Theoretical study of overstretching DNA–RNA hybrid duplex*

Abstract

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.

GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes

“…When temperature is above 16 C, or the NaCl concentration is low, DRH undergoes a hysteretic transition, indicating the presence of unpeeling process, which results in a stretched ssDNA and probably a coiled ssRNA (note that because of the configuration used in their experiments, only the RNA strand can be unpeeled there without breaking the tether), and such peeled single strands are difficult to anneal back to reform the hybrid duplex. Our previous theoretical study indicated that during overstretching, peeling from RNA strand is more favored than peeling from DNA (55). A recent experimental study performed by Melkonyan et al (56) also supports this point.…”

“…Therefore, three components, namely ssDNA, ssRNA, and S-form DRH (S-DRH), could remain after overstretching. Notice, here, we do not consider small DRH ''bubble'' formation because the theoretical calculation has shown that the ''bubble'' formation is energetically less favorable in comparison with unpeeling and formation of S-DRH, even for AT/UA-rich sequences (55). Then, for traces whose FECs do not show obvious hysteresis in the force range of 75-80 pN, we have developed a method (see Supporting Materials and Methods for details) to analyze the fraction of each components left at the end of stretching (i.e., F ¼ 80 pN).…”