Distamycin-stabilized Antiparallel-Parallel Combination (APC) DNA |
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| Authors: | Anna K Shchyolkina Lyudmila E Minchenkova Elvira E Minyat Yelena B Khomyakova Valery I Ivanov Reinhard Klement |
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| Institution: | 1. Engelhardt Institute of Molecular Biology, Russian Academy of Science , 117984 , Moscow , Russia;2. Department of Molecular Biology , Max Planck Institute for Biophysical Chemistry , D-37070 , G?ttingen , FRG |
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| Abstract: | Abstract The formation of Antiparallel-Parallel-Combination (APC) DNA, a liner duplex with a segment of parallel-stranded (ps) helix flanked by conventional B-DNA, was tested with a number of synthetic oligonucleotides. The groove-binding ligand distamycin A (DstA) was used to stabilize the ps segment comprising five A·T base pairs. Two drug molecules bound per APC, one in each of the two equivalent grooves characteristic of ps-DNA. APC-DNA, reference molecules and their complexes with DstA were analysed by several methods: circular dichroism and absorption spectroscopy, thermal denaturation, chemical modification, and molecular modeling. The dye binding stoichiometry differed significantly due to inherent structural differences in the groove geometries of ps-DNA (trans base pairs, similar grooves) and conventional antiparallel-stranded (aps) B-DNA (cis base pairs, distinct major and minor grooves). The data support the existence of APC folding in solution. |
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