花菁染料与DNA同源四链体及肽核酸- DNA异源四链体结构的非共价结合和荧光响应。
Noncovalent binding and fluorogenic response of cyanine dyes to DNA homoquadruplex and PNA-DNA heteroquadruplex structures.
作者信息
Mohammed Halimatu S, Delos Santos Junriz O, Armitage Bruce A
机构信息
Department of Chemistry and Center for Nucleic Acids Science and Technology; Carnegie Mellon University; Pittsburgh, PA USA.
出版信息
Artif DNA PNA XNA. 2011 Apr;2(2):43-49. doi: 10.4161/adna.2.2.16339.
Abstract
Two symmetrical cyanine dyes based on benzothiazole heterocycles and a trimethine bridge were found to bind to a parallel-stranded DNA guanine quadruplex based on the MYC oncogene promoter sequence with high nanomolar affinity and 1:1 stoichiometry. The dyes exhibited substantial fluorescence enhancements upon binding. In the presence of homologous guanine-rich peptide nucleic acid oligomers, PNA-DNA heteroquadruplexes were formed. The dyes retained their ability to bind to the heteroquadruplexes at low micromolar concentrations and with varying fluorescence enhancements, although indeterminate stoichiometries preclude quantitative comparison of the affinities with the DNA homoquadruplex precursor. The difference in fluorescence enhancement between DNA homoquadruplex and PNA-DNA heteroquadruplex allows the dyes to be used as fluorogenic indicators of hybridization in a facile method for determining PNA-DNA stoichiometry.
摘要
基于苯并噻唑杂环和三甲川桥的两种对称花青染料被发现能以高纳摩尔亲和力和1:1化学计量比与基于MYC癌基因启动子序列的平行链DNA鸟嘌呤四链体结合。染料结合后荧光显著增强。在富含鸟嘌呤的同源肽核酸寡聚物存在下，形成了PNA-DNA异源四链体。尽管不确定的化学计量比妨碍了与DNA同源四链体前体亲和力的定量比较，但染料在低微摩尔浓度下仍保留了与异源四链体结合的能力，且荧光增强程度各异。DNA同源四链体和PNA-DNA异源四链体之间荧光增强的差异使得这些染料能够作为杂交的荧光指示剂，用于一种简便的方法来确定PNA-DNA的化学计量比。
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J Fluoresc. 2011 Jan;21(1):223-30. doi: 10.1007/s10895-010-0709-y. Epub 2010 Sep 1.
2
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3
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4
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