螺旋度在DNA发状折叠动力学中的作用
Role of helicity in DNA hairping folding dynamics
摘要：
我们研究发夹折叠动力学通过广泛的计算机模拟，特别注意到螺旋度的折叠时间$τ$的影响。我们发现，在三维空间中，当双螺旋度被去除时，长度为N的发夹的反常标度$τ\sim N^α$的动力学指数$α$从1.6（$1+ν$）变为1.2（$2ν$）。无旋转发夹折叠中的$α= 2ν$关系在二维（$ν= 0.75$）和幽灵链（$ν= 0.5$）中得到进一步验证。据我们所知，这是对$α$的理论下限的第一次观察，该理论下限是早先根据聚合物通过孔移位的能量守恒来预测的。我们的研究结果表明，在长螺旋链的折叠动力学是由双链动力学，对比早期的理解的基础上的茎花图片的不成对的片段。我们提出了一个缩放参数$α= 1+ν$在螺旋链，假设双链松弛所需的定向定位的下一对基地是限速过程。
英文摘要：
We study hairpin folding dynamics by means of extensive computer simulations, with particular attention paid to the influence of helicity on the folding time $τ$. We find that the dynamical exponent $α$ of the anomalous scaling $τ\sim N^α$ for a hairpin with length N changes from 1.6 ($1+ν$) to 1.2 ($2ν$) in three dimensions, when duplex helicity is removed. The relation $α= 2ν$ in rotationless hairpin folding is further verified in two dimensions ($ν= 0.75$), and for a ghost-chain ($ν= 0.5$). This, to our knowledge, is the first observation of the theoretical lower bound on $α$, which was predicted earlier on the basis of energy conservation for polymer translocation through a pore. Our findings suggest that the folding dynamics in long helical chains is governed by the duplex dynamics, contrasting the earlier understanding based on the stem-flower picture of unpaired segments. We propose a scaling argument for $α= 1+ν$ in helical chains, assuming that duplex relaxation required for orientational positioning of the next pair of bases is the rate-limiting process.
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