Koch Lab:Protocols/Unzipping constructs

Principle

If DNA is attached to a surface (e.g. a coverglass) at one end and to another surface (e.g. a microsphere) in the middle, the DNA can be unzipped if there is a nick between the two attachments. This was first shown by Bockelmann, Essevaz-Roulet, and Heslot in the mid-1990s (PMID 9342340). Compared to DNA constructs for end-to-end DNA stretching (see, e.g. labeling DNA by PCR unzipping constructs are more challenging to produce. The method we describe here has a significant stretch of double-stranded DNA (dsDNA) between the first and second attachment labels (dig and biotin). A simpler construct can be made by directly hybridizing two end-labeled DNA oligos, producing a force construct. (See, e.g. Koch_Lab:Protocols/Fork unzipping constructs.)