Sequence Identification and Structural Mapping of Single DNA and RNA Molecules via Quantum Tunneling Spectroscopy

We present a method that uses scanning tunneling spectroscopy (STS) measurements on DNA and RNA molecules to directly identify the nucleotide sequence as well as to map both secondary structure and epigenetic modifications. The method relies on non-perturbative STS to probe the molecular orbitals of each base,[1] combined with a molecular identification algorithm that uses machine learning to recognize unique electronic fingerprints of the bases and their modifications.[2] Structural mapping of RNA at the single molecule level can be achieved using conformation-dependent chemical labeling followed by mapping of the labels via STS. We further describe the use of a ‘smear parameter’ to quantify the extent of smearing out of the nucleotide orbitals due to entropic factors, and we show how these effects can be mitigated through engineered surface chemistry to reduce conformational entropy, which plays an important role in molecular recognition.[3] This paves the way for probing the genome and transcriptome with a previously unattainable level of detail.

[1] Ribot, JC; Chatterjee, A & Nagpal, P. J. Phys. Chem. B 2015, 119, 4968.
[2] Korshoj, LE; Afsari, S; Khan, S, et al. Small 2017, 13, 1603033.
[3] Korshoj, LE; Afsari, S; Chatterjee, A, et al. J. Am. Chem. Soc. 2017, 139, 15420.