Bifunctional intercalator [N-MeCys3,N-MeCys7]TANDEM binds to the dinucleotide TpA

The binding of [N-MeCys3,N-MeCys7]TANDEM has been examined by DNase I footprinting and diethyl pyrocarbonate modification of several synthetic DNA fragments containing AT-rich regions. DNase I footprinting reveals that at low concentrations the ligand binds preferentially to the center of (AT)n regions. A fragment containing the tetranucleotide AATT was unaffected by the ligand. Diethyl pyrocarbonate modification of several fragments containing blocks of (AT)n revealed a pattern in which alternate adenines were rendered more reactive in the presence of the ligand. These reactive adenines were staggered across the two DNA strands in the 3'-direction, consistent with ligand binding to the dinucleotide TpA. In sequences of the type (TAA)n.(TTA)n, binding of [N-MeCys3,N-MeCys7]TANDEM resulted in strong modification of the second adenine in the sequence TAA, i.e., the base on the 3'-side of the ligand binding site. Data for binding to (AT)n are best explained by suggesting that the adenines sandwiched between the quinoxaline chromophores are rendered most reactive to diethyl pyrocarbonate.