Mesoscopic modelling of Cy3 and Cy5 dyes attached to DNA duplexes

•Cy3 and Cy5 attached to DNA can be modelled as if they were ordinary base pairs with mesoscopic models.•The interaction potentials of Cy3 and Cy5 are very similar to that of AT and CG base pairs.•Cy3-A was found to be the most rigidly stacked.•Cyanines appear to stabilize the AT hydrogen bonds, but CG is not affected.

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.

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