Gizem Celebi Torabfam, Güleser K. Demir, Durmuş Demir
{"title":"Quantum tunneling time delay investigation of \\({{\\varvec{K}}}^{+}\\) ion in human telomeric G-quadruplex systems","authors":"Gizem Celebi Torabfam, Güleser K. Demir, Durmuş Demir","doi":"10.1007/s00775-022-01982-z","DOIUrl":null,"url":null,"abstract":"<div><p>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 (<span>\\({{\\varvec{K}}}^{+}\\)</span>) 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 <span>\\({{\\varvec{K}}}^{+}\\)</span> 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 <span>\\({{\\varvec{K}}}^{+}\\)</span> 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 <span>\\({{\\varvec{K}}}^{+}\\)</span> in G-quadruplex. The computations have shown that ion tunneling takes picosecond times. In addition, average <span>\\({{\\varvec{K}}}^{+}\\)</span> accumulation rate is found to be in the picoampere range. Our results show that time delay during the <span>\\({{\\varvec{K}}}^{+}\\)</span> 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.</p><h3>Graphical abstract</h3>\n <figure><div><div><div><picture><source><img></source></picture></div></div></div></figure>\n </div>","PeriodicalId":603,"journal":{"name":"JBIC Journal of Biological Inorganic Chemistry","volume":"28 2","pages":"213 - 224"},"PeriodicalIF":2.7000,"publicationDate":"2023-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00775-022-01982-z.pdf","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"JBIC Journal of Biological Inorganic Chemistry","FirstCategoryId":"1","ListUrlMain":"https://link.springer.com/article/10.1007/s00775-022-01982-z","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
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.
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.