Staerk D, Hamed A A, Pedersen E B, Jacobsen J P
Department of Chemistry, Odense University, Denmark.
Bioconjug Chem. 1997 Nov-Dec;8(6):869-77. doi: 10.1021/bc970067k.
The thiazole orange dye 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)-bis[4-[3-methy l-2, 3-dihydro(benzo-1,3-thiazole)-2-methylidene]]quinolinium tetraiodide (TOTO) binds to double-stranded DNA (dsDNA) in a sequence selective bisintercalation. Each chromophore is sandwiched between two base pairs in a (5'-CpT-3'):(5'-ApG-3') site, and the linker spans over two base pairs in the minor groove. The binding of analogs of TOTO in which the linker has been modified is examined. The aim of the study is to utilize the sequence selectivity of the TOTO chromophores to enhance and/or alter the overall selectivity of the binding. One- and two-dimensional 1H-NMR investigations of complexes between TOTO analogs and various dsDNA oligonucleotides are reported. The following analogs were synthesized and used: 1,1'-(4,4,8,8-tetramethyl-4,8-diazadodecamethylene) -bis[4-[3-methyl-2,3-dihydro- (benzo-1,3-thiazole)-2-methylidene]]quinolinium tetraiodide (TOTO10), 1,1'-(5,5,9,9-tetramethyl-5,9-diazatridecamethylene)-bis[4-[3-meth yl-2, 3-dihydro(benzo-1,3-thiazole)-2-methylidene]]quinolinium tetraiodide (TOTO11), and 1,1'-(6,6,10,10-tetramethyl-6,10-diazapentadecamethylene)-bis[4-[3 -methyl-2, 3-dihydro(benzo-1,3-thiazole)-2-methylidene]]quinolinium tetraiodide (TOTO13). The results show that with a longer linker the dyes can bisintercalate into two (5'-CpT-3'):(5'-ApG-3') sites separated by one or two base pairs. Bisintercalation in two such "isolated" binding sites yields non-nearest-neighbor bisintercalation in which the linker spans over more than two base pairs. The investigations also showed that an exact length of the linker is not crucial for the site selectivity since TOTO, TOTO10, and TOTO11 are almost equally suitable in binding selectively to the (5'CTAG-3')2 sequence. Fluorescence measurements show that TOTO10, TOTO11, and TOTO13 have higher fluorescence quantum yields than TOTO when bound to d(CGCTAGCG)2. This indicates that the length of the linker in TOTO may not be the optimum one in terms of using the dye as a fluorescence marker.
噻唑橙染料1,1'-（4,4,8,8-四甲基-4,8-二氮杂十一亚甲基）-双[4-[3-甲基-2,3-二氢（苯并-1,3-噻唑）-2-亚甲基]]喹啉四碘化物（TOTO）以序列选择性双插入的方式与双链DNA（dsDNA）结合。每个发色团夹在（5'-CpT-3'）:（5'-ApG-3'）位点的两个碱基对之间，且连接体跨越小沟中的两个碱基对。对连接体已被修饰的TOTO类似物的结合情况进行了研究。该研究的目的是利用TOTO发色团的序列选择性来增强和/或改变结合的整体选择性。报道了TOTO类似物与各种dsDNA寡核苷酸之间复合物的一维和二维¹H-NMR研究。合成并使用了以下类似物：1,1'-（4,4,8,8-四甲基-4,8-二氮杂十二亚甲基）-双[4-[3-甲基-2,3-二氢-（苯并-1,3-噻唑）-2-亚甲基]]喹啉四碘化物（TOTO10）、1,1'-（5,5,9,9-四甲基-5,9-二氮杂十三亚甲基）-双[4-[3-甲基-2,3-二氢（苯并-1,3-噻唑）-2-亚甲基]]喹啉四碘化物（TOTO11）以及1,1'-（6,6,10,10-四甲基-6,10-二氮杂十五亚甲基）-双[4-[3-甲基-2,3-二氢（苯并-1,3-噻唑）-2-亚甲基]]喹啉四碘化物（TOTO13）。结果表明，连接体更长时，染料可双插入到被一个或两个碱基对隔开的两个（5'-CpT-3'）:（5'-ApG-3'）位点。在两个这样的“孤立”结合位点的双插入产生非近邻双插入，其中连接体跨越超过两个碱基对。研究还表明，连接体的确切长度对位点选择性并非至关重要，因为TOTO、TOTO10和TOTO11在选择性结合（5'CTAG-3'）₂序列方面几乎同样合适。荧光测量表明，与d（CGCTAGCG）₂结合时，TOTO10、TOTO11和TOTO13的荧光量子产率高于TOTO。这表明就将该染料用作荧光标记而言，TOTO中连接体的长度可能并非最佳长度。
