1
|
Riera Aroche R, Ortiz García YM, Martínez Arellano MA, Riera Leal A. DNA as a perfect quantum computer based on the quantum physics principles. Sci Rep 2024; 14:11636. [PMID: 38773193 PMCID: PMC11109248 DOI: 10.1038/s41598-024-62539-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
DNA is a complex multi-resolution molecule whose theoretical study is a challenge. Its intrinsic multiscale nature requires chemistry and quantum physics to understand the structure and quantum informatics to explain its operation as a perfect quantum computer. Here, we present theoretical results of DNA that allow a better description of its structure and the operation process in the transmission, coding, and decoding of genetic information. Aromaticity is explained by the oscillatory resonant quantum state of correlated electron and hole pairs due to the quantized molecular vibrational energy acting as an attractive force. The correlated pairs form a supercurrent in the nitrogenous bases in a single band π -molecular orbital ( π -MO). The MO wave function ( Φ ) is assumed to be the linear combination of the n constituent atomic orbitals. The central Hydrogen bond between Adenine (A) and Thymine (T) or Guanine (G) and Cytosine (C) functions like an ideal Josephson Junction. The approach of a Josephson Effect between two superconductors is correctly described, as well as the condensation of the nitrogenous bases to obtain the two entangled quantum states that form the qubit. Combining the quantum state of the composite system with the classical information, RNA polymerase teleports one of the four Bell states. DNA is a perfect quantum computer.
Collapse
Affiliation(s)
- R Riera Aroche
- Department of Research in Physics, University of Sonora, Hermosillo, Sonora, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - Y M Ortiz García
- Research Institute of Dentistry, University of Guadalajara, Guadalajara Jalisco, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - M A Martínez Arellano
- General Hospital of the State of Sonora, Boulevar José María Escrivá de Balaguer 157, Colonia Villa del Palmar, C.P. 83105, Hermosillo, Sonora, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - A Riera Leal
- General Hospital of the State of Sonora, Boulevar José María Escrivá de Balaguer 157, Colonia Villa del Palmar, C.P. 83105, Hermosillo, Sonora, Mexico.
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico.
| |
Collapse
|
2
|
Skrodzki D, Molinaro M, Brown R, Moitra P, Pan D. Synthesis and Bioapplication of Emerging Nanomaterials of Hafnium. ACS NANO 2024; 18:1289-1324. [PMID: 38166377 DOI: 10.1021/acsnano.3c08917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
A significant amount of progress in nanotechnology has been made due to the development of engineered nanoparticles. The use of metallic nanoparticles for various biomedical applications has been extensively investigated. Biomedical research is highly focused on them because of their inert nature, nanoscale structure, and similar size to many biological molecules. The intrinsic characteristics of these particles, including electronic, optical, physicochemical, and surface plasmon resonance, that can be altered by altering their size, shape, environment, aspect ratio, ease of synthesis, and functionalization properties, have led to numerous biomedical applications. Targeted drug delivery, sensing, photothermal and photodynamic therapy, and imaging are some of these. The promising clinical results of NBTXR3, a high-Z radiosensitizing nanomaterial derived from hafnium, have demonstrated translational potential of this metal. This radiosensitization approach leverages the dependence of energy attenuation on atomic number to enhance energy-matter interactions conducive to radiation therapy. High-Z nanoparticle localization in tumor issue differentially increases the effect of ionizing radiation on cancer cells versus nearby healthy ones and mitigates adverse effects by reducing the overall radiation burden. This principle enables material multifunctionality as contrast agents in X-ray-based imaging. The physiochemical properties of hafnium (Z = 72) are particularly advantageous for these applications. A well-placed K-edge absorption energy and high mass attenuation coefficient compared to elements in human tissue across clinical energy ranges leads to significant attenuation. Chemical reactivity allows for variety in nanoparticle synthesis, composition, and functionalization. Nanoparticles such as hafnium oxide exhibit excellent biocompatibility due to physiochemical inertness prior to incidence with ionizing radiation. Additionally, the optical and electronic properties are applicable in biosensing, optical component coatings, and semiconductors. The wide interest has prompted extensive research in design and synthesis to facilitate property fine-tuning. This review summarizes synthetic methods for hafnium-based nanomaterials and applications in therapy, imaging, and biosensing with a mechanistic focus. A discussion and future perspective section highlights clinical progress and elaborates on current challenges. By focusing on factors impacting applicational effectiveness and examining limitations this review aims to support researchers and expedite clinical translation of future hafnium-based nanomedicine.
