Pb. Arimondo et al., Triple helix-forming oligonucleotides conjugated to indolocarbazole poisons direct topoisomerase I-mediated DNA cleavage to a specific site, BIOCONJ CHE, 12(4), 2001, pp. 501-509
Topoisomerase I is an ubiquitous DNA-cleaving enzyme and an important thera
peutic target in cancer chemotherapy for camptothecins as well as for indol
ocarbazole antibiotics such as rebeccamycin. To achieve a sequence-specific
cleavage of DNA by topoisomerase I, a triple helix-forming oligonucleotide
was covalently linked to indolocarbazole-type topoisomerase I poisons. The
three indolocarbazole-oligonucleotide conjugates investigated were able to
direct topoisomerase I cleavage at a specific site based upon sequence rec
ognition by tripler formation. The efficacy of topoisomerase I-mediated DNA
cleavage depends markedly on the intrinsic potency of the drug. We show th
at DNA cleavage depends also upon the length of the linker arm between the
tripler-forming oligonucleotide and the drug. Based on a known structure of
the DNA-topoisomerase I complex, a molecular model of the oligonucleotide
conjugates bound to the DNA-topoisomerase I complex was elaborated to facil
itate the design of a potent topoisomerase I inhibitor-oligonucleotide conj
ugate with an optimized linker between the two moieties. The resulting olig
onucleotide-indolocarbazole conjugate at 10 nM induced cleavage at the trip
le helix site a-fold more efficiently than 5 muM of free indolocarbazole, w
hile the other drug-sensitive sites were not cleaved. The rational design o
f drug-oligonucleotide conjugates carrying a DNA topoisomerase poison may b
e exploited to improve the efficacy and selectivity of chemotherapeutic can
cer treatments by targeting specific genes and reducing drug toxicity.