Structures of the kinetically trapped i-motif DNA intermediates.
Structures of the kinetically trapped i-motif DNA intermediates.
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DOI：
10.1039/c6cp04418b
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发表时间：
2016-09-29
期刊：
影响因子：
--
通讯作者：
Fernandez-Lima F
中科院分区：
文献类型：
--
作者：
Garabedian A;Butcher D;Lippens JL;Miksovska J;Chapagain PP;Fabris D;Ridgeway ME;Park MA;Fernandez-Lima F
本文采用圆二色性（CD）、光声量热分析（PAC）、离子迁移谱-质谱（TIMS-MS）和分子动力学（MD）等方法，研究了i-motif DNA在溶液和气相中的构象动力学和折叠途径随溶液pH条件的变化。溶液研究表明，在热力学平衡下存在两态折叠机制，而在pH = 7.0→4.5过渡期间，观察到快速和慢相（ΔHfast+ ΔHslow = 43±7 kcal mol - 1）的体积变化与半质子化胞嘧啶碱基对的形成和伴随的i-motif寡核苷酸坍塌成紧凑的构象有关。TIMS-MS实验表明，纳米esi产生的i基序DNA中间体被保留了下来，其相对丰度取决于溶液的pH条件。特别是，在纳米esi - tims - ms中，在低pH条件下，在正负离子模式（例如z = +/−3至+/−5）的低电荷状态下，观察到折叠的i-motif DNA结构。随着溶液pH的增加，胞嘧啶去质子化导致CCC链中胞嘧啶-胞嘧啶+ （C•CH+）碱基配对的丢失，在这些条件下，我们在nanoESI-TIMS-MS中观察到部分展开的i-motif DNA构象在高电荷态（例如，z = - 6至- 9）。碰撞诱导激活先验TIMS-MS显示存在多个局部自由能极小值，这与i-motif DNA在z = - 6电荷态展开有关。首次提出了基于i-motif DNA展开途径的迁移率测量的候选气相结构。此外，对部分展开的i-motif DNA结构（z = - 7和z = - 8电荷态）的检查表明，内部阳离子的存在可能会或可能不会引起气相构象的变化。例如，铵加合物的加入不会导致主要的构象变化，而钠加合物可能会导致钠介导的键在两个带负电荷的侧之间形成，从而在新的局部自由能最小值中稳定为更紧凑的结构。
In the present work, the conformational dynamics and folding pathways of i-motif DNA were studied in solution and in the gas-phase as a function of the solution pH conditions using circular dichroism (CD), photoacoustic calorimetry analysis (PAC), trapped ion mobility spectrometry - mass spectrometry (TIMS-MS), and molecular dynamics (MD). Solution studies showed at thermodynamic equilibrium the existence of a two-state folding mechanism, whereas during the pH = 7.0 → 4.5 transition a fast and slow phase (ΔHfast+ ΔHslow = 43 ± 7 kcal mol−1) with a volume change associated with the formation of hemiprotonated cytosine base pairs and concomitant collapse of the i-motif oligonucleotide into a compact conformation were observed. TIMS-MS experiments showed that gas-phase, kinetically trapped i-motif DNA intermediates produced by nanoESI are preserved, with relative abundances depending on the solution pH conditions. In particular, a folded i-motif DNA structure was observed in nanoESI-TIMS-MS for low charge states in both positive and negative ion mode (e.g., z = +/− 3 to +/−5) at low pH conditions. As solution pH increases, the cytosine deprotonation leads to the loss of cytosine-cytosine+ (C•CH+) base pairing in the CCC strands and in those conditions we observe partially unfolded i-motif DNA conformations in nanoESI-TIMS-MS for higher charge states (e.g., z = − 6 to −9). Collisional induced activation prior TIMS-MS showed the existence of multiple local free energy minima, associated with the i-motif DNA unfolding at z = −6 charge state. For the first time, candidate gas-phase structures are proposed based on mobility measurements of the i-motif DNA unfolding pathway. Moreover, the inspection of partially unfolded i-motif DNA structures (z = −7 and z = −8 charge states) showed that the presence of inner cations may or may not induce conformational changes in the gas-phase. For example, incorporation of ammonium adducts does not lead to major conformational changes while sodium adducts may lead to the formation of sodium mediated bonds between two negatively charged sides inducing the stabilization towards more compact structures in new local, free energy minima in the gas-phase.
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DOI：
10.1007/s12127-015-0175-y
发表时间：
2015-10
期刊：
International journal for ion mobility spectrometry : official publication of the International Society for Ion Mobility Spectrometry
影响因子：
--
作者：
Benigni P;Marin R;Fernandez-Lima F
通讯作者：
Fernandez-Lima F
影响因子：
7.4
作者：
Benigni P;Thompson CJ;Ridgeway ME;Park MA;Fernandez-Lima F
通讯作者：
Fernandez-Lima F
影响因子：
3.3
作者：
Donten, Mateusz L.;Hamm, Peter;VandeVondele, Joost
通讯作者：
VandeVondele, Joost
影响因子：
1.8
作者：
Baker, Erin Shammel;Bernstein, Summer L.;Bowers, Michael T.
通讯作者：
Bowers, Michael T.
影响因子：
1.8
作者：
Drayss, Miriam K.;Blunk, Dirk;Schaefer, Mathias
通讯作者：
Schaefer, Mathias