Numerical Studies of 3-mer Oligo Hybridization on an ssDNA Molecule

In the proposed nanopore DNA sequencing, the 4th generation polymerase-free DNA sequencing technology, a key question is whether one can discriminate DNA bases using short, 3-mer, oligonucleotides hybridization. In this numerical study, we employed the molecular dynamics (MD) method to investigate the stability of trimers hybridized on an ssDNA molecule. For a trimer with fully matched Watson-Crick base-pairing with the host ssDNA, we found that the hybridization was stable during the entire simulation time (hundreds of nanoseconds). Thus the actual residence time (or dwell time) for such pairs should be much longer. However, with a single mismatched base-pair, the tested trimer could diffuse away from the hybridization site on the ssDNA within one nano-second. To estimate the residence time of a fully matched trimer bound on the ssDNA, we applied pulling/biasing forces F on the trimer to facilitate its unbinding with the ssDNA. Using the Bell theory, we can numerically calculate the residence time (when F=0) for a trimer on its hybridization site. We expect that these results, providing temporal constraints on the nanopore-based DNA sequencing, will lead to a more optimized design for the nanopore sequencing platform.