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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 processes.They are difficult to identify and have recently become the focus of singlemolecule investigations.Three single-molecule experiments were successively conducted to detect the effects of dna mismatch on the stability of dna hairpins.However,there was no consensus regarding the results of the intermediate state caused by dna mismatch.Based 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 loops.The intermediate state and its dependence on the position of the dna mismatch in the stem from the hairpin loop were systematically studied.The results indicated that dna mismatch definitely reduced the critical forces of dna hairpins.At 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 mismatch.Three 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],respectively.In the[0.55,0.85)range,the extension probability distribution of dna hairpins had unfolded,intermediate,and folded states.In contrast,in the other ranges[0,0.55)and[0.85,1],the extension probability distributions had unfolded and folded states.The 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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Selective Tumor Cell Death induced by Irradiated Riboflavin through Recognizing dna G-T mismatch

Selective Tumor Cell Death induced by Irradiated Riboflavin ...

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第十届全国化学生物学学术会议

作者： Yi Yuan Zhuo Tang Natural Products Research Center Chengdu Institute of Biology

Riboflavin（vitamin B2） has been thought to be a promising antitumoral agent in photodynamic therapy, though the further application of the method was limited by the unclear molecular mechanism. G-T mismatch was the most abundant mismatches that were generated by replication errors and endogenous damages.Our work reveals that riboflavin was able to recognize G-T mismatch specifically and induce single-strand breaks in duplex dna targets efficiently under irradiation. Riboflavin was proved selectively interacting with G-T bases. Certain cancer cells were certified deficient in mismatch repair system, generating high level of G-T mismatches. In the presence of riboflavin, the photo-irradiation could induce the death of tumor cells that are defective in mismatch repair system selectively, highlighting the G – T mismatch as potential drug target for tumor cells. Moreover, riboflavin is a promising leading compound for further drug design due to its inherent specific recognition of the G–T mismatch.

关键词： cell death riboflavin photocleavage tumor cells dna mismatch

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