The different DNA building block topologies include linear, circular, and branched DNA (bDNA). Complex molecular design has led to the production of various functional nanomaterials incorporating the significant properties of bDNA. In our study, we demonstrate two different methods for topology sampling of bDNA in modeling. The first method consists of sampling Ralstonia solanacearum cells and culturing them in a nutrient medium. The propagated cells are then stored from which their DNA is collected, and sequenced to form Y and X-shaped bDNA. The second method only took an in-silico approach where we formed branches Y and X of DNA in 3D mode using bioinformatics retainer databases. A set of sequences designed by software comprising Maya, bio-blender, and discovery studio (DS) software that can produce 3D models. These models will help us in the laboratory to carry out a precise laboratory simulation to detect bDNA design which can be useful in diagnostics. Although the first trial was unsuccessful, the use of a software simulation in a second trial was the most successful and yielded several 3D models of bDNA, which could be used in the laboratory simulation of molecular diagnostic strains that express genes. These models were used in molecular diagnostic assays which are sensitive, specific, and reliable tools in the detection of virulence genes of some diseases such as fusarium oxysporum, phytphthora fragariae, and botrytis cinerea. This platform not only offers a means for screening the potential activity of molecular diagnostics but also presents opportunities for time and cost savings.