Nanopore translocation reveals electrophoretic force on A- and B- form nucleic acids

Abstract

ABSTRACTElectrophoretic transport plays a pivotal role in advancing sensing technologies, with A-form nucleic acids, predominantly RNA-containing, emerging as the new frontier for nanopore sensing and sequencing. Here, we compare the less-explored dynamics of A-form electrophoretic transport with the well-researched transport of B-form DNA. Using DNA/RNA nanotechnology and solid-state nanopores, the translocation of RNA:DNA (RD) and DNA:DNA (DD) duplexes was examined. Notably, RD duplexes were found to translocate through nanopores up to 1.8 times faster than DD duplexes, despite containing the same number of base pairs. Our experiments reveal that A- and B-form duplex molecules with the same contour length move with comparable velocity through nanopores. We examined the physical characteristics of both duplex forms using atomic force microscopy, agarose gel electrophoresis, and dynamic light scattering measurements. With the help of coarse-grained and atomistic molecular dynamics simulations, we find the effective force applied by the electric field to a fragment of A-form or B-form duplex in a nanopore to be approximately the same. Our results shed light on the significance of helical form in nucleic acid translocation, with implications for RNA sensing, sequencing, and molecular understanding of electrophoretic transport.