Synthesis of DNA with Green Perylene Bisimides as DNA Base Substitutions

Abstract

Abstract Perylene‐3,4:9,10‐tetracarboxylic acid bisimide represents a particularly attractive building block for DNA‐based multichromophores and nanoassemblies due to its unique combination of optical and electronic properties. Despite the broad applicability of the perylene bisimide dye for DNA‐based assemblies, significant fluorescence quenching by photoinduced charge‐transfer processes to guanines in DNA represents a major disadvantage. In order to develop a redox actively and optically tuned perylene bisimide derivative with fluorescence that does not photooxidize guanines in DNA, we chose to attach two N ‐pyrrolidinyl substituents as strongly electron‐donating substituents at the 1‐ and 7‐positions of the bay area (“APBI”). The corresponding phosphoramidite 1 was synthesized and incorporated synthetically into oligonucleotides by using the automated DNA building block chemistry. The 2′‐deoxyribofuranoside of natural nucleosides was replaced by ( S )‐1‐aminopropane‐2,3‐diol as an acyclic linker between the phosphodiester bridges that is tethered to one of the imide nitrogen atoms of the APBI dye. Electrochemical and optical characterization of the isolated APBI dye shows that photoinduced charge transfer with guanines is indeed very unlikely. Single APBI DNA base substitutions show an exciplex‐type emission with pH sensitivity. The interstrand APBI dimer in DNA could be regarded as a hydrophobically interacting base pair that stabilizes the thermal stability of the double strand. The APBI dimer behaves like an H aggregate, and the fluorescence is quenched quantitatively.