Collapse
Affiliation(s)
- David Skrodzki
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Matthew Molinaro
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Richard Brown
- Department of Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Parikshit Moitra
- Department of Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dipanjan Pan
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, 101 Huck Life Sciences Building, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
3
|
Chevalier F, Schlathölter T, Poully JC. Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems. Chembiochem 2023; 24:e202300543. [PMID: 37712497 DOI: 10.1002/cbic.202300543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.
Collapse
Affiliation(s)
- François Chevalier
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen (The, Netherlands
- University College Groningen, University of Groningen, Groningen (The, Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| |
Collapse
|
4
|
Masi A, Capobianco A, Bobrowski K, Peluso A, Chatgilialoglu C. Hydroxyl Radical vs. One-Electron Oxidation Reactivities in an Alternating GC Double-Stranded Oligonucleotide: A New Type Electron Hole Stabilization. Biomolecules 2023; 13:1493. [PMID: 37892175 PMCID: PMC10605094 DOI: 10.3390/biom13101493] [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: 09/04/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
We examined the reaction of hydroxyl radicals (HO•) and sulfate radical anions (SO4•-), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO• to the G:C pair moiety, affording the [8-HO-G:C]• detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H+):C]• after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G]•+, in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C]• detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.
Collapse
Affiliation(s)
- Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
- Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznań, Poland
| |
Collapse
|
5
|
Zhu L, Li Q, Wan Y, Guo M, Yan L, Yin H, Shi Y. Short-Range Charge Transfer in DNA Base Triplets: Real-Time Tracking of Coherent Fluctuation Electron Transfer. Molecules 2023; 28:6802. [PMID: 37836645 PMCID: PMC10574627 DOI: 10.3390/molecules28196802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
The short-range charge transfer of DNA base triplets has wide application prospects in bioelectronic devices for identifying DNA bases and clinical diagnostics, and the key to its development is to understand the mechanisms of short-range electron dynamics. However, tracing how electrons are transferred during the short-range charge transfer of DNA base triplets remains a great challenge. Here, by means of ab initio molecular dynamics and Ehrenfest dynamics, the nuclear-electron interaction in the thymine-adenine-thymine (TAT) charge transfer process is successfully simulated. The results show that the electron transfer of TAT has an oscillating phenomenon with a period of 10 fs. The charge density difference proves that the charge transfer proportion is as high as 59.817% at 50 fs. The peak position of the hydrogen bond fluctuates regularly between -0.040 and -0.056. The time-dependent Marcus-Levich-Jortner theory proves that the vibrational coupling between nucleus and electron induces coherent electron transfer in TAT. This work provides a real-time demonstration of the short-range coherent electron transfer of DNA base triplets and establishes a theoretical basis for the design and development of novel biological probe molecules.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ying Shi
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China; (L.Z.); (Q.L.); (Y.W.); (M.G.); (L.Y.); (H.Y.)
| |
Collapse
|
6
|
Narayanan S J J, Tripathi D, Verma P, Adhikary A, Dutta AK. Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials. ACS OMEGA 2023; 8:10669-10689. [PMID: 37008102 PMCID: PMC10061531 DOI: 10.1021/acsomega.2c06776] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.
