NF-κB DNA-binding activity was compared in alcoholics and controls using EMSA. The assay identified three main complexes in both PFC and MC (Figure 3A). Two upper complexes (I, II) were specific since their formation was inhibited in the presence of unlabeled wt-κB oligonucleotide (Figure 3A, lane 2) but not m-κB oligonucleotide (Figure 3A, lane 3). Formation of the third, lower complex (III) was not blocked by wt- or m-κB oligonucleotide demonstrating low specificity and affinity of this factor for binding to DNA. We previously identified protein factors in the complexes I and II as NF-κB (p50/p65 heterodimer) and p50 homodimer, respectively, using the supershift/depletion assay with anti-p65- and p50-antibodies and also UV-crosslinking in extracts of human neuronal cell lines and rat brain [24], [47]. We also identified complex III as the Ku protein that binds to double-stranded DNA ends, does not recognize specific DNA sequences, and is present at high levels in the human brain [48], [49]. The levels of the constitutively active and total (active plus latent) NF-κB DNA-binding were measured in the presence of 0.03% and 0.6% DOC,
