DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single- or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarse-grained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic-inorganic nanomaterials.