Denaturation of DNA by Potassium Hydroxide

A lambda digest DNA sample was prepared for AFM imaging using a typical preparation where the DNA solution (1 μg/µL λDNA in 10 mM NiCl₂) is allowed to adsorb to a freshly cleaved mica disc. The sample was loaded in the Cypher VRS and prepared for imaging. Then a 100 mM potassium hydroxide solution was introduced, which was expected to denature the DNA (i.e. unravel the DNA double-helix, forming single stranded DNA). Video-rate AFM imaging immediately commenced using an Asylum Research Cypher VRS atomic force microscope, scanning at 625 lines per second with an Olympus AC10 probe at a scan size of 160 nm with 448 points per line and 52 lines, for an effective frame rate of 9.19 frames/second. The video plays back here in real-time (i.e. 1× the acquisition rate).

Initial image frames show the expected intact DNA structure, but finer strands corresponding to single-strand DNA quickly appear, oftentimes appearing to remain connected to the original DNA strand.

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