Verma Sachin Dev, Pal Nibedita, Singh Moirangthem Kiran, Sen Sobhan
Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University , New Delhi 110067, India.
J Phys Chem B. 2015 Aug 27;119(34):11019-29. doi: 10.1021/acs.jpcb.5b01977. Epub 2015 May 22.
Ligand binding to minor-grooves of DNA depends on DNA-base sequence near its binding-site. However, it is not known how base-sequences affect the local solvation of ligand inside minor-grooves of DNA. Here we present a comprehensive study on sequence-dependent solvation dynamics of ligand inside duplex-DNA by measuring the static and dynamic fluorescence Stokes shifts of a popular groove-binder, DAPI, inside DNA minor-grooves created by four different sequences; d(5'-CGCGAATTCGCG-3')2, d(5'-CGCGTTAACGCG-3')2, d(5'-CGCGCAATTGCGCG-3')2, and d(5'-CGCGCTTAAGCGCG-3')2, having different sequences near DAPI-binding site. Fluorescence up-conversion and time-correlated single photon counting techniques are employed to capture the dynamic Stokes shifts of DAPI over five decades in time from 100 fs to 10 ns. We show that the ligands sense different static and dynamic solvation inside minor-grooves created by different sequences: Only subtle change in the dynamics is seen in DNA containing -AATTG-, -TTAAG-, and -AATTC- sequences, which show power-law relaxation in initial time-decades, followed by biexponential decay in nanosecond time-scales. However, changing a single base (and the complementary base) near ligand-binding site from -TTAAG- to -TTAAC- drastically induces the dynamics to follow a single power-law relaxation over the entire five decades. The observed variation of dynamics possibly relate to the local DNA motions, coupled to the hydration dynamics near the ligand-binding site.
配体与DNA小沟的结合取决于其结合位点附近的DNA碱基序列。然而，尚不清楚碱基序列如何影响DNA小沟内配体的局部溶剂化作用。在此，我们通过测量一种常用的沟结合剂DAPI在由四种不同序列（d(5'-CGCGAATTCGCG-3')2、d(5'-CGCGTTAACGCG-3')2、d(5'-CGCGCAATTGCGCG-3')2和d(5'-CGCGCTTAAGCGCG-3')2）在DAPI结合位点附近具有不同序列所形成的DNA小沟内的静态和动态荧光斯托克斯位移，对双链DNA内配体的序列依赖性溶剂化动力学进行了全面研究。采用荧光上转换和时间相关单光子计数技术，在从100飞秒到10纳秒的五个数量级的时间内捕获DAPI的动态斯托克斯位移。我们表明，配体在由不同序列形成的小沟内感受到不同的静态和动态溶剂化作用：在含有-AATTG-、-TTAAG-和-AATTC-序列的DNA中，动力学仅出现细微变化，在初始的时间数量级上呈现幂律弛豫，随后在纳秒时间尺度上呈现双指数衰减。然而，将配体结合位点附近的单个碱基（及其互补碱基）从-TTAAG-改变为-TTAAC-，会极大地促使动力学在整个五个数量级上遵循单一的幂律弛豫。观察到的动力学变化可能与局部DNA运动有关，且与配体结合位点附近的水合动力学相耦合。
