Thermodynamics of DNA-RNA renaturation

DNA/RNA机械力解链的自旋振子模型

Spin-oscillator model for DNA/RNA unzipping by mechanical force

我们利用自旋振子系统模拟了DNA/RNA分子在外力作用下的解链过程。该系统包括由一维振荡器表示的宏观自由度和由具有最近邻相互作用的Glauber自旋和与振荡器位置成比例的耦合常数表示的内部自由度。在所施加的外力$F$的临界值$F_c$处，振子静止位置（序参量）突然改变，并且系统经历一阶相变。当外力以不同的速率循环时，由振荡器位置给出的延伸在高加载速率下表现出滞后循环，而在非常低的加载速率下，其在平衡力-延伸曲线上可逆地移动。在恒定的力下，在稳定和亚稳振荡器静止位置处的停留时间的对数与$(F-F_c)$成比例，如在阿克里乌斯定律中。

DNA轨道上的RNA聚合酶马达：相互作用、外力和扭矩的影响

RNA polymerase motor on DNA track: effects of interactions, external force and torque

RNA聚合酶（RNAP）是一个移动的分子作坊，它通过一个接一个地添加单体亚基来聚合RNA分子，同时在DNA模板本身上逐步移动。在这里，我们开发了一个理论模型，将空间相互作用的RNAP和他们的机械化学周期，明确捕捉每个电机的周期性形状变化。使用这个模型，我们不仅解释了依赖于外部施加的负载力的RNAP的平均速度，但也预测的{ \it nonmotonic}变化的平均速度的外部扭矩。我们还显示了马达的空间相互作用对RNA合成总速率的影响。原则上，我们的预测可以通过进行{ \it in-vitro}实验来测试，我们在这里建议。

Flexibility of nucleic acids: from DNA to RNA

The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid flexibility, extensive studies have been performed using various experimental methods and theoretical models. In this review, we will introduce the progress that has been made in understanding the flexibility of nucleic acids including DNAs and RNAs, and will emphasize the experimental findings and the effects of salt, temperature, and sequence. Finally, we will …

高密度寡核苷酸芯片中RNA/DNA杂交的热力学

Thermodynamics of RNA/DNA hybridization in high density oligonucleotide microarrays

我们分析了一系列公开可用的对照实验（拉丁方）的Affyellow高密度寡核苷酸微阵列使用一个简单的物理模型的杂交过程。我们绘制每个基因的信号强度与杂交自由能的RNA/DNA双链体在溶液中，完美匹配和不匹配的探针。两个值倾向于在单个主曲线上对齐，与朗缪尔吸附理论良好一致，前提是考虑到由于溶液中的靶-靶杂交导致的有效靶浓度的降低。我们给出了一个由于注释问题而偏离探针组1091\_at的预期化学行为的例子，即，由于设计阵列时公共数据库中存在的错误，表面结合的探针不是靶RNA序列的精确互补序列。我们表明，参数化的实验数据与RNA/DNA自由能提高了拟合的质量，并提高了拟合参数的稳定性相比，以前的研究。

Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA

Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Cobalt Hexammine ion (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that …

A biologically inspired two-species exclusion model: effects of RNA polymerase motor traffic on simultaneous DNA replication

We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles ($P$) represents RNAP motors while the other ($R$) represents replication forks. Motivated by the biological phenomena that this model is intended to capture, a maximum of only two $R$ particles are allowed to enter the lattice from two opposite ends whereas the unrestricted number of $P$ particl…