Hillebrand M, Kalosakas G, Bishop A R, Skokos Ch
Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa.
Department of Materials Science, University of Patras, GR-26504 Rio, Greece.
J Chem Phys. 2021 Sep 7;155(9):095101. doi: 10.1063/5.0060335.
Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the average lifetime at the mutation sites when the mutated promoter decreases transcription, while a corresponding enhancement of the bubble lifetime is observed in the case of mutations leading to increased transcription. The relative difference in bubble lifetimes between the mutated and wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length decreases.
在佩拉尔-毕晓普-多克索模型的框架内，给出了长度达十个碱基对的固有双链DNA开口的相对寿命，这些开口对应于不同的基因启动子以及相应的突变体，这些突变体要么增加要么降低转录活性。使用了广泛的微正则模拟，其能量对应于生理温度。沿DNA序列的气泡寿命分布表明，当突变启动子降低转录时，突变位点处的平均寿命显著缩短，而在导致转录增加的突变情况下，观察到气泡寿命相应延长。随着气泡长度减小，突变启动子与野生型启动子在突变位置的气泡寿命相对差异从20%到超过30%不等。
