Bifunctional Intercalator [N-MeCys³,N-MeCys⁷]TANDEM Binds to the Dinucleotide TpA

Waterloh, Kerstin, Fox, Keith R. and Olsen, Richard K. (1992) Bifunctional Intercalator [N-MeCys³,N-MeCys⁷]TANDEM Binds to the Dinucleotide TpA. Biochemistry, 31 (27), 6246-6253. (doi:10.1021/bi00142a012).

Abstract

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 3ʹ-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 3ʹ-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.

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Contributors

Author: Keith R. Fox

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