Structure And Flexibility Of DNA-RNA Hybrid Duplex Studied By All-atom Molecular Dynamics Simulations

DNA-RNA hybrids(DRH)are important intermediates in molecular biology.DRH duplexes play essential roles during the replication of DNA and reverse transcription of RNA viruses and their flexibility can be crucial for their biological functions and clinical applications such as the design of high stability and specificity to the RNase H-susceptible DRH and antisense therapy based on the activation of the RNase H mechanism.Recent experiments and theoretical studies have shown that the flexibility of RNA and DNA duplexes can be very different on stretching and twist-stretch coupling,and then there is still a lack of a quantitative and extensive characterization on the helical parameters and structural flexibility of DRH duplex.In this thesis,we employed microsecond all-atom molecular dynamics simulations with the new generation force fields to characterize the structure and flexibility of DRH duplexes,and major conclusions are as follow.First,we provided almost all the helical parameters for DRH duplex in a comparative way with DNA and RNA duplexes.Our analyses show that a DRH duplex adopts an intermediate conformation between canonical A-form and B-form and is biased to A-form,which may be attributed to the fact that RNA strand is more rigid than DNA strand.Second,we have explored the stretching flexibility of DRH duplex.The stretch modulus S of DRH duplex is ~834 pN,a value between those of DNA and RNA duplexes(the stretch modulus of ~1000-1500 pN for DNA duplex and of ~350-600 pN for RNA duplex),and is closer to that of RNA duplex.Such stretch modulus of DRH duplex is attributed to the base pair inclination and slide which are also between those of DNA and RNA duplexes and are closer to those of RNA duplex.Third,we have explored the twist-stretch coupling for DRH duplex.We found that a DRH duplex exhibits very weak twist-stretch coupling(~-0.06 nm/turn),while DNA and RNA duplexes(~-0.85 nm/turn for RNA duplex and ~ 0.59 nm/turn for DNA duplex)exhibit apparently negative and positive twist-stretch coupling,respectively.Such different twist-stretch coupling is attributed to the fact that the base pair inclination of DRH duplex is between those of DNA and RNA duplexes and is closer to that of RNA duplex,since the relationships between twist and H-rise are similar for DRH,DNA and RNA duplexes.This thesis provides a quantitative characterization on helical parameters,stretchmodulus and twist-stretch coupling,and provides comprehensive analyses on the flexibility in a comparative way with DNA and RNA duplexes.The thesis could be helpful for understanding the relative flexibility of DRH,DNA and RNA duplexes.