1H NMR and optical spectroscopic investigation of the sequence-dependent dimerization of a symmetrical cyanine dye in the DNA minor groove
1H NMR and optical spectroscopic investigation of the sequence-dependent dimerization of a symmetrical cyanine dye in the DNA minor groove
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DOI：
10.1021/bi051298e
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发表时间：
2005-12-06
期刊：
影响因子：
2.9
通讯作者：
Armitage, BA
中科院分区：
文献类型：
--
作者：
Hannah, KC;Gil, RR;Armitage, BA
此前已证明对称花青染料作为共面二聚体与双链DNA的交替A-T序列结合。间接证据表明，二聚化的染料发生在小沟。本文报道的1H-1 NMR实验证实了该模型，其基于由于腺嘌呤的碳2上的质子和11个碱基对双链体：5 '-GCGTATATGCG-3'/3 '-CGCATATACGC-5'的中心五个A-T对处的亚氨基质子引起的信号的加宽和移位。这种结合模式与偏端霉素A的结合模式相似，尽管染料缺乏偏端霉素用于序列特异性识别的氢键基团。令人惊讶的是，第三个碱基对（G-C）也涉及结合位点。UV-vis实验用于比较11种不同序列变体的染料二聚化程度。这些实验验证了第三位G-C对的重要性：用A-T取代该对抑制了二聚化。这些结果表明染料结合位点跨越六个碱基对：5 '-GTATAT-3'。最初的G-C对似乎对于加宽小沟而不是与染料分子进行重要接触是重要的，因为将其取向反转为C-G或用I-C取代它仍然导致染料的有利二聚化。
A symmetrical cyanine dye was previously shown to bind as a cofacial dimer to alternating A-T sequences of duplex DNA. Indirect evidence suggested that dimerization of the dye occurred in the minor groove. H-1 NMR experiments reported here verify this model based on broadening and shifting of signals due to protons on carbon 2 of adenine and imino protons at the central five A-T pairs of the 11 base pair duplex: 5'-GCGTATATGCG-3'/3'-CGCATATACGC-5'. This binding mode is similar to that of distamycin A, even though the dye lacks the hydrogen-bonding groups used by distamycin for sequence-specific recognition. Surprisingly, the third base pair (G-C) was also implicated in the binding site. UV-vis experiments were used to compare the extent of dimerization of the dye for 11 different sequence variants. These experiments verified the importance of a G-C pair at the third position: replacing this pair with A-T suppressed dimerization. These results indicate that the dye binding site spans six base pairs: 5'-GTATAT-3'. The initial G-C pair seems to be important for widening the minor groove rather than for making important contacts with the dye molecules since inverting its orientation to C-G or replacing it with I-C still led to favorable dimerization of the dye.