Summary
A bioRxiv preprint describes ModDNA, a sequence-design and cloning toolkit for building custom DNA molecules up to 100 kilobases. The researchers used the constructs in single-molecule visualisation assays, including an assay of DNA loop extrusion by human condensin I.
Researchers at Delft University of Technology and the Netherlands Cancer Institute describe ModDNA, a toolkit for designing and assembling customised DNA molecules up to 100 kilobases. The bioRxiv preprint, posted on October 10, 2026, reports that the team used the constructs in single-molecule visualisation assays, including one involving DNA loop extrusion by human condensin I.
How ModDNA builds custom DNA
Single-molecule biophysics experiments often use long DNA molecules as a substrate for observing molecular processes. The authors note that many studies rely on the λ-phage genome, which has a fixed sequence, an uneven distribution of GC bases and limited options for modification. Those constraints can make it difficult to place chosen features at specific positions in the DNA.
ModDNA combines computational sequence design with cloning. The researchers used curated databases in a workflow to design a motif-depleted DNA backbone, then inserted sequences selected by the user at specified positions. Golden Gate assembly—a method for joining DNA fragments—was used to build the constructs, which the team extended iteratively in defined increments to lengths of up to 100 kilobases.
The authors report precise placement of local features, including a fluorophore, a bound protein and a DNA-origami structure. This makes the DNA substrate itself more configurable: researchers can position features within a long molecule rather than relying only on the sequence and modification options available in a standard genome.
Demonstrations in single-molecule assays
The team used ModDNA constructs in visualisation assays, including experiments involving loop extrusion by human condensin I. In a loop-extrusion assay, researchers observe a protein-driven process that forms or enlarges a loop in DNA. The reported demonstration shows the toolkit being used in an experimental setting as well as for assembling designed DNA.
The work presents ModDNA as a sequence-programmable alternative to λ-DNA and other restrictive substrates. More broadly, having control over sequence context and feature placement could help researchers design experiments around specific molecular arrangements. The findings are reported as a bioRxiv preprint.