Ethidium and azidoethidium oligonucleotide derivatives: synthesis, complementary complex formation and sequence-specific photomodification of the single-stranded and double-stranded target oligo- and polynucleotides.
Oligodeoxyribonucleotide derivatives containing ethidium or azidoethidium residues attached to 3' and/or 5' end were prepared. These derivatives formed tight specific complexes with complementary oligodeoxyribonucleotides where each attached ethidium residue led to an increase of complex Tm by 20-30 degrees C. Tandem complexes of two oligodeoxyribonucleotides containing ethidium residues with an oligodeoxyribonucleotide having two adjacent complementary sequences for these oligonucleotides were investigated. Photoinduced reactions of a number of ethidium and azidoethidium oligodeoxyribonucleotide derivatives with target complementary single-stranded and double-stranded oligo- and polydeoxyribonucleotides were investigated. The irradiation led to direct photocleavage of the target oligo- or polynucleotide, to formation of hidden (piperidine cleavable) modifications of the target and to formation of covalent adducts between ethidium oligodeoxyribonucleotide derivative and the target. In a number of experiments, azidoethidium dyes were demonstrated to be considerably stronger photosensitizers than ethidium ones. Depending on the nature of the target (single- or double-stranded DNA) and on the irradiation conditions, the total damages to the target oligo- or polydeoxyribonucleotides ranged from 10-70% (for ethidium dyes) to 30-80% (for azidoethidium dyes).
Koshkin
A A
AA
Institute of Bioorganic Chemistry, Siberian Division, Russian Academy of Sciences, Novosibirsk.
Kropachev
K
K
Mamaev
S V
SV
Bulychev
N V
NV
Lokhov
S G
SG
Vlassov
V V
VV
Lebedev
A V
AV
D001386:Azides / Q000737:chemistry*; D001483:Base Sequence; D004396:Coloring Agents / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D018076:DNA, Complementary; D004591:Electrophoresis, Polyacrylamide Gel; D004996:Ethidium / Q000737:chemistry*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D015345:Oligonucleotide Probes; D011119:Polynucleotides / Q000737:chemistry
D001386:Azides; D004396:Coloring Agents; D018076:DNA, Complementary; D009838:Oligodeoxyribonucleotides; D015345:Oligonucleotide Probes; D011119:Polynucleotides; D004247:DNA; D004996:Ethidium