Bioorthogonal labeling methods represent an important tool for the visualization and subsequent tracking of biomolecules within living systems. Commonly used chemical reporters are cyclopropene derivatives, which can undergo Photoclick as well as inverse electron-demand Diels-Alder reactions. By differing the position of a single methyl substituent at the cyclopropene ring it is also possible to create an orthogonality between these two reactions and thereby enable the dual bioorthogonal labeling of two different biomolecules using two isomeric cyclopropenes. This work aims to transfer this system, which so far has only been used for the labeling of proteins, to an application for nucleic acids.