Chen Jixin, Poddar Nitesh K, Tauzin Lawrence J, Cooper David, Kolomeisky Anatoly B, Landes Christy F
Department of Chemistry and ‡Department of Electrical and Computer Engineering, Rice University , Houston, Texas 77251-1892, United States.
J Phys Chem B. 2014 Oct 23;118(42):12130-9. doi: 10.1021/jp507067p. Epub 2014 Oct 14.
We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.
我们使用单分子荧光共振能量转移(smFRET)方法直接测量了具有多个环的HIV反式激活应答(TAR)-DNA发夹的动力学。识别出了多个与发夹中间解链状态相对应的FRET状态。从smFRET数据计算出每个中间状态的稳定性。结果表明,发夹展开遵循“磨损和剥离”机制,并且在折叠过程中观察到了发夹末端塌陷的证据。这些结果表明,发夹环作为额外的磨损中心,在原本稳定的系统中增加展开速率,可能具有生物学功能。本文开发的实验和分析方法为研究多状态DNA发夹动力学机制以及具有多个平行化学反应途径的其他一般系统提供了有用的工具。