论文标题
DNA中气泡寿命和气泡长度的分布
Distributions of Bubble Lifetimes and Bubble Lengths in DNA
论文作者
论文摘要
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content on these分布。对于这两种模型，我们都发现，考虑要分离的互补核苷酸的碱基对依赖性（GC与AT）阈值能够重现观察到的熔化温度对DNA序列GC含量的依赖性。将这些阈值用于基础对开口，我们获得了气泡寿命分布，用于长度长达十个碱基对的气泡，因为序列的GC含量是多种多样的，它们可以准确地拟合到拉伸指数函数。我们发现，对于这两种模型，平均气泡寿命随着气泡长度或GC含量的增加而降低。此外，获得的气泡长度分布还通过适当的拉伸指数函数拟合，我们的结果表明，短气泡对于任何GC含量都具有相似的可能性，但是更长的气泡在富含的序列中更可能发生。我们还表明，与PBD系统相比，EPBD模型允许更多，更长的气泡。
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.
