Miranda Pâmella, Oliveira Luciana M, Weber Gerald
Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte-MG 31270-901, Brazil.
Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte-MG 31270-901, Brazil.
Biophys Chem. 2017 Nov;230:62-67. doi: 10.1016/j.bpc.2017.08.007. Epub 2017 Sep 27.
Cy3 and Cy5 dyes linked to the 5' end of a double stranded DNA molecule are known to attach to both strands in a way that is very similar to an additional base pair and has a stabilizing effect on the oligonucleotide. Here we adapt the Peyrard-Bishop mesoscopic model to incorporate cyanine dyes and use the technique of thermal equivalence to obtain the appropriate parameters from existing melting temperatures. We have found that the stacking parameters are in the same range of ordinary AT and CG base pairs, in particular Cy3-A was found to be most rigidly stacked. While the cyanines stabilize the AT hydrogen bonds quite strongly the CG bonds are mostly unaffected.
已知连接到双链DNA分子5'端的Cy3和Cy5染料会以一种与额外碱基对非常相似的方式附着在两条链上，并且对寡核苷酸具有稳定作用。在这里，我们采用佩拉尔 - 毕晓普介观模型来纳入花青染料，并使用热等效技术从现有的解链温度中获取合适的参数。我们发现堆积参数与普通的AT和CG碱基对处于相同范围内，特别是发现Cy3 - A堆积最为紧密。虽然花青染料相当强烈地稳定了AT氢键，但CG键大多不受影响。
