Direct Measurement of the Rates and Barriers on Forward and Reverse Diffusions of Intramolecular Collision in Overhang Oligonucleotides

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• 作者：Peng Qu ; Xinxing Yang ; Xun Li ; Xiaoxue Zhou ; Xin Sheng Zhao
• 刊名：Journal of Physical Chemistry B
• 出版年：2010
• 出版时间：June 24, 2010
• 年：2010
• 卷：114
• 期：24
• 页码：8235-8243
• 全文大小：362K
• 年卷期：v.114,no.24(June 24, 2010)
• ISSN：1520-5207

文摘

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).