Mobility shift electrophoresis (MSE) and methylation interference (M-I) with 5' end labeled double stranded oligonucleotides encompassing the sequences of DNase I protected domains prpA and prpB. (A) MSE with 5' end labeled double stranded oligonucleotides encompassing the sequences of domain prpA (lane 1, and lower panel). Brackets show binding complexes (bA1-bA3) and the free oligonucleotide (f). Mobility shift competition was performed with a 20-fold molar excess of unlabeled oligonucleotide prpB (lane2) and prpA (lane 3). Methylated G residues within domain prpA that partially interfere with binding of complex bA2 on the coding [(C), lanes 4-7] and noncoding [(N), lanes 8-11] strands are indicated by arrowheads. Lanes 4 and 8 show the methylation patterns of the free oligonucleotides. Lower panel shows the sequence of the double stranded oligonucleotide used and G-residues that interfere with binding to complex bA2. (B) Same as in A except that the sequence of DNase I protected domain prpB was used. Mobility shift electrophoresis shows the formation of binding complexes bB1-bB5 with sequence-specific competition of complex bB5 (lanes 1-3). The same binding complex also exhibits binding interference with indicated methylated G residues (bracket, arrowheads) on coding (lanes 4-9) and noncoding (lanes 10-15) strands. Lanes 4 and 10 show the methylation patterns of the free oligonucleotides.