Conformational study of a dinucleoside monophosphate in aqueous solution using the lanthanide probe method

Abstract

The conformation of the metal-bound dinucleoside monophosphate adenylyl-3′→5′-adenosine (ApA) in aqueous solution at different pH values and temperatures has been studied using the lanthanide probe method. The conformational analysis, based on a mixture of different conformations in fast exchange within the n.m.r. time scale, agrees well with the results from coupling constants, proton dimerization shifts, and ab initio molecular orbital calculations, obtained for the metal-free system. The unstacking process of ApA depends on the temperature and the state of protonation of the adenine bases. In particular the conformational populations about the phosphodiester bonds for the stacked and unstacked forms of ApA show that this part of the molecule has a noticeable preference for the gauche forms gg when the adenine bases are unprotonated, and for the gt,tg forms in the protonated species. A combination of proton dimerization shift data and lanthanide data indicate a two-state equilibrium for the unstacking process of ApA.