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Introduction

As our project revolved around functional nucleic acids we had to face the challenge of visualizing short ssRNAs and ssDNAs. When testing the activity of our designed ribozymes or DNAzymes it was especially important for us to distinguish between reacted and unreacted equivalents even if their sizes were very similar. Most scientists choose a radioactive labeling technique to visualize little amounts of RNA or DNA. We wanted to develop new approaches to give scientists the possibility to detect little amounts of nucleic acids without the necessity to employ radioactive isotopes. On the one hand we decided to use copper-catalyzed azide-alkyne cycloaddition to specifically label RNA or DNA with fluorophores as described in winz2012. On the other hand we came up with the idea of using the HRP-mimicking DNAzymetravascio1998 connecting it to our DNA or RNA of interest to make it visible on a Southern/Northern blot.