McKnight Ruel E, Onogul Bilgehan, Polasani Shivani R, Gannon Michael K, Detty Michael R
Department of Chemistry, State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA.
Bioorg Med Chem. 2008 Dec 15;16(24):10221-7. doi: 10.1016/j.bmc.2008.10.051. Epub 2008 Oct 25.
The DNA binding efficacy and preferred mode of binding of a series of rhodamine-related chalcogenoxanthylium dyes was investigated by isothermal titration calorimetry (ITC) using ctDNA, poly(dCdG) and poly(dAdT), and by a topoisomerase I DNA unwinding (Topo I) assay. The dyes of this study showed tight binding to ctDNA with binding constants, K(b), on the order of 10(6)-10(7)M(-1). The ITC and Topo I assay studies suggested that the 9-substituent has a strong impact on binding modes ranging from an apparent preference for intercalation with a 9-2-thienyl substituent (similar binding to poly(dCdG) and poly(dAdT), re-supercoiling of DNA in the Topo I assay at <10(-5)M dye), to mixed binding modes with 9-phenyl derivatives (2- to 3-fold preference for binding to poly(dAdT), re-supercoiling of DNA in the Topo I assay at approximately 2 x 10(-5)M dye), to minor groove binding in a 9-(2-thienyl-5-diethylcarboxamide) derivative (strong preference for binding to poly(dAdT), did not show complete re-supercoiling in the Topo I assay). No binding to ctDNA was observed in one derivative with a 9-(3-thienyl-2-diethylcarboxamide) substituent, which cannot be co-planar with the xanthylium core. In series of dyes where the chalcogen atom was varied, the selenoxanthylium derivatives had 2- to 3-fold higher values of K(b) than the corresponding xanthylium, thioxanthylium, or telluroxanthylium derivatives, which all showed comparable values of K(b). The chalcogen atom appeared to have little influence on binding mode.
通过等温滴定量热法（ITC），使用小牛胸腺DNA（ctDNA）、[聚（dCdG）]₂和[聚（dAdT）]₂，以及通过拓扑异构酶I DNA解旋（Topo I）测定法，研究了一系列罗丹明相关的硫属黄原鎓染料的DNA结合效率和偏好的结合模式。本研究中的染料显示出与ctDNA紧密结合，结合常数Kₐ在10⁶ - 10⁷M⁻¹量级。ITC和Topo I测定法研究表明，9-取代基对结合模式有强烈影响，范围从明显倾向于与9-2-噻吩基取代基发生嵌入（与[聚（dCdG）]₂和[聚（dAdT）]₂的结合相似，在Topo I测定法中，染料浓度<10⁻⁵M时DNA重新超螺旋），到与9-苯基衍生物的混合结合模式（对[聚（dAdT）]₂的结合偏好高2至3倍，在Topo I测定法中，染料浓度约为2×10⁻⁵M时DNA重新超螺旋），再到9-（2-噻吩基-5-二乙酰胺）衍生物中的小沟结合（对[聚（dAdT）]₂的结合有强烈偏好，在Topo I测定法中未显示完全重新超螺旋）。在一种具有9-（3-噻吩基-2-二乙酰胺）取代基且不能与黄原鎓核心共平面的衍生物中，未观察到与ctDNA的结合。在硫属原子不同的一系列染料中，硒黄原鎓衍生物的Kₐ值比相应的黄原鎓、硫代黄原鎓或碲黄原鎓衍生物高2至3倍，而后三者的Kₐ值相当。硫属原子似乎对结合模式影响不大。
