Examining DNA Breathing with pyDNA-EPBD.
Examining DNA Breathing with pyDNA-EPBD.
复制标题
使用 pyDNA-EPBD 检查 DNA 呼吸。
DOI：
10.1101/2023.09.09.557010
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Alexandrov,BoianS
中科院分区：
文献类型：
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作者：
Kabir,Anowarul;Bhattarai,Manish;Rasmussen,KimØ;Shehu,Amarda;Usheva,Anny;Bishop,AlanR;Alexandrov,BoianS
在活细胞中，由于DNA固有的热运动，DNA双螺旋的两条链局部自发地分离和重组。这种动态导致双螺旋结构的瞬间打开，被称为“DNA呼吸”或“DNA气泡”。形成局部瞬时开口的倾向在广泛的生物过程中是重要的，如转录、复制和转录因子结合。然而，由于温度、盐含量、DNA序列、氢键、碱基堆叠等众多因素的复杂相互作用，这些现象的建模和计算机模拟仍然是一个挑战。我们提出了pyDNA-EPBD，一个扩展peyard - bishop - dauxois （EPBD）非线性DNA模型的并行软件实现，使我们能够详细描述DNA动力学的一些特征。pyDNA-EPBD生成平均碱基对开度、碱基翻转概率、DNA泡概率的基因组尺度谱，并使用马尔可夫链蒙特卡罗算法计算特征动态长度，表明受单点突变统计显著影响的碱基对数量。可用性和实现pydna - epbd在大多数操作系统上都得到支持，可以在https://github.com/lanl/pyDNA_EPBD上免费获得。可以在https://lanl.github.io/pyDNA_EPBD/上找到大量文档。
MotivationThe two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as “DNA breathing” or “DNA bubbles.” The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others.ResultsWe present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm.Availability and implementationpyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.