The effects of pore geometry for DNA entering and clogging nanopore

Solid state nanopores have a capability to detect single DNA molecules with sub-molecule resolution. However, long chain DNA molecules frequently clog at a pore although DNA enters individually. The clogging probabilities exceed 0.3 for lambda DNA (48.5kbp) and 0.7 for T4 DNA (166kbp). We have investigated a cause of such clogging enhanced by electroosmosis by DNA itself since negatively charged DNA attracts positive ions as well as pore wall, which generates counterflow for DNA translocation. Focused ion beams were used on SiN (200 nm) thin films to create nanopores. Fluorescently stained DNA molecules were directly observed by using an optical microscope. To reduce such counterflow, we have tested nanopores with various shapes with the diameter from 100 to 500 nm. We found a pore with sharp corners rather than circular reduced clogging probabilities for both lambda DNA (48.5kbp) and T4 DNA (166kbp). Further investigations showed the traces of DNA entering pores are strongly affected by the nanopore shape. To evaluate the flow by electroosmosis and electrophoresis quantitatively, a finite element analysis was also performed. Finally, we discuss the interactions between nanopore wall and highly crowded DNA inside pores.