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

Abstract

SummaryThe Nile Blue chromophore was incorporated into oligonucleotides using “click” chemistry for the postsynthetic modification of oligonucleotides. These were synthesized using DNA building block 3 bearing an alkyne group and reacted with the azide 4. (R)-3-amino-1,2-propanediol was applied as the linker between the phosphodiester bridges. Two sets of DNA duplexes were prepared. One set carried the chromophore in an A-T environment, the second set in a G-C environment. Both were characterized by optical spectroscopy. Sequence-dependent fluorescence quenching was applied as a sensitive tool to compare the stacking interactions with respect to the chirality of the acyclic linker attachment. The results were compared to recent results from duplexes that carried the Nile Blue label in a sequentially and structurally identical context, except for the opposite chirality of the linker ((S)-3-amino-1,2-propandiol). Only minor, negligible differences were observed. Melting temperatures, UV–vis absorption spectra together with fluorescence quenching data indicate that Nile Blue stacks perfectly between the adjacent base pairs regardless of whether it has been attached via an S- or R-configured linker. This result was supported by geometrically optimized DNA models.

DNA and RNA “Traffic Lights”: Synthetic Wavelength-Shifting Fluorescent Probes Based on Nucleic Acid Base Substitutes for Molecular Imaging

“…(ii) How important is the S -configuration of the linker? Fluorescence quenching studies with nile blue revealed that the interactions between the fluorophore and the adjacent base pairs seem to be similar with the S - and R -configurated linker …”

Hybridization-Sensitive Fluorescent Probes for DNA and RNA by a Modular “Click” Approach

“…In former work, we already showed that 2′-deoxyribofuranoside can be replaced by a clickable acyclic linker 31 using both enantiomers. 32 Glycol is the smallest possible connection between the phosphodiester bridges as evidenced by the glycol nucleic acids (GNAs). 33 To place the dyes into the DNA base stack, we designed the clickable components 1 with the (S)configuration and 2 with the (R)-configuration at the central carbon atom.…”

Copper‐Free Postsynthetic Labeling of Nucleic Acids by Means of Bioorthogonal Reactions

“…As alternatives to natural‐like nucleosides, acyclic nucleoside substitutes—containing, for example, 3‐aminopropane‐1,2‐diol as an acyclic linker between the phosphodiester units and the propargyl group for the click‐type reactivity attached through a carbamate function—have also been applied 19. The S configuration of the linker in 4 was chosen in analogy to the chirality of position 3′ in the 2′‐deoxyribofuranoside moiety of a natural nucleoside; however, the R configuration (building block 5 ) could also be applied 22…”