Motor enzymes that interact with DNA are essential for replicative biological processes. In nanopore sequencing, a motor enzyme controls the motion of a nucleic acid through a protein nanopore, and sequence-dependent blockages of an ion current flowing through the nanopore are used to decode the DNA sequence. The kinetics of these enzymes are sequence-dependent and can serve as an additional source of information during sequencing. Here, we use Mutual Information (MI) to quantify the sequence-dependent kinetics of a Hel308 helicase during nanopore sequencing. We use MI to identify sites in Hel308 that are responsible for sequence-dependent kinetics and develop “k-mer” models of Hel308 kinetics that map kinetics to DNA sequence. We estimate that enzyme kinetics can improve nanopore sequencing accuracy by ~5-fold at high sequencing depth. We mutate Hel308 to identify amino acids involved in DNA translocation and suggest pathways for engineering molecular motors with enhanced responsiveness to DNA sequence. Motor enzymes that translocate DNA are an essential element of nanopore sequencing. Here, authors use mutual information to quantify the sequence-dependence of helicase kinetics and show that such kinetics can be used to improve the sequencing accuracy of all standard DNA bases.
Craig et al. (Thu,) studied this question.