E, C4''.sbd.C5'' .simeq. 60.degree., C5''.sbd.O5'' .simeq. 180.degree., C3''.sbd.O3'' .simeq. 205.degree. and .chi.CN .simeq. 40.degree., the trimers display a variety of spatial configurations, an important one being a bulged configuration in which the central nucleotide unit is bulged out, enabling stacking interactions between the end units. The 3'' acceptor end of tRNA, CpCpA, displays considerable flexibility for the terminal adenine nucleotide unit. Theoretical NMR calculations demonstrate that the predominant solution conformation does not conform to the CCA terminus of tRNA as reported by 4 independent crystallographic studies of tRNAPhe. The preferred intramolecular order of CCA in solution is such that .chi.1 = .chi.2 = .chi.3 = 40.degree., all the 3 sugars are in 3E, .psi.1 = .psi.2 = .psi.3 = 60.degree., .vphi.2 and .vphi.3 = 170 and 180.degree., respectively; .vphi.1'' = .vphi.2'' = 205.degree., and .omega.1/.omega.1'' and .omega.2/.omega.2'' = 240/205.degree. and 295/265.degree., respectively.