1
|
Winokan M, Slocombe L, Al-Khalili J, Sacchi M. Multiscale simulations reveal the role of PcrA helicase in protecting against spontaneous point mutations in DNA. Sci Rep 2023; 13:21749. [PMID: 38065963 PMCID: PMC10709646 DOI: 10.1038/s41598-023-48119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Proton transfer across hydrogen bonds in DNA can produce non-canonical nucleobase dimers and is a possible source of single-point mutations when these forms mismatch under replication. Previous computational studies have revealed this process to be energetically feasible for the guanine-cytosine (GC) base pair, but the tautomeric product (G[Formula: see text]C[Formula: see text]) is short-lived. In this work we reveal, for the first time, the direct effect of the replisome enzymes on proton transfer, rectifying the shortcomings of existing models. Multi-scale quantum mechanical/molecular dynamics (QM/MM) simulations reveal the effect of the bacterial PcrA Helicase on the double proton transfer in the GC base pair. It is shown that the local protein environment drastically increases the activation and reaction energies for the double proton transfer, modifying the tautomeric equilibrium. We propose a regime in which the proton transfer is dominated by tunnelling, taking place instantaneously and without atomic rearrangement of the local environment. In this paradigm, we can reconcile the metastable nature of the tautomer and show that ensemble averaging methods obscure detail in the reaction profile. Our results highlight the importance of explicit environmental models and suggest that asparagine N624 serves a secondary function of reducing spontaneous mutations in PcrA Helicase.
Collapse
Affiliation(s)
- Max Winokan
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford, GU2 7XH, UK
| | - Louie Slocombe
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, GU2 7XH, UK
| | - Jim Al-Khalili
- School of Mathematics and Physics, University of Surrey, Guildford, GU2 7XH, UK
| | - Marco Sacchi
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, GU2 7XH, UK.
| |
Collapse
|
2
|
Ghasemi F, Tirandaz A. Environment assisted quantum model for studying RNA-DNA-error correlation created due to the base tautomery. Sci Rep 2023; 13:10788. [PMID: 37402822 PMCID: PMC10319750 DOI: 10.1038/s41598-023-38019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/30/2023] [Indexed: 07/06/2023] Open
Abstract
The adaptive mutation phenomenon has been drawing the attention of biologists for several decades in evolutionist community. In this study, we propose a quantum mechanical model of adaptive mutation based on the implications of the theory of open quantum systems. We survey a new framework that explain how random point mutations can be stabilized and directed to be adapted with the stresses introduced by the environments according to the microscopic rules dictated by constraints of quantum mechanics. We consider a pair of entangled qubits consist of DNA and mRNA pair, each coupled to a distinct reservoir for analyzing the spreed of entanglement using time-dependent perturbation theory. The reservoirs are physical demonstrations of the cytoplasm and nucleoplasm and surrounding environments of mRNA and DNA, respectively. Our predictions confirm the role of the environmental-assisted quantum progression of adaptive mutations. Computing the concurrence as a measure that determines to what extent the bipartite DNA-mRNA can be correlated through entanglement, is given. Preventing the entanglement loss is crucial for controlling unfavorable point mutations under environmental influences. We explore which physical parameters may affect the preservation of entanglement between DNA and mRNA pair systems, despite the destructive role of interaction with the environments.
Collapse
Affiliation(s)
- Fatemeh Ghasemi
- Department of Energy Engineering, Sharif University of Technology, P.O. Box 11365-9516, Tehran, Iran.
| | - Arash Tirandaz
- Department of Chemistry, Bu-Ali Sina University, Hamedan, Iran.
| |
Collapse
|
3
|
Peng HC, Castro GL, Karthikeyan V, Jarrett A, Katz MA, Hargrove JA, Hoang D, Hilber S, Meng W, Wang L, Fick RJ, Ahn JM, Kreutz C, Stelling AL. Measuring the Enthalpy of an Individual Hydrogen Bond in a DNA Duplex with Nucleobase Isotope Editing and Variable-Temperature Infrared Spectroscopy. J Phys Chem Lett 2023; 14:4313-4321. [PMID: 37130045 DOI: 10.1021/acs.jpclett.3c00178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
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 (ΔHf). 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.
