The ability to create nanoscaffolds within living cells using DNA has the potential to become a powerful tool in synthetic biology. However, to date, genetically encoded DNA nanostructures are limited to simple architecture due to the lack of genetic parts that can produce multiple ssDNAs in a single bacterium. Here, we develop a system that overcomes this challenge by using a single oligo gene mimicking operons. This was achieved by converting a noncoding RNA into a long ssDNA that self-cleaves into multiple ssDNAs using R3-DNAzymes (DNAzyme-based operon). We demonstrate the ability to apply the DNAzyme-based operon to produce a four-ssDNA crossover nanostructure (25 nm) that recruits split YFPs when properly assembled. This system enables the formation of more complex DNA nanostructures in vivo and thus paves the way to further integrate the field of DNA nanotechnology into living bacteria for basic biology, bioengineering, and medicine applications.