Single-Molecule Conductance and Conformational Analysis with Engineered Nano-Junctions for Nucleic Acid Sequencing

DNA sequencing on the single-molecule level can be used to study cellular heterogeneity and stochasticity with reduced time, cost, and complexity compared to traditional sequencing methods. However, sample noise and signature overlap due to varying nucleotide conformations prevent accurate sequencing results. We address these issues by engineering nano-junctions for conductance measurements on conformationally constrained single nucleotides within electrostatically bound DNA molecules on a self-assembled cysteamine monolayer. From STM break junctions with biochemical moieties in individual nucleobases, the unique conductance signature of each nucleobase is analyzed with machine learning algorithms [1]. Additionally, conformational variation, or smear, is quantified from the distance over which molecular junctions are maintained during each conductance measurement [2]. We demonstrate >93% accuracy for DNA nucleotide recognition with 20 repeat measurements. These results are a significant improvement over contemporary methods and show the potential for using simple surface modifications and existing biochemical moieties in nucleobases for single-molecule, nanoelectronic nucleotide identification.

[1] Afsari, et al. ACS Nano 2017; [2] Korshoj, et al. JACS 2017