Synthetic route to novel zwitterionic pentamethine indocyanine fluorophores with various substitutions

Abstract Two series of novel zwitterionic water-soluble pentamethine cyanine dyes with geometrically balanced structures were synthesized and characterized. One series of cyanine dyes is the «zwitterionic» fluorophores, which contain positively charged trimethylammonioalkyl and negatively charged sulfonate groups. The second series of cyanine dyes contains a sulfonate group on one indolenine nucleus and a carboxyl group linked through an N- acylsulfonamide bond on the other indolenine nucleus. Dye-modified deoxyuridine triphosphates were synthesized and evaluated as reagents for nucleic acid labeling using PCR with Taq DNA-polymerase. The efficiency of the incorporation of labeled nucleotides was investigated via real-time PCR and using a «KRAS-Biochip» commercial testing system.