Bianco Simona, Hu Tianyu, Henrich Oliver, Magennis Steven W
School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK.
Department of Physics, University of Strathclyde, Glasgow G4 0NG, UK.
Biophys Rep (N Y). 2022 Sep 14;2(3):None. doi: 10.1016/j.bpr.2022.100070.
It is unclear how the length of a repetitive DNA tract determines the onset and progression of repeat expansion diseases, but the dynamics of secondary DNA structures formed by repeat sequences are believed to play an important role. It was recently shown that three-way DNA junctions containing slip-out hairpins of CAG or CTG repeats and contiguous triplet repeats in the adjacent duplex displayed single-molecule FRET (smFRET) dynamics that were ascribed to both local conformational motions and longer-range branch migration. Here we explore these so-called "mobile" slip-out structures through a detailed kinetic analysis of smFRET trajectories and coarse-grained modeling. Despite the apparent structural simplicity, with six FRET states resolvable, most smFRET states displayed biexponential dwell-time distributions, attributed to structural heterogeneity and overlapping FRET states. Coarse-grained modeling for a (GAC) repeat slip-out included trajectories that corresponded to a complete round of branch migration; the structured free energy landscape between slippage events supports the dynamical complexity observed by smFRET. A hairpin slip-out with 40 CAG repeats, which is above the repeat length required for disease in several triplet repeat disorders, displayed smFRET dwell times that were on average double those of 3WJs with 10 repeats. The rate of secondary-structure rearrangement via branch migration, relative to particular DNA processing pathways, may be an important factor in the expansion of triplet repeat expansion diseases.
目前尚不清楚重复DNA片段的长度如何决定重复序列扩增疾病的发生和发展，但据信由重复序列形成的二级DNA结构的动力学起着重要作用。最近的研究表明，包含CAG或CTG重复序列的滑出式发夹以及相邻双链体中连续三联体重复序列的三链DNA连接体表现出单分子荧光共振能量转移（smFRET）动力学，这归因于局部构象运动和长程分支迁移。在这里，我们通过对smFRET轨迹的详细动力学分析和粗粒度建模来探索这些所谓的“移动”滑出结构。尽管表面结构简单，可分辨出六种FRET状态，但大多数smFRET状态显示出双指数驻留时间分布，这归因于结构异质性和重叠的FRET状态。对（GAC）重复序列滑出的粗粒度建模包括与一轮完整的分支迁移相对应的轨迹；滑移事件之间的结构化自由能景观支持了smFRET观察到的动力学复杂性。具有40个CAG重复序列的发夹滑出结构，其长度超过了几种三联体重复序列疾病发病所需的重复长度，其smFRET驻留时间平均是具有10个重复序列的三链连接体的两倍。相对于特定的DNA加工途径，通过分支迁移进行二级结构重排的速率可能是三联体重复序列扩增疾病扩展的一个重要因素。
