Abstract: Methods are provided for identification and production of new DNA binding proteins that up or down regulate the expression of pre-determined target genes. Such genes include DNA sequences that encode proteins that regulate such target genes as well as gene constructs and biological materials that contain such DNA binding proteins and/or their DNA sequences. Discovery methods also are provided for transcriptional promoters that allow identification of the desired target gene specific DNA binding proteins, methods for targeting DNA binding protein variants to the desired DNA binding sequence, the methods for removing undesired DNA binding protein variants from the total pool of all variants, as well as the media used for assaying in vivo DNA binding. The invention further encompasses kits for the identification and production of DNA binding protein variants and/or their DNA sequences.