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A New Family of Sequence‐Specific DNA‐Cleaving Agents Directed by Triple‐Helical Structures: Benzopyridoindole‐EDTA Conjugates
Author(s) -
Marchand Christophe,
Nguyen Chi Hung,
Ward Brian,
Sun JianSheng,
Bisagni Emile,
Garestier Thérèse,
Hélène Claude
Publication year - 2000
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/(sici)1521-3765(20000502)6:9<1559::aid-chem1559>3.0.co;2-z
Subject(s) - triple helix , dna , oligonucleotide , cleavage (geology) , nucleotide , biochemistry , stereochemistry , biology , chemistry , microbiology and biotechnology , gene , paleontology , fracture (geology)
Sequence‐specific DNA recognition can be achieved by oligonucleotides that bind to the major groove of oligopyrimidine ⋅ oligopurine sequences. These intermolecular structures could be used to modulate gene expression and to create new tools for molecular biology. Here we report the synthesis and biochemical characterization of triple helix‐specific DNA cleaving reagents. It is based on the previously reported triplex‐specific ligands, benzo[e]pyridoindole (BePI) and benzo[g]pyridoindole (BgPI), covalently attached to ethylenediaminotetraacetic acid (EDTA). In the presence of iron, a reducing agent and molecular oxygen, BgPI‐EDTA ⋅ Fe II but not BePI‐EDTA ⋅ Fe II induced a double‐stranded cut in a plasmid DNA at the single site where a triplex‐forming oligonucleotide binds. At single nucleotide resolution, it was found that upon triplex formation BePI‐EDTA ⋅ Fe II led to cleavage of the pyrimidine strand and protection of the purine strand. BgPI‐EDTA ⋅ Fe II cleaved both strands with similar efficiency. The difference in cleavage efficiency between the two conjugates was rationalized by the location of the EDTA ⋅ Fe II moiety with respect to the grooves of DNA (major groove: BePI‐EDTA ⋅ Fe II , minor groove: BgPI‐EDTA ⋅ Fe II ). This work paves the way to the development of a new class of triple helix directed DNA cleaving reagents. Such molecules will be of interest for sequence‐specific DNA cleavage and for investigating triple‐helical structures, such as H‐DNA which could play an important role in the control of gene expression in vivo.