Minor groove DNA alkylation directed by major groove triplex forming oligodeoxyribonucleotides

Abstract

We describe sequence-specific alkylation in the minor groove of double-stranded DNA by a hybridization-triggered reactive group conjugated to a triplex forming oligodeoxyribonucleotide (TFO) that binds in the major groove. The 24 nt TFOs (G/A motif) were designed to form triplexes with a homopurine tract within a 65 bp target duplex. They were conjugated to an N 5-methyl-cyclopropapyrroloindole (MCPI) residue, a structural analog of cyclopropapyrroloindole (CPI), the reactive subunit of the potent antibiotic CC-1065. These moieties react in the DNA minor groove, alkylating adenines at their N3 position. In order to optimize alkylation efficiency, linkers between the TFO and the MCPI were varied both in length and composition. Quantitative alkylation of target DNA was achieved when the dihydropyrroloindole (DPI) subunit of CC-1065 was incorporated between an octa(propylene phosphate) linker and MCPI. The required long linker traversed one strand of the target duplex from the major groove-bound TFO to deliver the reactive group to the minor groove. Alkylation was directed by relative positioning of the TFOs. Sites in the minor groove within 4-8 nt from the end of the TFO bearing the reactive group were selectively alkylated.

A Bis-Alkylating Triplex Forming Oligonucleotide Inhibits Intracellular Reporter Gene Expression and Prevents Triplex Unwinding Due to Helicase Activity

“…This conclusion is in accordance with data demonstrating that a TFO conjugated to psoralen on both ends was also less efficiently repaired within cells compared to a single adduct (). Higher efficiency may be attained with other novel DNA binding agents that undergo hybridization triggered DNA adduct formation to improve adduct formation in cells, such as cyclopropapyrroloindole (CPI) () or pyrrolo-1,4-benzodiazepine (PBD) reactive moieties (unpublished observations) ( , ).…”

Hybridization-Promoted and Cytidine-Selective Activation for Cross-Linking with the Use of 2-Amino-6-vinylpurine Derivatives

“…A promising approach to overcome such problems is the use of agents that have inducible reactivity by triggering signals such as UV-irradiation, enzymatic, or chemical reactions. Some compounds, such as ET-743 and CC-1065, are furnished with inducible reactivity that is activated in the microenvironments of the DNA. − Psoralen and its analogues have enjoyed remarkable successes as T-selective photo-cross-linking agents that are applied to a wide variety of in vitro as well as in vivo studies. − However, as UV irradiation might cause damages to other sites of DNA and UV light might not be suitable for in vivo study, researchers have been seeking other types of alkylating agents with inducible reactivity. Rokita's group developed the intermediates of a quinone methide as inducible alkylating agents that can be activated by enzymatic reduction , or chemical reaction. − Quinone methide derivatives have been used to propose a general strategy for target-promoted alkylation .…”

Conjugation of Benzylvanillin and Benzimidazole Structure Improves DNA Binding with Enhanced Antileukemic Properties

“…The viscosity studies hints that the DNA interaction that could have possibly taken place may perhaps be via minor groove binding for 2XP and DNA alkylation for 3BS. It is also possible that 3BS may also interact covalently in the minor groove region similar to some alkylating minor groove binders [ 50 , 51 , 52 ]. Monofunctional alkylation can occur on the most nucleophilic sites on the DNA mainly the N7 of guanine, O6 of Thymine, N3 of adenine etc [ 53 , 54 , 55 ].…”