Direct Measurement of the Rates and Barriers on Forward and Reverse Diffusions of Intramolecular Collision in Overhang Oligonucleotides
Direct Measurement of the Rates and Barriers on Forward and Reverse Diffusions of Intramolecular Collision in Overhang Oligonucleotides
复制标题
直接测量悬垂寡核苷酸分子内碰撞正向和反向扩散的速率和势垒
DOI：
10.1021/jp101173y
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发表时间：
2010-06-24
影响因子：
3.3
通讯作者：
Zhao, Xin Sheng
中科院分区：
文献类型：
--
作者：
Qu, Peng;Yang, Xinxing;Zhao, Xin Sheng
通过结合光致电子转移（PET）和荧光相关光谱（FCS）在不同温度下监测鸟苷残基对四甲基罗丹明（TMR）的荧光猝灭，研究了锚定在双链DNA （dsDNA）上的悬垂物端到端（I型）和端到端（II型）碰撞的动力学。TMR和鸟苷残基由双螺旋状的悬垂碱基2 - 16分开。通过分析FCS数据，我们得到了正向和反向链内扩散速率常数和各自的势垒。对于I型和II型碰撞，链内扩散速率遵循高斯链模型的标度规律。相反的链内扩散速率对碱基长度不敏感。正反扩散的激活焓和激活熵均与长度无关。第一类和第二类碰撞的比较表明，端到端内部的碰撞速率比端到端慢。通过一系列分离长度相同但尾长不同的悬垂DNA （III型）进一步详细检查了这一现象。
The dynamics of end-to-interior (Type I) and end-to-end (Type II) collisions in a dangling overhang anchored on a double-stranded DNA (dsDNA) was studied by monitoring the fluorescence quenching of tetramethylrhodamine (TMR) by guanosine residues through combining photoinduced electron transfer (PET) with fluorescence correlation spectroscopy (FCS) at different temperatures. TMR and guanosine residues are separated by a double helix with dangling bases ranging from 2 to 16. By analyzing the FCS data, we obtained the forward and reverse intrachain diffusion rate constants and respective barriers. For both Type I and Type II collisions, the intrachain diffusion rates followed the scaling law of the Gaussian chain model. Especially, the reverse intrachain diffusion rate was insensitive to the base length of separation. Both the activation enthalpy and activation entropy of the forward and reverse diffusions were length independent. The comparison between Type I and Type II collisions shows that the collision rate of end-to-interior is slower than that of end-to-end. The phenomenon is further checked in detail by a series of dangling DNA with the same separation length but different tail lengths (Type III).