It has been suggested that the structure that results when double-stranded DNA (dsDNA) is pulled from the 3′3′ ends differs from that which results when it is pulled from the 5′5′ ends. In this work, we demonstrate, using λ phage dsDNA, that the overstretched states do indeed show different properties, suggesting that they correspond to different structures. For 3′3′ pulling versus 5′5′ pulling, the following differences are observed: (i) the forces at which half of the molecules in the ensemble have made a complete force-induced transition to single stranded DNA are 141 ± 3 pN and 122 ± 4 pN, respectively; (ii) the extension vs. force curve for overstretched DNA has a marked change in slope at 127 ± 3 pN for 3′3′ and 110 ± 3 pN for 5′5′; (iii) the hysteresis (H) in the extension vs. force curves at 150 mM NaCl is 0.3 ± 0.8 pN μm for 3′3′ versus 13 ± 8 pN for 5′5′; and (iv) 3′3′ and 5′5′ molecules show different changes in hysteresis due to interactions with β-cyclodextrin, a molecule that is known to form stable host-guest complexes with rotated base pairs, and glyoxal that is known to bind stably to unpaired bases. These differences and additional findings are well-accommodated by the corresponding structures predicted on theoretical grounds.
展开▼
