Site-specific one-pot triple click labeling for DNA and RNA

Abstract

We report site-specific triple click labeling for DNA and RNA in a one-pot setup by performing inverse electron demand Diels–Alder reaction and strain-promoted and copper catalyzed click reactions sequentially.

Covalent labeling of nucleic acids

“…This triple labeling can be used to study the dynamics of nucleic acid structures during folding and the population of multiple folding states using FRET. 102…”

“…With this approach, it was possible to triple label, for instance, the preQ1 riboswitch RNA, rendering this strategy applicable for folding and dynamic studies. 102 For RNA labeling, the polymerase-based approaches are, in principle, similar to the DNA-labeling approaches, but based on in vitro transcription with a DNA-dependent RNA polymerase, such as T7. In 2014, a cytidine triphosphate analog bearing a trans-cyclooctene at the 5-position (CTP tco ) was synthesized and incorporated into RNA by T7 RNA polymerase (Fig.…”

Synthesis, Structural, and Conformational Analysis of 4′‐C‐Alkyl‐2′‐O‐Ethyl‐Uridine Modified Nucleosides

“…Also, dual modifications at 2′‐ and 4′‐ sugar positions such as 4′‐ C ‐aminomethyl‐2′‐ O ‐methyl (4′‐AM‐2′‐OMe), 4′‐ C ‐aminoethyl‐2′‐ O ‐methyl (4′‐AMEt‐2′‐OMe), and 4′‐ C ‐aminopropyl‐2′‐ O ‐methyl (4′‐AMPr‐2′‐OMe) analogs have adopted C2′‐ endo (South , DNA ‐type) sugar conformation [21,22] . In contrast, other bi‐functional sugar modifications such as 4′‐ C ‐aminomethyl‐2′‐deoxy‐2′‐fluoro (4′‐AM‐2′‐F), 4′‐ C ‐aminoethyl‐2′‐deoxy‐2′‐fluoro (4′‐AMEt‐2′‐F), 2′,4′‐diF, 2′‐OMe‐4′‐F, 2′‐F‐4′‐OMe, 2′,4′‐diOMe, 2′‐F‐4′‐OMe‐araU, 2′,4′‐diF‐araU tuned the sugar conformation predominantly toward C3′‐ endo ( North , RNA ‐type), which has been attributed to the small size, high electronegativity of fluorine, and additional C−H⋅⋅⋅F interactions [23–30] . From the above observations, it is clear that 2′ and 4′‐ modifications can alter the sugar conformation, structural stability, and functional role of the duplex.…”

The Sulfo‐Click Reaction and Dual Labeling of Nucleosides

“…For this purpose orthogonal reactions are required. Although several examples of multiple labeling of nucleic acids have been described in the literature (Meyer et al., 2010; Reisacher et al., 2019; Schoch, Staudt, Samanta, Wiessler, & Jäschke, 2012; Winz, Linder, Becker, & Jäschke, 2018), new orthogonal click reactions are needed to expand the potential of multiple labeling strategies. The sulfo‐click reaction is an emergent alternative click reaction which involves a thioacid and a sulfonyl azide.…”