A rule of seven in Watson-Crick base pairing of mismatched sequences

Sequence recognition through base pairing is essential for DNA repair and gene regulation but the basic rules governing this process remain elusive. In particular, the kinetics of annealing between two imperfectly matched strands is not well characterized despite its potential importance in nucleic acids-based biotechnologies and gene silencing. Here we use single molecule fluorescence to visualize the multiple annealing and melting reactions of two untethered strands inside a porous vesicle, allowing us to quantify precisely the annealing and melting rates. The data as a function of mismatch position suggest that seven contiguous base pairs are needed for rapid annealing of DNA and RNA. This phenomenological rule of seven may underlie the requirement of seven nucleotides complementarity to seed gene silencing by small non-coding RNA and may help guide performance improvement in DNA and RNA-based bio- and nano-technologies where off-target effects can be detrimental.