Collapse
Affiliation(s)
- Jishnu Narayanan S J
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Pooja Verma
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Amitava Adhikary
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Achintya Kumar Dutta
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
7
|
Aminzare M, Jiang J, Mandl GA, Mahshid S, Capobianco JA, Dorval Courchesne NM. Biomolecules incorporated in halide perovskite nanocrystals: synthesis, optical properties, and applications. NANOSCALE 2023; 15:2997-3031. [PMID: 36722934 DOI: 10.1039/d2nr05565a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Halide perovskite nanocrystals (HPNCs) have emerged at the forefront of nanomaterials research over the past two decades. The physicochemical and optoelectronic properties of these inorganic semiconductor nanoparticles can be modulated through the introduction of various ligands. The use of biomolecules as ligands has been demonstrated to improve the stability, luminescence, conductivity and biocompatibility of HPNCs. The rapid advancement of this field relies on a strong understanding of how the structure and properties of biomolecules influences their interactions with HPNCs, as well as their potential to extend applications of HPNCs towards biological applications. This review addresses the role of several classes of biomolecules (amino acids, proteins, carbohydrates, nucleotides, etc.) that have shown promise for improving the performance of HPNCs and their potential applications. Specifically, we have reviewed the recent advances on incorporating biomolecules with HP nanomaterials on the formation, physicochemical properties, and stability of HP compounds. We have also shed light on the potential for using HPs in biological and environmental applications by compiling some recent of proof-of-concept demonstrations. Overall, this review aims to guide the field towards incorporating biomolecules into the next-generation of high-performance HPNCs for biological and environmental applications.
Collapse
Affiliation(s)
- Masoud Aminzare
- Department of Chemical Engineering, McGill University, 3610 University Street, Wong Building, Room 4180, Montréal, QC, H3A 0C5, Canada.
| | - Jennifer Jiang
- Department of Chemical Engineering, McGill University, 3610 University Street, Wong Building, Room 4180, Montréal, QC, H3A 0C5, Canada.
| | - Gabrielle A Mandl
- Department of Chemistry and Biochemistry and Centre for NanoScience Research, 7141 Rue Sherbrooke Ouest, Concordia University, Montreal, QC, H4B 1R6, Canada
| | - Sara Mahshid
- Department of Bioengineering, McGill University, 817 Sherbrooke Street West, Macdonald Engineering Building, Room 355, Montréal, QC, H3A 0C3, Canada
| | - John A Capobianco
- Department of Chemistry and Biochemistry and Centre for NanoScience Research, 7141 Rue Sherbrooke Ouest, Concordia University, Montreal, QC, H4B 1R6, Canada
| | - Noémie-Manuelle Dorval Courchesne
- Department of Chemical Engineering, McGill University, 3610 University Street, Wong Building, Room 4180, Montréal, QC, H3A 0C5, Canada.
| |
Collapse
|
8
|
Vasca E, Siano F, Caruso T. Fluorescence Detecting of Paraquat and Diquat Using Host-Guest Chemistry with a Fluorophore-Pendant Calix[6]arene. SENSORS (BASEL, SWITZERLAND) 2023; 23:1120. [PMID: 36772161 PMCID: PMC9920563 DOI: 10.3390/s23031120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Paraquat (PQ) and diquat (DQ), some of the most widely used herbicides in the world, both present a high mortality index after intentional exposure. In this paper, a fluorescence sensing method for PQ and DQ, based on host-guest molecular recognition, is proposed. Calix[6]arene derivatives containing anthracene or naphthalene as pendant fluorophore at their lower rim recognize DQ and PQ in hydroalcoholic solution with a broad linear response range at the μg L-1 level concentration. The linear response ranges were found from 1.0 to 18 μg L-1 with the detection limit of 31 ng L-1 for paraquat, and from 1.0 to 44 μg L-1 with the detection limit of 0.16 μg L-1 for diquat. The recognition process is detected by following the decrease in the fluorescence emission consequent to complexation. The proposed quenching method has been applied to the determination of paraquat in drinking water samples.
Collapse
Affiliation(s)
- Ermanno Vasca
- Department of Chemistry and Biology, University of Salerno, 84084 Fisciano, Italy
| | - Francesco Siano
- Institute of Food Science, National Research Council, 83100 Avellino, Italy
| | - Tonino Caruso
- Department of Chemistry and Biology, University of Salerno, 84084 Fisciano, Italy
| |
Collapse
|
9
|
Electron Transfer Rates in Solution: Toward a Predictive First Principle Approach. CHEMISTRY 2023. [DOI: 10.3390/chemistry5010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Using a very recently proposed theoretical model, electron transfer rates in solution are calculated from first principles for different donor-acceptor pairs in tetrahydrofuran. We show that this approach, which integrates tunneling effects into a classical treatment of solvent motion, is able to provide reliable rate constants and their temperature dependence, even in the case of highly exergonic reactions, where Marcus’ theory usually fails.
