Insights into the Discrepancy between Single Molecule Experiments |
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Authors: | Qian Zhou Min Zhang Yang-Tao Fan Yu-Kang Wang Lin Bao Guang-Ju Zhao Hu Chen Yan-Hui Liu |
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Institution: | 1. College of Physics, Guizhou University, Guiyang 550025, China;2. College of Big Data and Information Engineering, Guizhou University, Guiyang 550025, China;3. Department of Physics, Xiamen University, Xiamen 361005, China;4. Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China |
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Abstract: | Sharp bending as one of the mechanical properties of double-stranded DNA(dsDNA) on the nanoscale is essential for biological functions and processes. Force sensors with optical readout have been designed to measure the forces inside short, strained loops composed of both dsDNA and single-stranded DNA(ssDNA). Recent FRET singlemolecule experiments were carried out based on the same force sensor design, but provided totally contrary results. In the current work, Monte Carlo simulations were performed under three conditions to clarify the discrepancy between the two experiments. The criterion that the work done by the force exerted on dsDNA by ssDNA should be larger than the nearest-neighbor(NN) stacking interaction energy is used to identify the generation of the fork at the junction of dsDNA and ssDNA. When the contour length of dsDNA in the sensor is larger than its critical length, the fork begins to generate at the junction of dsDNA and ssDNA, even with a kink in dsDNA. The forces inferred from simulations under three conditions are consistent with the ones inferred from experiments, including extra large force and can be grouped into two different states, namely, fork states and kink states. The phase diagrams constructed in the phase space of the NN stacking interaction energy and excited energy indicate that the transition between the fork state and kink state is difficult to identify in the phase space with an ultra small or large number of forks, but it can be detected in the phase space with a medium number of forks and kinks. |
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Keywords: | force sensor Monte Carlo simulation kink structure fork structure nearest-neighbouring stacking interaction energy |
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