Comparative Behavior Analysis of Cy5-Pyrimidine Nucleotides in the Rolling Circle Amplification

Two pairs of Cy-5-labeled dU and dC triphosphates with similar electroneutral fluorophore structures differing in the length of the hydrocarbon linker between the fluorophore and the nitrogenous base were synthesized. A comparative analysis of their substrate behavior in the rolling circle amplification (RCA) using Bst 3.0 DNA polymerase was carried out. It was found that nucleotides with a long linker between the fluorophore and pyrimidine base are more efficiently incorporated into the growing DNA chain, while nucleotides with a short linker inhibit RCA less. In each of the dU and dC pairs with similar fluorophores and linkers, fluorescently labeled uridine derivatives demonstrated a high embedding density. It was found that with simultaneous incorporation of labeled dU and dC, the inhibitory effect does not summarise. This gives grounds for a more careful study of various Cy5-dC variants in order to increase a sensitivity of the analysis with simultaneous introduction of labeled dU and dC.