Collapse
|
10
|
Capobianco A, Landi A, Peluso A. Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations. Int J Mol Sci 2022; 23:ijms232214452. [PMID: 36430930 PMCID: PMC9697240 DOI: 10.3390/ijms232214452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/09/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
Molecular dynamics simulations and geometry optimizations carried out at the quantum level as well as by quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations very similar to those observed in crystallographic double-stranded B-DNA, with rise coordinates close to ≈3.3 Å. In agreement with the experimental evidence, the computational results show that DNA single strands rich in adjacent purine nucleobases assume more regular arrangements than poly-thymine. The preliminary results suggest that single-stranded poly-cytosine DNA should also retain a substantial helical order in solution. A comparison of the structures of single and double helices confirms that the B-DNA motif is a favorable arrangement also for single strands. Indeed, the optimal geometry of the complementary single helices is changed to a very small extent in the formation of the duplex.
Collapse
|
11
|
Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases. Molecules 2022; 27:molecules27217408. [DOI: 10.3390/molecules27217408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical–computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.
Collapse
|
12
|
Biomimetic Radical Chemistry and Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072042. [PMID: 35408441 PMCID: PMC9000372 DOI: 10.3390/molecules27072042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/16/2022] [Indexed: 01/02/2023]
Abstract
Some of the most interesting aspects of free radical chemistry that emerged in the last two decades are radical enzyme mechanisms, cell signaling cascades, antioxidant activities, and free radical-induced damage of biomolecules. In addition, identification of modified biomolecules opened the way for the evaluation of in vivo damage through biomarkers. When studying free radical-based chemical mechanisms, it is very important to establish biomimetic models, which allow the experiments to be performed in a simplified environment, but suitably designed to be in strict connection with cellular conditions. The 28 papers (11 reviews and 17 articles) published in the two Special Issues of Molecules on "Biomimetic Radical Chemistry and Applications (2019 and 2021)" show a remarkable range of research in this area. The biomimetic approach is presented with new insights and reviews of the current knowledge in the field of radical-based processes relevant to health, such as biomolecular damages and repair, signaling and biomarkers, biotechnological applications, and novel synthetic approaches.
Collapse
|
13
|
Landi A, Capobianco A, Peluso A. The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study. Molecules 2021; 26:molecules26185497. [PMID: 34576968 PMCID: PMC8465834 DOI: 10.3390/molecules26185497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 12/28/2022] Open
Abstract
The time needed to establish electronic resonant conditions for charge transfer in oxidized DNA has been evaluated by molecular dynamics simulations followed by QM/MM computations which include counterions and a realistic solvation shell. The solvent response is predicted to take ca. 800–1000 ps to bring two guanine sites into resonance, a range of values in reasonable agreement with the estimate previously obtained by a kinetic model able to correctly reproduce the observed yield ratios of oxidative damage for several sequences of oxidized DNA.
Collapse
|
14
|
LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability. MATERIALS 2021; 14:ma14174930. [PMID: 34501020 PMCID: PMC8434186 DOI: 10.3390/ma14174930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022]
Abstract
To describe the molecular electronic structure of nucleic acid bases and other heterocycles, we employ the Linear Combination of Atomic Orbitals (LCAO) method, considering the molecular wave function as a linear combination of all valence orbitals, i.e., 2s, 2px, 2py, 2pz orbitals for C, N, and O atoms and 1s orbital for H atoms. Regarding the diagonal matrix elements (also known as on-site energies), we introduce a novel parameterization. For the non-diagonal matrix elements referring to neighboring atoms, we employ the Slater–Koster two-center interaction transfer integrals. We use Harrison-type expressions with factors slightly modified relative to the original. We compare our LCAO predictions for the ionization and excitation energies of heterocycles with those obtained from Ionization Potential Equation of Motion Coupled Cluster with Singles and Doubles (IP-EOMCCSD)/aug-cc-pVDZ level of theory and Completely Normalized Equation of Motion Coupled Cluster with Singles, Doubles, and non-iterative Triples (CR-EOMCCSD(T))/aug-cc-pVDZ level of theory, respectively, (vertical values), as well as with available experimental data. Similarly, we calculate the transfer integrals between subsequent base pairs, to be used for a Tight-Binding (TB) wire model description of charge transfer and transport along ideal or deformed B-DNA. Taking into account all valence orbitals, we are in the position to treat deflection from the planar geometry, e.g., DNA structural variability, a task impossible for the plane Hückel approach (i.e., using only 2pz orbitals). We show the effects of structural deformations utilizing a 20mer evolved by Molecular Dynamics.
