Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers

• Published in: Science advances Vol. 5; no. 6; p. eaav1697
• Main Authors: Shon, Min Ju, Rah, Sang-Hyun, Yoon, Tae-Young
• Format: Journal Article
• Language: English
• Published: United States American Association for the Advancement of Science 01.06.2019
• Subjects: Base Composition; Biomechanical Phenomena; Biophysics; DNA - chemistry; DNA Methylation; Elasticity; Inverted Repeat Sequences; Magnetic Fields; Nucleic Acid Conformation; Optical Tweezers; SciAdv r-articles; Solutions
• ISSN: 2375-2548; 2375-2548
• DOI: 10.1126/sciadv.aav1697

Submicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under 1 μm is limited. We developed an MT-based method for precise force-extension measurements in the 100-nm regime that enables in situ correction of the error in DNA extension measurement, and normalizes the force variability across beads by exploiting DNA hairpins. The method reduces the lower limit of tractable dsDNA length down to 198 base pairs (bp) (67 nm), an order-of-magnitude improvement compared to conventional tweezing experiments. Applying this method and the finite worm-like chain model we observed an essentially constant persistence length across the chain lengths studied (198 bp to 10 kbp), which steeply depended on GC content and methylation. This finding suggests a potential sequence-dependent mechanism for short-DNA elasticity.