PROTON MAGNETIC RESONANCE STUDIES OF RIBOSE DINUCLEOSIDE MONOPHOSPHATES IN AQUEOUS SOLUTION .2. NATURE OF BASE-STACKING INTERACTION IN ADENYLYL-(3'-]5')-CYTIDINE AND CYTIDYLYL-(3'-]5')-ADENOSINE

The nature of the intramolecular base-stacking interaction in aqueous solution between the adenine and cytosine bases in adenylyl-(3ʹ→5ʹ)-cytidine (ApC) and cytidylyl-(3ʹ→5ʹ)-adenosine (CpA) has been investigated by proton magnetic resonance spectroscopy. The pmr spectra of both dinucleoside monophosphates were studied as a function of concentration and temperature. The results of these pmr studies indicate that the intramolecular base-stacking interaction between the adenine and cytosine bases in these dinucleoside monophosphates is rather strong, and that the stacking tendencies are comparable for the two sequence isomers. A comparison of the data obtained in this work for ApC and CpA with those previously reported for adenylyl-(3ʹ→5ʹ)-adenosine (ApA) suggests that the intramolecular stacking interaction is somewhat stronger in ApA than in ApC and CpA. The chemical shifts of the cytosine H5 and adenine H2 protons, and their variations with temperature, were shown to be consistent with stacked conformations in which both bases of the dinucleoside monophosphates are preferentially oriented in the anti conformation as in similar dApdC and dCpdA (dA = deoxyadenosine; dC = deoxycytidine) segments of double-helical DNA. The intramolecular stacking interaction was found to have a pronounced effect on the conformation of the ribose moieties, and these conformational changes are discussed. This work also reveals a small magnetic anisotropy for the cytosine base, which had not been detected in previous work. The concentration studies indicate extensive self-association of these dinucleoside monophosphates, and analysis of the concentration data facilitated determination of the dimerization constant for the association process as well as the nature of the intermolecular complexes. © 1969, American Chemical Society. All rights reserved.