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A common rule for the intermediate state caused by DNA mismatch in single-molecule experiments

Communications in Theoretical Physics 2023年第5期75卷 158-166页

作者： Xiaoya Song Chao Yang Yuyu Feng Hu Chen Yanhui Liu College of Physics Guizhou UniversityGuiyang 550025China Research Institute for Biomimetics and Soft Matter Fujian Provincial Key Lab for Soft Functional Materials ResearchDepartment of PhysicsXiamen UniversityXiamen 361005China State Key Laboratory of Public Big Data Guizhou UniversityGuiyang 550025China Kechuang Industrial Development Company Limited Guian New AreaGuiyang 550025China

Defective structures,such as DNA mismatches,occur in DNA with a high frequency in some biological *** are difficult to identify and have recently become the focus of singlemolecule *** single-molecule experiments were successively conducted to detect the effects of DNA mismatch on the stability of DNA ***,there was no consensus regarding the results of the intermediate state caused by DNA *** on the extended ox-DNA model,DNA mismatch was introduced to the stem of DNA hairpins with different stem lengths(12-20 bps)and 4T in hairpin *** intermediate state and its dependence on the position of the DNA mismatch in the stem from the hairpin loop were systematically *** results indicated that DNA mismatch definitely reduced the critical forces of DNA *** the same time,a common rule about the dependence of the intermediate state on the position of DNA mismatch was generalized in a phase diagram constructed in a phase space of a scaled position of DNA *** segments on its diagonal line corresponded to the ranges of the scaled position of DNA mismatch[0,0.55),[0.55,0.85),and[0.85,1],*** the[0.55,0.85)range,the extension probability distribution of DNA hairpins had unfolded,intermediate,and folded *** contrast,in the other ranges[0,0.55)and[0.85,1],the extension probability distributions had unfolded and folded *** scaled positions of DNA mismatch for the DNA hairpins used in the three single-molecule experiments(0.65,0.4736,and 0.5)fell in the ranges[0.55,0.85)and[0,0.55).Obviously,the common rule generalized in the phase diagram not only clarifies the nonconsensus between the three single-molecule experiments but also highlights the design of single-molecule experiments in the future.

关键词： DNA mismatch intermediate state DNA hairpin Bell’s Model extended Ox-DNA model single-molecule experiment

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