Fig. 3.

Repetitive unwinding of a short duplex stretch. (A) Partial duplex with ds18 and ss30 tail with cy3 and cy5 at ds/ss junction was blocked at the duplex end via biotin-streptavidin (PD3). (B) Majority of molecules (75%) showed repetitive unwinding pattern where the enzyme appear to snap/slip back to near junction upon encountering a blockade. (C) Partial duplex with ds18 and ss20 tail was labeled with cy5 at the ds/ss junction and cy3 at the end of duplex end (PD4). (D) The repetitive cycles of gradual FRET increase followed by a rapid decrease indicates that the displaced strand is brought close to the duplex end by NS3, then snaps/slips back to the junction rapidly after encountering the blockade.