Secondary structure plays critical roles in nucleic acid function. Mismatches in DNA can lead to mutation and disease, and some mismatches involve a protonated base. Among protonated mismatches, A+.C wobble pairs form near physiological pH and have relatively minor effects on helix geometry, making them especially important in biology. Herein, we investigate effects of helix position, temperature, and ionic strength on pKa shifting in A+.C wobble pairs in DNA. We observe that pKa shifting is favored by internal A+.C wobbles, which have low cooperativities of folding and make large contributions to stability, and disfavored by external A+.C wobbles, which have high folding cooperativities but make small contributions to stability. An inverse relationship between pKa shifting and temperature is also found, which supports a model in which protonation is enthalpically favored overall and entropically correlated with cooperativity of folding. We also observe greater pKa shifts as the ionic strength decreases, consistent with anticooperativity between proton binding and counterion-condensed monovalent cation. Under the most favorable temperature and ionic strength conditions tested, a pKa of 8.0 is observed for the A+.C wobble pair, which represents an especially large shift (4.5 pKa units) from the unperturbed pKa value of adenosine. This study suggests that protonated A+.C wobble pairs exist in DNA under biologically relevant conditions, where they can drive conformational changes and affect replication and transcription fidelity.