Experimental and theoretical studies are carried out to determine the influence of thioketo substitution on the properties of uracil and its noncovalent interactions with alkali metal ions. Bond dissociation energies of alkali metal ion-thiouracil complexes, M+(SU), are determined using threshold collision-induced dissociation techniques in a guided ion beam mass spectrometer, where M+ = Li+, Na+, and K+ and SU = 2-thiouracil, 4-thiouracil, 2,4-dithiouracil, 5-methyl-2-thiouracil, and 6-methyl-2-thiouracil. Ab initio electronic structure calculations are performed to determine the structures and theoretical bond dissociation energies of these complexes and provide molecular constants necessary for thermodynamic analysis of the experimental data. Theoretical calculations are also performed to examine the influence of thioketo substitution on the acidities, proton affinities, and A::SU Watson-Crick base pairing energies. In general, thioketo substitution leads to an increase in both the proton affinity and the acidity of uracil. 2-Thio substitution generally results in an increase in the alkali metal ion binding affinities but has almost no affect on the stability of the A::SU base pair. In contrast, 4-thio substitution results in a decrease in the alkali metal ion binding affinities and a significant decrease in the stability of the A::SU base pair. In addition, alkali metal ion binding is expected to lead to an increase in the stability of both single-stranded and double-stranded nucleic acids by reducing the charge on the nucleic acid in a zwitterion effect as well as through additional noncovalent interactions between the alkali metal ion and the nucleobases.