Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, 34956, Istanbul, Turkey.
Department of Electrical and Electronics Engineering, Dokuz Eylül University, Buca, 35390, İzmir, Turkey.
J Biol Inorg Chem. 2023 Mar;28(2):213-224. doi: 10.1007/s00775-022-01982-z. Epub 2023 Jan 19.
Guanine-rich quadruplex DNA (G-quadruplex) is of interest both in cell biology and nanotechnology. Its biological functions necessitate a G-quadruplex to be stabilized against escape of the monovalent metal cations. The potassium ion ([Formula: see text]) is particularly important as it experiences a potential energy barrier while it enters and exits the G-quadruplex systems which are normally found in human telomere. In the present work, we analyzed the time it takes for the [Formula: see text] cations to get in and out of the G-quadruplex. Our time estimate is based on entropic tunneling time-a time formula which gave biologically relevant results for DNA point mutation by proton tunneling. The potential energy barrier experienced by [Formula: see text] ions is determined from a quantum mechanical simulation study, Schrodinger equation is solved using MATLAB, and the computed eigenfunctions and eigenenergies are used in the entropic tunneling time formula to compute the time delay and charge accumulation rate during the tunneling of [Formula: see text] in G-quadruplex. The computations have shown that ion tunneling takes picosecond times. In addition, average [Formula: see text] accumulation rate is found to be in the picoampere range. Our results show that time delay during the [Formula: see text] ion tunneling is in the ballpark of the conformational transition times in biological systems, and it could be an important parameter for understanding its biological role in human DNA as well as for the possible applications in biotechnology. To our knowledge, for the first time in the literature, time delay during the ion tunneling from and into G-quadruplexes is computed.
富含鸟嘌呤的四链体 DNA（G-四链体）在细胞生物学和纳米技术领域都具有重要意义。其生物学功能需要稳定 G-四链体，以防止单价金属阳离子逃逸。钾离子（[Formula: see text]）特别重要，因为它在进入和离开通常存在于人类端粒中的 G-四链体系统时会遇到势能障碍。在本工作中，我们分析了[Formula: see text]阳离子进出 G-四链体所需的时间。我们的时间估计基于熵隧穿时间——一种通过质子隧穿对 DNA 点突变给出生物学相关结果的时间公式。[Formula: see text]离子经历的势能障碍是通过量子力学模拟研究确定的，Schrödinger 方程使用 MATLAB 求解，计算出的本征函数和本征能用于熵隧穿时间公式，以计算 G-四链体中[Formula: see text]隧穿时的延迟时间和电荷积累率。计算表明，离子隧穿需要皮秒时间。此外，发现平均[Formula: see text]积累率在皮安范围内。我们的结果表明，[Formula: see text]离子隧穿过程中的延迟时间与生物系统中构象转变时间相当，这可能是理解其在人类 DNA 中生物学作用以及在生物技术中可能应用的重要参数。据我们所知，这是文献中首次计算出 G-四链体中离子隧穿的延迟时间。
