Synthetic incorporation of Nile Blue into DNA using 2′-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

• Daniel Lachmann,
• Sina Berndl,
• Otto S. Wolfbeis and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2010, 6, No. 13, doi:10.3762/bjoc.6.13

• was supported by geometrically optimized DNA models. Keywords: cycloaddition; fluorescence; glycol; oligonucleotide; phenoxazinium; phosphoramidite; Introduction Chemical bioanalysis and imaging of nucleic acids require synthetic incorporation of fluorescent DNA probes for an optical readout [1][2

• explore how important the chirality of the 3-amino-1,2-propanediol linker is with respect to the optical properties of an attached fluorophore. We chose Nile Blue as the fluorescent probe for these experiments since the redox properties of this phenoxazinium label exhibit a potential sufficient for

• photooxidizing guanines in the sequential neighborhood [17]. As a result, fluorescence quenching is observed in DNA and it is important to note that we decided to use this property as a sensitive tool to compare the electronic interactions of the phenoxazinium chromophore with the DNA base stack in order to