Distamycin-stabilized antiparallel-parallel combination (APC) DNA.
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.
Shchyolkina
A K
AK
Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow.
Minchenkova
L E
LE
Minyat
E E
EE
Khomyakova
Y B
YB
Ivanov
V I
VI
Klement
R
R
Jovin
T M
TM
D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004214:Distamycins / Q000378:metabolism*; D006361:Heating; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry* / Q000378:metabolism; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000378:metabolism
D004214:Distamycins; D009692:Nucleic Acid Heteroduplexes; D009838:Oligodeoxyribonucleotides; C030000:stallimycin; D004247:DNA