Conformational analysis of a modified ribotetranucleoside triphosphate: m62A-U-m62A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz1

Abstract

The complete and unequivocal assignment of the 24 ribose proton signals of $m62A(1)-U(2)-m62A(3)-U(4)$ by means of 500 MHz NMR spectroscopy at 17°C is given. This assignment is based on scrupulous decoupling experiments carried out at various temperatures. Analysis of the observed chemical shifts and coupling constants of the tetramer shows that the two fragments $-m62A(3)-U(4)$ comprising the 3′-end occur mainly in the classical right-handed stack conformation, whereas at the 5′-end the -U(2)- residue appears bulged out in favour of a less well-defined stacking interaction between the bases $-m62A(1)-$ and $-m62A(3)-$. Conformational populations about each of the torsional degrees of freedom along the backbone are discussed. A modernized version of pseudo-rotation analysis is used to delineate the conformational behaviour of the four ribose rings.