Quantum tunneling time delay investigation of \({{\varvec{K}}}^{+}\) ion in human telomeric G-quadruplex systems

IF 2.7 3区 化学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Gizem Celebi Torabfam, Güleser K. Demir, Durmuş Demir
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引用次数: 0

Abstract

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 (\({{\varvec{K}}}^{+}\)) 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 \({{\varvec{K}}}^{+}\) 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 \({{\varvec{K}}}^{+}\) 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 \({{\varvec{K}}}^{+}\) in G-quadruplex. The computations have shown that ion tunneling takes picosecond times. In addition, average \({{\varvec{K}}}^{+}\) accumulation rate is found to be in the picoampere range. Our results show that time delay during the \({{\varvec{K}}}^{+}\) 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.

Graphical abstract

Abstract Image

人类端粒g -四重体系统中\({{\varvec{K}}}^{+}\)离子的量子隧穿时延研究
富鸟嘌呤四重体DNA (g -四重体)是细胞生物学和纳米技术研究的热点。它的生物学功能需要一个稳定的g -四联体来防止单价金属阳离子的逃逸。钾离子(\({{\varvec{K}}}^{+}\))尤其重要,因为它在进入和退出通常在人类端粒中发现的g -四重体系统时经历了势能障碍。在目前的工作中,我们分析了\({{\varvec{K}}}^{+}\)阳离子进入和离开g -四重体所需的时间。我们的时间估计是基于熵隧穿时间,这是一个时间公式,它给出了质子隧穿DNA点突变的生物学相关结果。通过量子力学模拟研究确定了\({{\varvec{K}}}^{+}\)离子所经历的势能势垒,利用MATLAB求解薛定谔方程,将计算得到的本征函数和本征能量用于g -四重体中\({{\varvec{K}}}^{+}\)离子隧穿过程中的时间延迟和电荷积累速率。计算表明,离子隧穿时间为皮秒级。此外,发现平均\({{\varvec{K}}}^{+}\)积累速率在皮安范围内。我们的研究结果表明,\({{\varvec{K}}}^{+}\)离子隧穿过程中的时间延迟与生物系统中的构象转变时间大致相同,这可能是理解其在人类DNA中的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,在文献中第一次计算了离子从g -四重丛隧穿和进入g -四重丛的时间延迟。图形摘要
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来源期刊
JBIC Journal of Biological Inorganic Chemistry
JBIC Journal of Biological Inorganic Chemistry 化学-生化与分子生物学
CiteScore
5.90
自引率
3.30%
发文量
49
审稿时长
3 months
期刊介绍: Biological inorganic chemistry is a growing field of science that embraces the principles of biology and inorganic chemistry and impacts other fields ranging from medicine to the environment. JBIC (Journal of Biological Inorganic Chemistry) seeks to promote this field internationally. The Journal is primarily concerned with advances in understanding the role of metal ions within a biological matrix—be it a protein, DNA/RNA, or a cell, as well as appropriate model studies. Manuscripts describing high-quality original research on the above topics in English are invited for submission to this Journal. The Journal publishes original articles, minireviews, and commentaries on debated issues.
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