Seminar: Dr. Wooli Bae

SEMINAR INFORMATION

Title: Rapid DNA four-way branch migration by introducing a bulge in toehold

Speaker: Wooli Bae

DNA nanotechnology enabled construction of nanostructures and reaction circuits made of DNA. Dynamic DNA nanotechnology aims building composable molecular reaction circuits made of DNA. The core molecular reaction for dynamic DNA nanotechnology is DNA strand exchange reaction. While most of the current DNA circuits use three-way branch migration, the alternative of four-way branch migration has the advantage of using two input toeholds for double recognition and having less crosstalk from single-stranded species. However, four-way branch migration is slower than three-way branch migration as the migration of the junction requires simultaneous opening of two base pairs in different arms of the junction while the opening of a single base pair is sufficient in three-way branch migration.

Here, we introduce a bulge at the DNA junction to change the molecular mechanism of four-way branch migration so that the opening of a single base pair is sufficient to induce migration of the branches by a half base pair. We show that the introduction of a bulge accelerates the DNA strand exchange reaction. Introduction of two bulges also accelerates the DNA strand exchange reaction, decreasing the stepping time by 100-fold, making it similar to the stepping time of a three-way branch migration. Therefore, our method opens up the possibility of constructing composable four-way branch migration-based DNA circuits that rival the speed of their three-way branch migration counterparts.