State of the Art Review

Naveen Kumar (JR3) | University of Leipzig | Supervisor: Prof. Ralf Seidel

State of the Art Prior to DYNAMO (2022)

DNA Origami as a Platform for Hybrid Nanostructures

By 2022, DNA origami had matured into a versatile three-dimensional construction platform with sub-nanometre positional precision[cite: 41]. At Leipzig, Seidel and co-workers had pioneered DNA origami molds for shape-controlled metallic nanoparticle synthesis — casting gold nanorods inside tubular cavities (Helmi et al., 2014) and developing a modular construction kit for complex metal nanostructures[cite: 42]. The platform had been extended to palladium nanostructures (Ye et al., 2021)[cite: 43]. DNA origami nanopores had been demonstrated in solid-state platforms and lipid bilayers[cite: 44]. However, the integration of thermal control with these nanostructures — to reversibly gate molecular access or dynamically reconfigure sensing elements — remained unrealised[cite: 45].

DNA Hybridization Kinetics

Equilibrium thermodynamics of DNA duplex formation were well described by the nearest-neighbour model (SantaLucia, 1998), but kinetic parameters — association and dissociation rates — were poorly characterised[cite: 47]. Single-molecule techniques (smFRET, DNA-PAINT) provided dwell-time information for specific systems, but systematic temperature-dependent measurements across diverse sequences were absent[cite: 48]. Whether association rates increased, decreased, or remained constant with temperature was actively debated[cite: 49]. No high-throughput platform existed to measure sequence-specific kon and koff across temperatures simultaneously[cite: 50].

Strand Displacement Dynamics

Toehold-mediated strand displacement (Zhang & Winfree, 2009) had become the standard mechanism for dynamic DNA nanotechnology[cite: 52]. While displacement kinetics had been characterised in bulk at room temperature (Srinivas et al., 2013; Irmisch et al., 2020), the temperature dependence of displacement rate constants and the activation barriers governing strand invasion and branch migration were not systematically characterised[cite: 53]. This gap was critical for designing thermally switchable DNA devices that must operate across a range of temperatures[cite: 54].

Plasmonic Sensing and SERS

Surface-enhanced Raman scattering (SERS) in plasmonic nanostructures had achieved single-molecule sensitivity[cite: 56]. DNA origami provided scaffolds for assembling nanoparticle dimers with defined gap sizes (~2–10 nm), creating electromagnetic hotspots with enhancement factors exceeding 108. However, systematic methods for reproducible analyte positioning and orientation control within hotspots were lacking[cite: 57]. The DNA origami mould technology offered a promising route for casting metal nanostructures with programmable gap geometries, but quantitative integration with thermally switchable DNA elements had not been demonstrated[cite: 58].

Temperature Measurement at the Nanoscale

Fluorescence thermometry using Rhodamine B and other temperature-sensitive dyes had been demonstrated in microfluidic contexts, but integration with TIRF microscopy for surface-temperature calibration during single-molecule experiments was not established[cite: 60]. Sub-diffraction temperature mapping — essential for characterising thermal gradients around plasmonic heaters — remained an unmet challenge[cite: 61].

Selected Output

1. N. Kumar, F. Ricci, R. Seidel, P. Irmisch. "Engineering the temperature response of DNA strand displacement." Nature Communications [Under Review] [cite: 63, 64]
2. N. Kumar, A. Overchenko, A. Sivaraman, C. Bastiaanssen, P. Irmisch, F. Cichos, R. Seidel, C. Joo. "Temperature- and sequence-dependent DNA hybridization kinetics from high-throughput single-molecule measurements." [In Preparation — Nature Chemistry] [cite: 65, 66]
3. N. Kumar et al. "Probing sequence-specific DNA hybridization dynamics using ThermoSPARXS." Biophysical Journal, 125(4), 287a (2026). [cite: 67]
4. S. Banerjee, C. Hadlich, M. Scherf, N. Kumar, R. Seidel, J. Kneipp. "SERS detects site-specific labeling of DNA nanocages via hexynyl modifications." [In Preparation] [cite: 68, 69]
5. N. Kumar, A. Sivaraman, P. Irmisch, D. Renger, C. Joo, R. Seidel. "DNA Origami-Enabled Single-Molecule Ratiometric Thermometry with Nanoscale Spatial Resolution." [In Preparation] [cite: 70, 71]

References

Key references: Rothemund 2006; SantaLucia 1998; Helmi & Seidel 2014; Ye & Seidel 2021; Zhang & Winfree 2009; Srinivas et al. 2013; Irmisch et al. 2020; Kemper & Seidel 2023; Rodriguez-Barea & Seidel 2026; Ghamari et al. 2025; Kanehira et al. 2026; Kumar & Seidel (ThermoSPARXS, in prep). [cite: 72, 73, 74]

This project has received funding from the European Union’s Horizon Europe programme under the Marie Skłodowska-Curie grant agreement No. 101072818. [cite: 75]