Effect of PNA Backbone Modifications on Cyanine Dye Binding to PNA−DNA Duplexes Investigated by Optical Spectroscopy and Molecular Dynamics Simulations
作者:Isil Dilek、Marcela Madrid、Rojendra Singh、Christian P. Urrea、Bruce A. Armitage
DOI:10.1021/ja045145a
日期:2005.3.1
used to study the interaction between a cationic cyanine dye and peptide nucleic acid (PNA)-DNA duplexes. This recognition event is important because it leads to a visible color change, signaling successful hybridization of PNA with a complementary DNA strand. We previously proposed that the dye recognized the minor groove of the duplex, using it as a template for the assembly of a helical aggregate
光谱学和分子动力学模拟已被用于研究阳离子花青染料和肽核酸 (PNA)-DNA 双链体之间的相互作用。这种识别事件很重要,因为它会导致可见的颜色变化,表明 PNA 与互补 DNA 链成功杂交。我们之前提出染料识别双链体的小沟,将其用作组装螺旋聚集体的模板。与此一致,我们现在报告说,当取代基突出到小沟中时,向 PNA 主链添加异丁基会阻碍染料的聚集,但如果被引导出小沟,则效果较弱。紫外-可见光和圆二向色光谱用于比较不同 PNA-DNA 双链体上的聚集,而分子动力学模拟用于确认取代基在不同程度上阻断了小沟,这取决于起始氨基酸的构型。除了取代基的简单空间阻断效应外,模拟表明,将异丁基基团引入小沟会导致沟变窄,双链体变得更加刚性,结构扰动与对骨架修饰的兴趣日益增长有关PNA 在生物和材料科学中的应用。