c-Myc family proteins, encoded by c-myc family proto-oncogenes, play critical roles in mechanisms associated with proliferation, differentiation and apoptotic death in eukaryotic cells. These functions are mediated by transcriptional activity of these proteins through binding to the E-box core sequence CACGTG referred to as a Myc core element located at a promoter or enhancer region of the individual target genes in the nucleus. Recent studies have demonstrated the presence of novel nuclear proteins that specifically recognize a Myc core element, in addition to c-Myc, Max, Mad and Mxi1. On the other hand, a Myc core element has alternating purine/pyrimidine repeats which could undergo a conformational transition from right-handed (B-DNA) to left-handed (Z-DNA) forms in the presence of a high concentration of salts such as Mg2+ and polyamines. Similarly, a Myc element has a homopurine-homopyrimidine site that may take a triplex configuration in particular situations. We have searched for nuclear proteins that can specifically recognize a Myc core element in different topological variations in murine brain.