Time delay during the proton tunneling in the base pairs of the DNA double helix

Çelebi, Gizem; Ozcelik, Elif; Vardar, Emre; Demir, Durmuş A.

doi:10.1016/j.pbiomolbio.2021.06.001

Cited by 7 publications

(18 citation statements)

References 27 publications

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“…It is concordant with the wavefront delay, and respects therefore fundamentals of the relativity and quantum. Needless to say, (ATT) F gives the durations of tunneling-enabled phenomena in nature, which range from nuclear fusion [1] in physics to smell perception [45] in chemistry to DNA mutation [46,47,48,49] in biology. Likewise, it sets operation speeds of all tunneling-driven processes such as quantum annealing [50,51] -a tunneling-enabled quantum computation mechanism [52,53,26] which has already been implemented on an 1,800-qubit chip [27] by D-Wave Systems.…”

Section: Discussionmentioning

confidence: 99%

Tunneling time from spin fluctuations in Larmor clock

Demir

2022

Preprint

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Tunneling time, time needed for a quantum particle to tunnel through a potential energy barrier, can be measured by a duration marker. One such marker is spin reorientation due to Larmor precession. With a weak magnetic field in z direction, the Larmor clock reads two times, τ y and τ z , for a potential energy barrier along the y axis. The problem is to determine the actual tunneling time (ATT). Büttiker defines τ 2 y + τ 2 z to be the ATT. Steinberg and others, on the other hand, identify τ y with the ATT. The Büttiker and Steinberg times are based on average spin components but in non-commuting spin system average of one component requires the other two to fluctuate. In the present work, we study the effects of spin fluctuations and show that the ATT can well be τ y + τ 2 z τy . We analyze the ATT candidates and reveal that the fluctuation-based ATT acts as a transmission time in all of the low-barrier, high-barrier, thick-barrier and classical dynamics limits. We extract this new ATT using the most recent experimental data by the Steinberg group. The new ATT qualifies as a viable tunneling time formula.

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Section: Discussionmentioning

confidence: 99%

Tunneling time from spin fluctuations in Larmor clock

Demir

2022

Preprint

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“…There are two statements for enabling quantum mechanics in complex biological systems: (i) quantum phenomena can take place over very short time scales before wash away by its surroundings and (ii) quantum dynamics can be enhanced by a finely tuned and constructive interplay with its surroundings [16]. In the last decades, the growing number of theoretical and experimental studies supported quantum tunneling and quantum coherence effects on biology [22,27,28], however, other areas of quantum biology remain speculative such as magnetoreception [29] and olfaction [30,31]. Even though its fast progression, the main limitation of studies in quantum biology is the difficulty of monitoring experimental systems for precise physical measurement.…”

Section: Introductionmentioning

confidence: 99%

“…Our end goal is to estimate the duration of the K + transfer, namely time it takes for the ion to make a tunneling transition. Our estimates are based on the time formulae used for other quantum-biological processes [28] and will be found to give biologically relevant time scales also in K + transfer in G-quadruplexes.…”

Section: Introductionmentioning

confidence: 99%

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

Çelebi

Demir

2023

J Biol Inorg Chem

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

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“…The main difference between the A-T and G-C PES is that A-T has a considerable forward barrier for tautomer formation but a small reverse barrier that causes its tautomeric form to be unstable. − On the contrary, G-C has a sizable reverse barrier, giving a tautomeric lifetime comparable to that of the replication process. Moreover, quantum tunnelling leads to a fast proton exchange between the bases, such that the time scale of the helicase cleavage is much slower than the proton transfer dynamics . Consequently, using a semiclassical interpretation, , the potentially mutagenic tautomer is continuously formed and destroyed over time scales several orders of magnitude quicker than that of helicase cleavage, after which, the bases are split into their monomeric forms.…”

mentioning

confidence: 99%

Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerism

Slocombe

Winokan

Al-Khalili

et al. 2022

J. Phys. Chem. Lett.

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The misincorporation of a noncomplementary DNA base in the polymerase active site is a critical source of replication errors that can lead to genetic mutations. In this work, we model the mechanism of wobble mispairing and the subsequent rate of misincorporation errors by coupling firstprinciples quantum chemistry calculations to an open quantum systems master equation. This methodology allows us to accurately calculate the proton transfer between bases, allowing the misincorporation and formation of mutagenic tautomeric forms of DNA bases. Our calculated rates of genetic error formation are in excellent agreement with experimental observations in DNA. Furthermore, our quantum mechanics/molecular mechanics model predicts the existence of a short-lived "tunnellingready" configuration along the wobble reaction pathway in the polymerase active site, dramatically increasing the rate of proton transfer by a hundredfold, demonstrating that quantum tunnelling plays a critical role in determining the transcription error frequency of the polymerase.

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Time delay during the proton tunneling in the base pairs of the DNA double helix

Cited by 7 publications

References 27 publications

Tunneling time from spin fluctuations in Larmor clock

Tunneling time from spin fluctuations in Larmor clock

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

Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerism

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