A nonlinear dynamic model of DNA with a sequence-dependent stacking term.
A nonlinear dynamic model of DNA with a sequence-dependent stacking term.
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DOI：
10.1093/nar/gkp016
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发表时间：
2009-04
影响因子：
14.9
通讯作者：
Usheva A
中科院分区：
文献类型：
--
作者：
Alexandrov BS;Gelev V;Monisova Y;Alexandrov LB;Bishop AR;Rasmussen KØ;Usheva A
没有简单的模型可以准确地描述双链DNA的解链行为和呼吸动力学随核苷酸序列的变化。这是特别真实的同质和周期性的DNA序列，表现出很大的偏差，从预测的熔融温度添加剂的热力学贡献。目前，没有方法存在的重复和高度G/C-或A/T-丰富的区域的DNA呼吸动力学的分析，即使这样的序列是广泛存在于脊椎动物基因组。在这里，我们扩展的非线性Peyrard-Bishop-Dauxois（PBD）模型的DNA，包括序列依赖的堆叠项，从而在一个模型，可以准确地描述熔化行为的均匀和周期性的序列。我们收集了几种DNA寡核苷酸的解链数据，并应用Monte Carlo模拟来建立10个二核苷酸步骤（CG，CA，GC，AT，AG，AA，AC，TA，GG，TC）的力常数。实验和数值模拟证实了GG/CC二核苷酸堆积与GC/CG和CG/GC二核苷酸堆积相比是非常不稳定的。扩展的PBD模型将有助于重要的基因组区域，如CpG岛和疾病相关的重复序列的热力学和动力学模拟。
No simple model exists that accurately describes the melting behavior and breathing dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially true for homogenous and periodic DNA sequences, which exhibit large deviations in melting temperature from predictions made by additive thermodynamic contributions. Currently, no method exists for analysis of the DNA breathing dynamics of repeats and of highly G/C- or A/T-rich regions, even though such sequences are widespread in vertebrate genomes. Here, we extend the nonlinear Peyrard–Bishop–Dauxois (PBD) model of DNA to include a sequence-dependent stacking term, resulting in a model that can accurately describe the melting behavior of homogenous and periodic sequences. We collect melting data for several DNA oligos, and apply Monte Carlo simulations to establish force constants for the 10 dinucleotide steps (CG, CA, GC, AT, AG, AA, AC, TA, GG, TC). The experiments and numerical simulations confirm that the GG/CC dinucleotide stacking is remarkably unstable, compared with the stacking in GC/CG and CG/GC dinucleotide steps. The extended PBD model will facilitate thermodynamic and dynamic simulations of important genomic regions such as CpG islands and disease-related repeats.
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影响因子：
8.6
作者：
Voulgarakis, N. K.;Redondo, A.;Rasmussen, K. O.
通讯作者：
Rasmussen, K. O.
影响因子：
10.8
作者：
Voulgarakis, NK;Kalosakas, G;Bishop, AR
通讯作者：
Bishop, AR
影响因子：
4.3
作者：
Sponer, J;Jurecka, P;Hobza, P
通讯作者：
Hobza, P
影响因子：
8.6
作者：
PEYRARD, M;BISHOP, AR
通讯作者：
BISHOP, AR
影响因子：
8.6
作者：
Ares, S;Voulgarakis, NK;Bishop, AR
通讯作者：
Bishop, AR