Geometrical and electronic structures of uracil nucleobase pair containing Ag-I ions have been studied theoretically and computationally. Four stable conformers are expected to co-exist under normal experimental conditions, and transition state structures among the conformers are also presented. The replacement of protons with AgI ions increases the size of the mismatch nucleobase pairs and leads to a better match of the size stabilizing the duplex. From the calculated infrared, Raman and UV absorption spectra of each conformer and mixtures of all conformers, all the conformers are expected to make significant contributions to the experimental spectroscopic profiles. (C) 2010 Elsevier B.V. All rights reserved.