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Chin. Phys. B, 2019, Vol. 28(6): 068701    DOI: 10.1088/1674-1056/28/6/068701

Theoretical study of overstretching DNA-RNA hybrid duplex

Dong-Ni Yang(杨东尼)1,2, Zhen-Sheng Zhong(钟振声)1,2, Wen-Zhao Liu(刘文钊)1,2, Thitima Rujiralai3, Jie Ma(马杰)1,2
1 School of Physics, Sun Yat-sen University, Guangzhou 510275, China;
2 State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China;
3 Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand

DNA-RNA hybrid (DRH) plays important roles in many biological processes. Here, we use a thermodynamic theory to analyze the free energy and unpeeling properties of the overstretching transition for the DRH molecule and compare the results with double-helix DNA. We report that the RNA strand of DRH is easier to get unpeeled than the DNA strand while the difficulty in unpeeling the double helix DNA lies in between. We also investigate the sequence effect, such as GC content and purine content, on the properties of unpeeling the DRH. Further, to study the temperature effect, the force-temperature phase diagram of DRH and DNA are calculated and compared. Finally, using a kinetic model, we calculate the force-extension curves in the DRH stretching and relaxation process under different pulling rates and temperatures. Our results show that both pulling rate and temperature have important influences on the stretching and relaxation kinetics of unpeeling the DRH. Putting all these results together, our work provides a comprehensive view of both the thermodynamics and kinetics in DRH overstretching.

Keywords:  DNA-RNA hybrid      mechanical properties      overstretching      thermodynamic and kinetic model  
Received:  11 March 2019      Revised:  08 April 2019      Accepted manuscript online: 
PACS:  87.14.G- (Nucleic acids)  
  87.15.La (Mechanical properties)  
  87.15.A- (Theory, modeling, and computer simulation)  
  87.10.Pq (Elasticity theory)  

Project supported by the National Natural Science Foundation of China (Grant No. 11674403), the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 31700809), the Fundamental Research Funds for the Central Universities (Grant No. 18lgzd16), and the Open Fund of the State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University.

Corresponding Authors:  Jie Ma     E-mail:

Cite this article: 

Dong-Ni Yang(杨东尼), Zhen-Sheng Zhong(钟振声), Wen-Zhao Liu(刘文钊), Thitima Rujiralai, Jie Ma(马杰) Theoretical study of overstretching DNA-RNA hybrid duplex 2019 Chin. Phys. B 28 068701

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