Abstract
The bending of double-stranded(ds) DNA on the nano-meter scale plays a key role in many cellular processes such as nucleosome packing, transcription-control, and viral-genome packing. In our recent study, a nanometer-sized dsDNA bent into a D shape was formed by hybridizing a circular single-stranded(ss) DNA and a complementary linear ssDNA. Our fluorescence resonance energy transfer (FRET) measurement of D-DNA revealed two types of conformational states: a less-bent state and a kinked state, which can transform into each other. To understand the origin of the two deformed states of D-DNA, here we study the presence of open base-pairs in the ds portion by using the breathing-DNA model to simulate the system. We provide strong evidence that the two states are due to the emergence of local denaturation, i.e., a bubble in the middle and two forks at ends of the dsDNA portion. We also study the system analytically and find that the free-energy landscape is bistable with two minima representative of the two states. The kink and fork sizes estimated by the analytical calculation are also in excellent agreement with the results of the simulation. Thus, this combined experimental-simulation-analytical study corroborates that highly bent D-DNA reduces bending stress via local denaturation.
Highlights
The two peaks have been attributed to the two conformational states of D-shaped DNA: a kinked state with short end-to-end distance (EED) and a less-bent state with long EED18 Inserting a 3-bp mismatch in the middle of the arc, as shown in Fig. 3(b), for n0 = 10 bp, gives a fluorescence resonance energy transfer (FRET) efficiency E = 0.8
With a single-molecule experiment, we detect that a short dsDNA strongly bent into a D-shape has two conformational states
One state is the ds short-EED state caused by a kink, as suggested by the same experiment with a mismatch placed in the middle of the dsDNA contour
Summary
D-shaped DNA: Effects of local denaturation received: 16 March 2016 accepted: 26 May 2016 Published: 24 June 2016. In a more recent study, for D-shaped DNA without nick formed by hybridizing an ss loop with a linear complementary ss, they showed that the ds portion transforms from a less-bent state to sharply kinked state when the bending torque on the ds exceeds a certain value[17] Their studies, based on electrophoresis gel experiments for bulk DNA, are quite limited with regard to detailing the conformations and conditions for DNA transition and coexistence. The experiment[18] showed that D-shaped DNA with a 3-bp size mismatch in the center of the ds portion yields a FRET signal indistinguishable from that of the short-EED state This result suggested that local melting was responsible for the short-EED state, which arises to release the large bending stress. We develop an analytical model that indicates that the bistability arises via the formation of a kink of about 5-bp length and two forks of about 3-bp length in order to release the large bending stress
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