Shchyolkina AK, Minchenkova LE, Minyat EE, Khomyakova YB, Ivanov VI, Klement R, Jovin TM. Distamycin-stabilized antiparallel-parallel combination (APC) DNA.
J Biomol Struct Dyn 1998;
15:823-39. [PMID:
9619506 DOI:
10.1080/07391102.1998.10508205]
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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 x 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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