Optimization of triple-helix-directed DNA cleavage by benzoquinoquinoxaline-ethylenediaminetetraacetic acid conjugates.
The formation of triple-helical structures of DNA is based on sequence-specific recognition of oligopyrimidine.oligopurine stretches of double-helical DNA. Triple-helical structures can be stabilized by DNA-binding ligands. Benzoquinoquinoxaline (BQQ) derivatives are among the most potent intercalating-type agents known to stabilize DNA triple-helical structures. We previously reported the conversion of BQQ into a triplex-directed DNA cleaving agent, namely BQQ-ethylenediaminetetraacetic acid (EDTA), by coupling of 6-(3-aminopropylamino)BQQ to a suitable ethylenediaminetetraacetic acid derivative, and we demonstrated the ability of this conjugate to cause double-stranded cleavage of DNA at the triplex site. However, this prototype derivative BQQ-EDTA conjugate showed lower affinity towards triplex DNA than BQQ itself. In the light of this observation, and guided by molecular modeling studies, we synthesized a second generation of BQQ-EDTA conjugates based on 6-[bis(2-aminoethyl)amino]- and 6-(3,3'-diamino-N-methyldipropylamino)-BQQ derivatives. We confirmed by DNA melting experiments that the new conjugates displayed an increased specific affinity towards triple helices when compared to the previously synthesized BQQ-EDTA. In addition, the efficiency of these new agents in triplex-specific binding and cleavage was demonstrated by triplex-directed double-stranded cleavage of plasmid DNA.
Zain
Rula
R
Department of Molecular Biology & Functional Genomics, Stockholm University, 10691 Stockholm, Sweden.
Polverari
David
D
Nguyen
Chi-Hung
CH
Blouquit
Yves
Y
Bisagni
Emile
E
Garestier
Thérèse
T
Grierson
David S
DS
Sun
Jian-Sheng
JS
D004247:DNA / Q000737:chemistry*; D004492:Edetic Acid / Q000138:chemical synthesis* / Q000737:chemistry; D007364:Intercalating Agents / Q000138:chemical synthesis* / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000737:chemistry; D011810:Quinoxalines / Q000138:chemical synthesis* / Q000737:chemistry; D013816:Thermodynamics
C403231:BQQ-EDTA conjugate; D007364:Intercalating Agents; D011810:Quinoxalines; D004247:DNA; D004492:Edetic Acid