Converting Multiple- to Single-DNA-Tethered Beads and Removing Only-One-End-Tethered DNA in High-Throughput Stretching

Abstract

S-DNA is a double-stranded DNA that forms under tensions of >65 pN. Here, we report that S-DNA resists the cleavage of Cas12a and the restriction endonuclease SmaI. Taking advantage of this resistance, in magnetic tweezer experiments, we developed an assay to convert multiple-DNA-tethered beads into single-DNA-tethered beads and remove the only-one-end-tethered DNA molecule by cleaving the DNA that does not transition to S-DNA at about 80 pN. When multiple DNA molecules are tethered to a single bead, they share the tension, exist in the B-form, and allow the cleavage. Only-one-end-tethered DNA molecules, free of tension, are also cleaved. In versatile types of experiments, we proved the broad applications of this assay: measuring the correct DNA elasticity and DNA condensation dynamics by avoiding the false results due to interference of only-one-end-tethered DNA molecules and quantifying the accurate cleavage rates of Cas12a and the restriction endonucleases by eliminating the error caused by multiple-DNA-tethered beads. This convenient assay ensures correct and accurate results in high-throughput DNA stretching experiments.