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Journal Article

Distamycin-stabilized antiparallel-parallel-combination (APC) DNA


Klement,  R.
Emeritus Group Laboratory of Cellular Dynamics, MPI for biophysical chemistry, Max Planck Society;


Jovin,  T. M.
Department of Molecular Biology, MPI for biophysical chemistry, Max Planck Society;

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Shchyolkina, A. K., Minchenkova, L. E., Minyat, E. E., Khomyakova, Y. B., Ivanov, V. I., Klement, R., et al. (1998). Distamycin-stabilized antiparallel-parallel-combination (APC) DNA. Journal of Biomolecular Structure and Dynamics, 15, 823-839.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0012-FE05-C
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 AT 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.