Bullard Kaitlin, Okyere Deborah, Foster Shelbi J, Sadoon Asmaa A, Li Jiali, Chen Jingyi, Wang Yong
Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA.
Materials Science and Engineering Program, University of Arkansas, Fayetteville, AR 72701, USA.
Biosensors (Basel). 2025 Apr 26;15(5):272. doi: 10.3390/bios15050272.
Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics of sharply bent DNA molecules in the absence and presence of Mg ions at different concentrations. The simulations show that Mg ions reduce the fluctuations of DNA strands, enhance base-pairing, and stabilize bent DNA molecules. The computational results are further verified by both melting curve experiments and ensemble FRET measurements, highlighting the mechanical instability and sensitivity of bent DNA molecules.
弯曲DNA扩增传感器最近被开发出来，用于扩增和量化DNA与各种盐和分子的相互作用。然而，对其机制仍缺乏全面的定量理解。在这里，我们使用全原子分子动力学（MD）模拟，研究了在不同浓度的镁离子存在和不存在的情况下，急剧弯曲的DNA分子的行为和动力学。模拟结果表明，镁离子减少了DNA链的波动，增强了碱基配对，并稳定了弯曲的DNA分子。熔解曲线实验和系综荧光共振能量转移（FRET）测量进一步验证了计算结果，突出了弯曲DNA分子的机械不稳定性和敏感性。
