In-Situ ssDNA Isolation from dsDNA Sources as a Streamlined Pathway to DNA Origami Assembly and Testing

Ruiz, E. O.; Neyra, K.; Lopez, D.; Chen, R.-W.; Paramasamy, D.; Bizjak, Q.; Halley, P. D.; Wei, Y.; Sotomayor, M.; Poirier, M. G.; Mathur, D.; Castro, C. E.; Pfeifer, W. G.

doi:10.64898/2026.03.19.709872

bioRxiv · 10.64898/2026.03.19.709872

In-Situ ssDNA Isolation from dsDNA Sources as a Streamlined Pathway to DNA Origami Assembly and Testing

Ruiz, E. O.·Neyra, K.·Lopez, D.·Chen, R.-W.·Paramasamy, D.·Bizjak, Q.·Halley, P. D.·Wei, Y.·Sotomayor, M.·Poirier, M. G.·Mathur, D.·Castro, C. E.·Pfeifer, W. G.

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Abstract

Scaffolded DNA origami has become a valuable nanoscale tool for applications in biomedical and physical sciences. Critical to leveraging the modular and programmable properties of DNA origami nanodevices is access to the scaffold strand, a long single-stranded DNA (ssDNA) of precise length and sequence, which is folded into a compact shape via piecewise base-pairing with many staple strands, short ssDNA oligonucleotides. Current methods to produce and manipulate long ssDNA scaffolds can be costly, time-consuming, and cumbersome. In contrast, methods to produce and manipulate the sequence of double-stranded DNA (dsDNA) are efficient and scalable. Here, we present a method for the rapid isolation of target ssDNA sequences from a variety of dsDNA sources using oligonucleotides as blocking strands that bind continuously to the undesired strand, thereby releasing the target scaffold strand. We report successful ssDNA isolation from linear and supercoiled dsDNAs of various sequences and lengths, ranging from 769 to 15,101 nucleotides. In addition to isolating ssDNA, we demonstrated this approach enables folding of DNA origami directly from dsDNA templates using both blocking and staple strands in a single-pot thermally controlled reaction. Furthermore, we explore multi-scaffold and gene-encoding DNA origami structures, expanding the framework for application-based designs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/709872v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@f7ada7org.highwire.dtl.DTLVardef@a9bab8org.highwire.dtl.DTLVardef@121b695org.highwire.dtl.DTLVardef@5a1dea_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Ruiz, E. O., Neyra, K., Lopez, D., Chen, R.-W., Paramasamy, D., Bizjak, Q., Halley, P. D., Wei, Y., Sotomayor, M., Poirier, M. G., Mathur, D., Castro, C. E., Pfeifer, W. G.. 2026-03-23. In-Situ ssDNA Isolation from dsDNA Sources as a Streamlined Pathway to DNA Origami Assembly and Testing. https://doi.org/10.64898/2026.03.19.709872

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