• Design of a neuron- inspierd DNA walker for use in molecular genetics researches
  • Hossein Aftabi,1,* Hadi Ravan,2 Nasrollah Saleh- Gohari,3
    1. Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Iran
    2. Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Iran
    3. Department of Medical Genetics, Faculty of Medicine, University of Medical Sciences, Kerman, Iran


  • Introduction: Introduction: DNA walkers are advanced biological nanomachines include precise and programmable architectures in single- pedal, bipedal, and multi- pedal forms. By exploiting one, two and three-dimensional pathways, they provide remarkable adaptability for diverse applications. Powered by strand displacement, enzymatic, chemical, and photonic reactions, DNA walkers achieve highly precise nanoscale movements and play a key role in next-generation biosensor development, enabling early disease diagnosis and biomolecule detection.
  • Methods: Methods: In this study, a DNA walker was designed and analyzed using both manual and bioinformatics-based approaches with NUPACK software, focusing on the formation and optimization of toehold-mediated strand displacement (TMSD) reactions. Structural validation was performed through electrophoresis and colorimetric methods.
  • Results: Results: Electrophoretic analysis revealed that single strands, due to their lighter nature, migrate rapidly through the gel without leaving a trace, while heavier double strands remain visible at the gel’s end. The bands corresponding to tracks with and without input strands (positive and negative controls, respectively) were clearly identified, with the input-free track positioned slightly higher than the input-containing track due to its greater weight. To optimize the performance parameters, critical factors including TMSD reaction time, Hemin concentration, glycerol volume, and strand concentrations were systematically evaluated. Optimal performance was achieved at 90 minutes, with strand concentration of 0.8 μM Hemin and 2 μM. On surface-based assays, using glycerol as the substrate, the strongest colorimetric signal was observed after 4 hours with 30 μL volume and with strand concentration of 0.5 μM Hemin, and 2 μM. In the presence of input (positive control), successful walking occurred, leading to DNAzyme formation and subsequent color signal generation, whereas in the absence of input (negative control), no walking and no signal were detected.
  • Conclusion: Conclusion: These findings demonstrate the successful design and validation of a DNA walker capable of efficient toehold-mediated strand displacement. The optimized system shows strong potential for application in biosensing and molecular diagnostics.
  • Keywords: DNA walker, Strand displacement, DNA nanotechnology, Nucleic acid circuit