Collapse
Affiliation(s)
- Hao-Che Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Gabrielle L Castro
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Varshini Karthikeyan
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Alina Jarrett
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Melanie A Katz
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - James A Hargrove
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - David Hoang
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Stefan Hilber
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Wenting Meng
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Robert J Fick
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| |
Collapse
|
4
|
Warman H, Slocombe L, Sacchi M. How proton transfer impacts hachimoji DNA. RSC Adv 2023; 13:13384-13396. [PMID: 37143915 PMCID: PMC10152326 DOI: 10.1039/d3ra00983a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023] Open
Abstract
Hachimoji DNA is a synthetic nucleic acid extension of DNA, formed by an additional four bases, Z, P, S, and B, that can encode information and sustain Darwinian evolution. In this paper, we aim to look into the properties of hachimoji DNA and investigate the probability of proton transfer between the bases, resulting in base mismatch under replication. First, we present a proton transfer mechanism for hachimoji DNA, analogous to the one presented by Löwdin years prior. Then, we use density functional theory to calculate proton transfer rates, tunnelling factors and the kinetic isotope effect in hachimoji DNA. We determined that the reaction barriers are sufficiently low that proton transfer is likely to occur even at biological temperatures. Furthermore, the rates of proton transfer of hachimoji DNA are much faster than in Watson-Crick DNA due to the barrier for Z-P and S-B being 30% lower than in G-C and A-T. Suggesting that proton transfer occurs more frequently in hachimoji DNA than canonical DNA, potentially leading to a higher mutation rate.
Collapse
Affiliation(s)
- Harry Warman
- School of Physics and Maths, University of Surrey Guildford GU2 7XH UK
| | - Louie Slocombe
- School of Chemistry and Chemical Engineering, University of Surrey Guildford GU2 7XH UK
| | - Marco Sacchi
- School of Chemistry and Chemical Engineering, University of Surrey Guildford GU2 7XH UK
| |
Collapse
|
5
|
King B, Winokan M, Stevenson P, Al-Khalili J, Slocombe L, Sacchi M. Tautomerisation Mechanisms in the Adenine-Thymine Nucleobase Pair during DNA Strand Separation. J Phys Chem B 2023; 127:4220-4228. [PMID: 36939840 DOI: 10.1021/acs.jpcb.2c08631] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
The adenine-thymine tautomer (A*-T*) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A*-T* while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A*-T* as the DNA strands unzip and the hydrogen bonds between the bases stretch. Molecular Dynamics simulations reveal the time scales and dynamics of DNA strand separation and the statistical ensemble of opening angles present in a biological environment. Our results demonstrate that the unwinding of DNA, an inherently out-of-equilibrium process facilitated by helicase, will change the energy landscape of the adenine-thymine tautomerization reaction. We propose that DNA strand separation allows the stable tautomerization of adenine-thymine, providing a feasible pathway for genetic point mutations via proton transfer between the A-T bases.
Collapse
Affiliation(s)
- Benjamin King
- Department of Physics, University of Surrey, Guildford GU2 7XH, U.K
| | - Max Winokan
- Leverhulme Quantum Biology Doctoral Training Centre, University of Surrey, Guildford GU2 7XH, U.K
| | - Paul Stevenson
- Department of Physics, University of Surrey, Guildford GU2 7XH, U.K
| | - Jim Al-Khalili
- Department of Physics, University of Surrey, Guildford GU2 7XH, U.K
| | - Louie Slocombe
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, U.K
| | - Marco Sacchi
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, U.K
| |
Collapse
|
6
|
Slocombe L, Winokan M, Al-Khalili J, Sacchi M. Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerism. J Phys Chem Lett 2023; 14:9-15. [PMID: 36562711 PMCID: PMC9841559 DOI: 10.1021/acs.jpclett.2c03171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/19/2022] [Indexed: 05/22/2023]
Abstract
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.
Collapse
Affiliation(s)
- Louie Slocombe
- Leverhulme
Quantum Biology Doctoral Training Centre, University of Surrey, GuildfordGU2 7XH, U.K.
- Department
of Chemistry, University of Surrey, GuildfordGU2 7XH, U.K.
| | - Max Winokan
- Leverhulme
Quantum Biology Doctoral Training Centre, University of Surrey, GuildfordGU2 7XH, U.K.
| | - Jim Al-Khalili
- Department
of Physics, University of Surrey, GuildfordGU2 7XH, U.K.
| | - Marco Sacchi
- Department
of Chemistry, University of Surrey, GuildfordGU2 7XH, U.K.
| |
Collapse
|
7
|
Tian B, Fang Y, Lei S, Xu K, He C, Li S, Ren H. Selective conformer detection of short-lived base pair tautomers: A computational study of the unusual guanine-cytosine pairs using ultrafast resonance Raman spectroscopy. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|