Inosine incorporation in DNA nanostructures and 3D DNA crystals
Abstract
DNA nanotechnology is based on programmable base pairing, resulting in the precise construction of nanoscale structures. Sequence variability in DNA nanostructure self-assembly is achieved by the use of xeno nucleic acids, chemically modified bases and base analogs. The naturally occurring base inosine, while well studied in RNA editing, has not been used in the context of DNA nanotechnology. In this work, I demonstrate the use of inosine in DNA nanostructures, specifically by incorporating inosine within the duplex regions or junctions of a double crossover DNA motif. In strand displacement and competition assays, I show that canonical complements do not displace inosine containing strands post-assembly but dominate in product formation when competing with inosine containing strands during assembly. Finally, sticky ends with inosine base pairs enable the formation of rationally designed 3D DNA crystals based on the tensegrity triangle motif. Overall, this work shows that inosine is a useful addition to the library of sequence variations in DNA nanotechnology.
Full-text reasoning
From the deep-tier full-text analysis of this preprint.
Reasoning review — 6 key claims, 3 well-supported, 3 with gaps
- supported Inosine can be incorporated into DNA nanostructures (DX motif) with proper assembly.
- supported Inosine incorporation in DX motifs leads to a minimal decrease in thermal stability.
- supported Inosine-containing sticky ends enable hierarchical self-assembly of 3D DNA crystals.
- unsupported Canonical complements do not displace inosine-containing strands post-assembly. gap: No data or methodology for this specific finding from strand displacement assays is presented in the excerpt.
- unsupported Canonical complements dominate product formation when competing with inosine-containing strands during assembly. gap: No data or methodology for this specific finding from competition assays is presented in the excerpt.
- partial Inosine is a useful addition to the library of sequence variations in DNA nanotechnology. gap: This overarching claim is partially supported by successful incorporation and crystal formation, but weakened by the lack of evidence for the strand displacement and competition assay claims.
Claims and gaps are read from the full text by a language model, shown for transparency; they do not affect ranking or selection.
Lifecycle
- biorxiv v1 2026-06-07 source ↗
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