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

Measuring the Enthalpy of an Individual Hydrogen Bond in a DNA Duplex with Nucleobase Isotope Editing and Variable-Temperature Infrared Spectroscopy

The level of interest in probing the strength of noncovalent interactions in DNA duplexes is high, as these weak forces dictate the range of suprastructures the double helix adopts under different conditions, in turn directly impacting the biological functions and industrial applications of duplexes that require making and breaking them to access the genetic code. However, few experimental tools can measure these weak forces embedded within large biological suprastructures in the native solution environment. Here, we develop experimental methods for detecting the presence of a single noncovalent interaction [a hydrogen bond (H-bond)] within a large DNA duplex in solution and measure its formation enthalpy (ΔH_f). We report that introduction of a H-bond into the TC2═O group from the noncanonical nucleobase 2-aminopurine produces an expected decrease ∼10 ± 0.76 cm^-1 (from ∼1720 cm^-1 in Watson-Crick to ∼1710 cm^-1 in 2-aminopurine), which correlates with an enthalpy of ∼0.93 ± 0.066 kcal/mol for this interaction.

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

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 first-principles 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 "tunnelling-ready" 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.

Demir G, Demir D. Quantum tunneling time delay investigation of [Formula: see text] ion in human telomeric G-quadruplex systems

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.

Time delay during intra-base proton tunneling in the guanine base of the single stranded DNA

Spontaneous point mutations are one of the main actors in evolution, and the tautomerization of organic bases in the DNA is hypothesized to be the underlying mechanism of this crucial process. Tautomerization can be induced by proton tunneling, and if it occurs in single-stranded DNA (ssDNA) during the replication process, tautomerized bases might give rise to a mismatch, which will eventually defect the genetic code. In the present work, we report on the tautomerization time in the guanine base of the ssDNA. The model we use includes an intra-base tunneling mechanism such that time tunneling (delay time) is estimated to be around a few pico-seconds. The time delay is found to be biologically relevant which indicates that it is long enough to induce point mutations. Our results close a gap in the literature and sheds light on the importance of point mutations originating from quantum effects in the ssDNA.