The impact of base stacking on the conformations and electrostatics of single-stranded DNA.
The impact of base stacking on the conformations and electrostatics of single-stranded DNA.
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DOI：
10.1093/nar/gkx140
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发表时间：
2017-04-20
影响因子：
14.9
通讯作者：
Pollack L
中科院分区：
文献类型：
--
作者：
Plumridge A;Meisburger SP;Andresen K;Pollack L
单链DNA（ssDNA）在DNA修复和复制等重要的生物学过程中与ssDNA结合蛋白（SSB）相互作用。先前的工作已经开始表征与SSB相关的ssDNA的构象和静电性质。然而，游离ssDNA的构象分布一直难以确定。为了捕获溶液中大量的ssDNA构象，我们将小角X射线散射与新颖的系综拟合方法配对，获得关键参数，如具有不同序列的链的大小，形状和堆叠特性。使用电感耦合等离子体原子发射光谱法的互补离子计数测量被用来确定在生理离子强度下的离子气氛的组成。将这种组合方法应用于多聚dA和多聚dT，我们发现这些序列的整体性质非常相似，尽管它们的单链螺旋堆叠倾向有很大不同。这些结果表明，一个相对简单的机制，结合ssDNA的非特异性SSB可能在发挥作用，这解释了这些系统中观察到的结合亲和力的差异。
Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems.