CPM Seminar

DNA and RNA translocation and unzipping using nanopore force spectroscopy

Amit Meller

Rowland Institute
Harvard University

DNA and RNA molecules can be electrophoreticaly driven through nanoscale pores, such as the ~1.5 nm a-Hemolysin pore. Information about the translocation dynamics is obtained by probing the ionic current flowing through the pore during the passage of each biopolymer. We experimentally study the translocation process of unstructured and structured DNA molecules through the a-Hemolysin pore. We find that for unstructured polymers this process is highly sensitive to the DNA properties, such as its sequence and its direction of entry, and to physical parameters such as the driving field. Secondary structure in the polynucleotide leads to orders of magnitude slowing down in the translocation process. At large enough electrical field intensities structured DNA and RNA can be unzipped in a highly controlled way, and the unzipping kinetics can be directly quantified. We have extensively studied the unzipping kinetics of DNA and RNA molecules at wide range of voltage loading rates. We find that the unzipping kinetics is characterized by two limiting regimes: the strong field limit in which the system is unzipped in an irreversible process, and the weak field regime, in which it is in quasi equilibrium. A theoretical model that accounts for our experimental results will be discussed.