Zain Rula, Polverari David, Nguyen Chi-Hung, Blouquit Yves, Bisagni Emile, Garestier Thérèse, Grierson David S, Sun Jian-Sheng
Department of Molecular Biology & Functional Genomics, Stockholm University, 10691 Stockholm, Sweden.
Chembiochem. 2003 Sep 5;4(9):856-62. doi: 10.1002/cbic.200300621.
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.
DNA三螺旋结构的形成基于对双螺旋DNA中寡嘧啶-寡嘌呤片段的序列特异性识别。三螺旋结构可通过DNA结合配体得以稳定。苯并喹喔啉（BQQ）衍生物是已知的最有效的嵌入型试剂之一，可稳定DNA三螺旋结构。我们之前报道了通过将6-(3-氨丙基氨基)BQQ与合适的乙二胺四乙酸衍生物偶联，将BQQ转化为一种三链定向DNA切割剂，即BQQ-乙二胺四乙酸（EDTA），并且我们证明了这种缀合物能够在三链位点引起DNA双链切割。然而，这种原型衍生物BQQ-EDTA缀合物对三链DNA的亲和力低于BQQ本身。鉴于这一观察结果，并在分子建模研究的指导下，我们基于6-[双(2-氨基乙基)氨基]-和6-(3,3'-二氨基-N-甲基二丙基氨基)-BQQ衍生物合成了第二代BQQ-EDTA缀合物。我们通过DNA熔解实验证实，与先前合成的BQQ-EDTA相比，新的缀合物对三螺旋显示出更高的特异性亲和力。此外，这些新试剂在三链特异性结合和切割方面的效率通过质粒DNA的三链定向双链切割得以证明。
