Photophysics and binding constant determination of the homodimeric dye BOBO-3 and DNA oligonucleotides.
Photophysics and binding constant determination of the homodimeric dye BOBO-3 and DNA oligonucleotides.
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同二聚体染料 BOBO-3 和 DNA 寡核苷酸的光物理学和结合常数测定。
DOI：
10.1021/jp909863c
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发表时间：
2010
期刊：
影响因子：
--
通讯作者：
J. M. Alvarez
中科院分区：
文献类型：
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作者：
M. Ruedas;Á. Orte;L. Crovetto;E. Talavera;J. M. Alvarez
利用吸收光谱、稳态荧光光谱和时间分辨荧光光谱详细研究了单链和双链DNA与三甲氰同二聚体染料BOBO-3（1,1′-（4,4,7,7-四甲基-4,7-重氮十一亚甲基）-双-4-[3-甲基-2,3-二氢-（苯并1,3-噻唑）-2-甲基]四碘吡啶）的相互作用。染料在各种条件下与单链和双链DNA相互作用，并改变其光谱特征。结果表明，BOBO-3染料与DNA寡核苷酸之间形成的复合物不能用单一的插层机制来解释；因此，提出了不同的交互模式。通过时间分辨荧光方法和对荧光衰减轨迹的深入分析，我们得到了不同形式BOBO-3的贡献：游离于溶液中，低亲和力，与DNA的静电驱动相互作用，以及DNA双螺旋结构内完整的双插层机制。利用这些信息，我们将mcgee - von Hippel理论应用于两种重叠的非合作结合模式，得到了平衡结合常数和每种结合模式所占据的位点数。染料/dsDNA完全双插层和外部结合的结合常数分别为（8.8 +/- 1.1）× 10(5)和（2.6 +/- 0.3）× 10(5) M（-1）。每种模式对应的覆盖碱基对恢复数分别为5.9 +/- 0.2和3.5 +/- 0.5个位点。
The interactions between single- and double-stranded DNA and the trimethine cyanine homodimer dye, BOBO-3 (1,1'-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)-bis-4-[3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene]pyridinium tetraiodide), have been investigated in detail using absorption and steady-state and time-resolved fluorescence spectroscopy. The dye interacts with both single-stranded and double-stranded DNA, under a variety of conditions, with changes in its spectral characteristics. Our results indicated that the complex formed between BOBO-3 dye and DNA oligonucleotides could not be explained with a simple, single intercalation mechanism; therefore, different modes of interaction were proposed. By using time-resolved fluorescence methodology and in-depth analysis of the fluorescence decay traces, we obtained the contribution of the different forms of BOBO-3: free in solution, a low affinity, electrostatically driven interaction with DNA, and a full bis-intercalation mechanism within the DNA double helix. With this information, we applied the McGhee-Von Hippel theory for two overlapping, noncooperative binding modes to obtain equilibrium binding constants and the number of sites occupied for each binding mode. Binding constants for dye/dsDNA complexes in complete bis-intercalation and externally bound were (8.8 +/- 1.1) x 10(5) and (2.6 +/- 0.3) x 10(5) M(-1), respectively. The corresponding recovered number of base pairs covered were 5.9 +/- 0.2 and 3.5 +/- 0.5 sites for each mode.