Determination of RNA orientation during translocation through a biological nanopore

We investigate single-molecule electrophoretic translocation of A(50), C-50, A(25)C(50), and C(50)A(25) RNA molecules through the alpha-hemolysin transmembrane protein pore. We observe pronounced bilevel current blockages during translocation of A(25)C(50) and C(50)A(25) molecules. The two current levels observed during these bilevel blockages are very similar to the characteristic current levels observed during A(50) and C-50 translocation. From the temporal ordering of the two levels within the bilevel current blockages, we infer whether individual A(25)C(50) and C(50)A(25) molecules pass through the pore in a 3'-> 5' or 5'-> 3' orientation. Correlation between the level of current obstruction and the inferred A(25)C(50) or C(50)A(25) orientation indicates that 3'-> 5' translocation of a poly C segment causes a significantly deeper current obstruction than 5'-> 3' translocation. Our analysis also suggests that the 39 ends of C-50 and A(25)C(50) RNA molecules are more likely to initiate translocation than the 59 ends. Orientation dependent differences in a smaller current blockage that immediately precedes many translocation events suggest that this blockage also contains information about RNA orientation during translocation. These findings emphasize that the directionality of polynucleotide molecules is an important factor in translocation and demonstrate how structure within ionic current signals can give new insights into the translocation process.