Indodicarbocyanine phosphoramidites with bathochromically shifted absorption and emission, and tunable hydrophobicity

Abstract

New phosphoramidite Cy5 derivatives can be used in automated DNA synthesis, allowing the labeling of DNA sequences with a wider array of chromophores than are presently commercially available. In addition to varying dye hydrophobicity/hydrophilicity, the 5,5′-substituents (including hexyloxy, triethyleneglycol monomethyl ether, tert-butyl, and chloro groups) can modulate electron donating/withdrawing character while also tuning resulting absorption and emission properties. Modification of the Cy5 periphery enables the tuning of photophysical properties, such as absorption and emission maxima, fluorescence quantum yield, and fluorescence lifetime.

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