Research On Micromechanics Problems In DNA Single Molecule Experiments

Sharp bending as one of the mechanical properties of double-stranded DNA on the nanoscale is essential for biological functions and processes.Based on fluorescence resonance energy transfer,force sensor has been designed to measure the forces inside short,strained loops composed of both double-stranded DNA and single-stranded DNA.But there were obvious differences between experimental value and theoretical value,and two similar FRET single-molecule experiments were carried out based on the same force sensor design,but provided totally contrary results.The key to solve the differences between the experimental value with the theoretical value and the discrepancy between the two FRET experiments is to identify the Kink generation in the double-stranded DNA of the force sensor and the Fork generation at the junction of double-stranded DNA and single-strand DNA,In view of this,three force sensor models were designed in current work based on experiment force sensor design as following,Model I: with kink structure and Fork structure in double-stranded DNA of the force sensor and at the the junction of the single-stranded DNA and double-stranded DNA,sepertately;Model II: with kink structure in double-stranded DNA of force sensor,but without Kink structure at the junction of double-stranded DNA and single-strand DNA;Model III: without Kink structure and Fork structure in double-stranded DNA of force sensor and at the junction of double-stranded DNA and single-strand DNA,seperately.The following works were carried out based on three models mentioned above by Monte Carlo simulation method,(1)Identification of Fork generation at junctions in force sensor.Focus on the dependence of Fork generation at junctions of double-stranded DNA and single-straned DNA in force sensor on the Kink generation in double-stranded DNA.It is found that the Fork began to generate at the junction of double-stranded DNA and single-stranded DNA when the counter length of double-stranded DNA in the sensor is larger than its critical length,even with a Kink in double-stranded DNA;(2)Identification of forces in three force sensor models.By establishing the function of the forces as the counter length of double-stranded DNA,the forces inferred from three models can be grouped into two different states,namely,Fork states and Kink states,the larger forces and the small ones are consistent with the ones inferred from experiments;(3)The transition between the Fork state and Kink state in force sensor.In the phase space composed of the NN stacking interaction energy and excited energy,the transition between the Fork state and Kink state is difficult to be identified,while the number of Forks is ultrasmall or large,by contrast,it can be detected in the phase space with a medium number of Forks and Kinks.Through the comparision between simulation results and the experimental results,it is justified that the discrepancy between the two FRET experiments results from the different experimental conditions.At the same time,based on the Arrhenius plot,the equivalent relationship between excitation energy and temperature was established.The effects of temperature on the transition between the Fork state and Kink state were determined,which was in agreement with the experimental results.