Dynamics in the DNA recognition by DAPI: Exploration of the various binding modes
Dynamics in the DNA recognition by DAPI: Exploration of the various binding modes
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DOI：
10.1021/jp077090f
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发表时间：
2008-01-24
影响因子：
3.3
通讯作者：
Pal, Samir Kumar
中科院分区：
文献类型：
--
作者：
Banerjee, Debapriya;Pal, Samir Kumar
荧光探针4 '，6-二脒基-2-苯基吲哚（DAPI）的两种不同的相互作用模式，取决于DNA的序列，已在文献中报道。在本研究中，溶剂化动力学已被用来探讨DAPI的结合相互作用的DNA寡聚体的不同序列。皮秒分辨荧光和偏振门控各向异性已被用来表征DAPI的结合到不同的低聚物。在序列CGCGAATTCGCG（oligo 1）的双链十二聚体中，探针的溶剂化弛豫动力学揭示了0.130 ns（75%）和2.35 ns（25%）的时间常数。使用另一种众所周知的小沟结合剂Hoechst 33258（H258）对寡聚物I的小沟环境的独立探索显示了类似的时间尺度，进一步证实了DAPI与寡聚物1的小沟结合。在具有序列GCGCGCGCGCGC的双链十二聚体（oligo 2）中，在文献中已经报道了嵌入，在我们的实验窗口中没有观察到溶剂化。与缓冲液中的DAPI相比，与oligo 2结合的DAPI显示荧光淬灭。嵌入DNA中的DAPI的荧光的淬灭也通过荧光寿命中30 ps的快速组分的出现得到证实，揭示了电子从其嵌入的GC碱基对转移到DAPI。除此之外，DAPI-DNA复合物中探针的激发态寿命也显示出与缓冲液中染料的时间常数类似的时间常数，表明与游离染料相关的激发态光过程也可在这种结合模式下操作，与DNA中DAPI C C的结合几何结构一致。具有随机碱基对序列的小牛胸腺DNA中DAPI的动力学类似于与DNA小沟相关的动力学。我们的研究清楚地探索了DAPI与DNA相互作用的两种不同模式下DAPI-DNA复合物的结构-动力学相关性。
Two distinct modes of interaction of the fluorescent probe 4',6-diamidino-2-phenylindole (DAPI), depending on the sequence of DNA, have been reported in the literature. In the present study, the dynamics of solvation has been utilized to explore the binding interaction of DAPI to DNA oligomers of different sequences. Picosecond-resolved fluorescence and polarization-gated anisotropy have been used to characterize the binding of DAPI to the different oligomers. In the double-stranded dodecamer of sequence CGCGAATTCGCG (oligo 1), the solvation relaxation dynamics of the probe reveals time constants of 0.130 ns (75%) and 2.35 ns (25%). Independent exploration of the minor-groove environment of oligo I using another well-known minor-groove binder Hoechst 33258 (H258) shows similar timescales, further confirming minor-groove binding of DAPI to oligo1. In the double-stranded dodecamer (oligo2) having the sequence GCGCGCGCGCGC, where intercalation has been reported in the literature, no solvation is observed in our experimental window. DAPI bound to oligo2 shows quenching of fluorescence compared to that of DAPI in a buffer. The quenching of fluorescence of DAPI intercalated in DNA is also borne out by the appearance of a fast component of 30 ps in the fluorescence lifetime, revealing electron transfer to DAPI from GC base pairs, between which it intercalates. In addition to this, the excited-state lifetime of the probe in the DAPI-DNA complex also shows a time constant similar to that of the dye in a buffer, indicating that the excited-state photoprocesses associated with the free dye is also operative in this binding mode, consistent with the binding geometry of the DAPI C C, in the DNA. The dynamics of DAPI in calf thymus DNA having a random sequence of base pairs is similar to that associated with the DNA minor groove. Our studies clearly explore the structure-dynamics correlation of the DAPI-DNA complex in the two distinct modes of interaction of DAPI with DNA.