Bubble lifetimes in DNA gene promoters and their mutations affecting transcription
arXiv:2106.15244 · doi:10.1063/5.0060335
Abstract
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 of bubble lifetimes between the mutated and the wild type promoters at the position of mutation varies from 20% to more than 30% as the bubble length is decreasing
arXiv comment6 pages, 4 figures
References in corpus (17)
- Helicoidal model for DNA opening
- Theory of Bubble Nucleation and Cooperativity in DNA Melting
- Structurally specific thermal fluctuations identify functional sites for DNA transcription
- Bubble dynamics in DNA
- Theoretical study of collective modes in DNA at ambient temperature
- Physics of base-pairing dynamics in DNA
- Bubble Statistics and Dynamics in Double-Stranded DNA
- Probing the mechanical unzipping of DNA
- Probability distribution of bubble lengths in DNA
- Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model
- Lengthscales and Cooperativity in DNA Bubble Formation
- Thermal and mechanical properties of a DNA model with solvation barrier
- Dependence on temperature and GC content of bubble length distributions in DNA
- End-to-end distance and contour length distribution functions of DNA helices
- Distributions of Bubble Lifetimes and Bubble Lengths in DNA
- Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences
- Base pair fluctuations in helical models for nucleic acids