3′ Exonuclease-mediated DNA assembly at room temperature and below

DNA assembly is a cornerstone of synthetic biology, enabling the construction of bespoke genetic systems for applications ranging from metabolic engineering to DNA nanotechnology. Conventional Gibson Assembly (GA), the most widely used method, relies on 5′ exonucleolytic resection and elevated temperatures (∼50 °C), which together prevent the retention of 5′ modifications and restrict compatibility with temperature-sensitive functionalities.

Here, we report a DNA assembly strategy, 3’ exonuclease-mediated low-temperature DNA assembly (3LTDA), which generates complementary 5′ overhangs while preserving 5′ end integrity. This approach enables the efficient assembly of blunt-ended, 5′-functionalised DNA fragments into both linear and circular constructs at ambient temperature (21 °C), with some assembly observed at temperatures as low as 4°C. We systematically optimise reaction conditions and demonstrate that this method supports efficient plasmid re-circularisation and multi-fragment assembly, including the construction of a ∼12.5 kbp plasmid from multiple DNA components. Comparative analysis across several DNA substrates shows that, under their respective optimal conditions, this approach matches or exceeds GA performance, improving assembly efficiency by up to 12.8%. Sequence analysis confirms high fidelity with no detectable base-pairing errors across assembled junctions.

Crucially, this method preserves chemically functionalised 5′ termini, enabling downstream conjugation and biochemical functionality. Retention of azide and biotin modifications was verified through fluorescence imaging, bead-based co-localisation, and enzymatic activity in ELISA-based assays. This is in contrast to GA-assembled controls, which showed complete loss of functionality under comparable conditions. We further assembled 5 kbp dsDNA using 3LTDA from four independent segments, three with different fluorescence reporters, and the fourth containing a biotin group for microparticle conjugation, each on the 5’ end. Under fluorescence illumination, bead-bound DNA with all three fluorescence markers were detected. Conventional GA assembled constructs, on the other hand, failed to retain the reporter groups and the fluorescent images did not show the presence of any fluorescent markers.

In addition to enhanced performance, the method could also reduce reagent cost and eliminate the need for elevated temperatures, simplifying workflows and expanding the applicability of multi-functionalised DNA constructs. Collectively, this work establishes 3LTDA as a robust, low-temperature alternative to conventional GA, with advantages for applications requiring precise chemical modification, temperature-sensitive components, or deployment outside conventional laboratory environments.