DNA-binding complexes were identified in the PFC and MC in 24 out of 30 subjects analyzed. In contrast, the NF-κB, p50 homodimer and Ku DNA-binding activity was much lover or virtually undetectable in extracts from other 4 control and 2 alcoholic subjects (Figure 3B, lanes 3 and 15). Stepwise linear regression identified pH (p<0.05) as a covariate for the DNA binding activities in the PFC and MC when 30 subjects were analyzed. The six subjects, which extracts failed to produce complexes, had the lowest brain tissue pH ranging from 5.66 to 6.24; the average brain pH for the remaining subjects was 6.61±0.19 and 6.54±0.14 for the control and alcoholic groups, respectively. Thus, DNA binding proteins including NF-κB, p50 homodimer and Ku were probably inactivated due to the low pH level of the sample. When these six subjects were excluded from the analysis, the remaining samples showed no correlation between pH and DNA binding activity.