Collapse
|
15
|
The Two Faces of the Guanyl Radical: Molecular Context and Behavior. Molecules 2021; 26:molecules26123511. [PMID: 34207639 PMCID: PMC8227002 DOI: 10.3390/molecules26123511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
The guanyl radical or neutral guanine radical G(-H)• results from the loss of a hydrogen atom (H•) or an electron/proton (e–/H+) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC•+ pair. The role of the two G(-H)• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.
Collapse
|
16
|
Dong Y, Liao H, Gao Y, Cloutier P, Zheng Y, Sanche L. Early Events in Radiobiology: Isolated and Cluster DNA Damage Induced by Initial Cations and Nonionizing Secondary Electrons. J Phys Chem Lett 2021; 12:717-723. [PMID: 33400538 DOI: 10.1021/acs.jpclett.0c03341] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Radiobiological damage is principally triggered by an initial cation and a secondary electron (SE). We address the fundamental questions: What lesions are first produced in DNA by this cation or nonionizing SE? What are their relative contributions to isolated and potentially lethal cluster lesions? Five monolayer films of dry plasmid DNA deposited on graphite or tantalum substrates are bombarded by 0.1-100 eV electrons in a vacuum. From measurements of the current transmitted through the films, 3.5 and 4.5 cations per incident 60 and 100 eV electrons, respectively, are estimated to be produced and stabilized within DNA. Damage analysis at 6, 10, 20, 30, 60, and 100 eV indicates that essentially all lesions, but preferentially cluster damages, are produced by non-ionizing or weakly ionizing electrons of energies below 12 eV. Most of these lesions are induced within femtosecond times, via transient anions and electron transfer within DNA, with little contributions from the numerous cations.
Collapse
Affiliation(s)
- Yanfang Dong
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Hong Liao
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Yingxia Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Pierre Cloutier
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, P.R. China
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
| |
Collapse
|
17
|
Velardo A, Landi A, Borrelli R, Peluso A. Reliable Predictions of Benzophenone Singlet-Triplet Transition Rates: A Second-Order Cumulant Approach. J Phys Chem A 2021; 125:43-49. [PMID: 33369419 DOI: 10.1021/acs.jpca.0c07848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fermi golden rule and second-order cumulant expansion of the time-dependent density matrix have been used to compute from first principles the rate of intersystem crossing in benzophenone, using minimum-energy geometries and normal modes of vibrations computed at the TDDFT/CAM-B3LYP level. Both approaches yield reliable values of the S1 decay rate, the latter being almost in quantitative agreement with the results of time-dependent spectroscopic measurements (0.154 ps-1 observed vs 0.25 ps-1 predicted). The Fermi golden rule slightly overestimates the decay rate of S1 state (kd = 0.45 ps-1) but provides better insights into the chemico-physical parameters, which govern the transition from a thermally equilibrated population of S1, showing that the indirect mechanism is much faster than the direct one because of the vanishingly small Franck-Condon weighted density of states at ΔE of transition.
Collapse
Affiliation(s)
- Amalia Velardo
- Department of Chemistry, University of Torino, Via P. Giuria, 7, 10125 Torino, Italy.,Dipartimento di Chimica e Biologia Adolfo Zambelli, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA, Italy
| | - Alessandro Landi
- Dipartimento di Chimica e Biologia Adolfo Zambelli, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA, Italy
| | - Raffaele Borrelli
- Department of Agricultural, Forestry and Food Science, University of Torino, I-10195 Grugliasco, Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia Adolfo Zambelli, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA, Italy
| |
Collapse
|
18
|
Maciá E. Base-Pairs' Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E5119. [PMID: 33202814 PMCID: PMC7697525 DOI: 10.3390/ma13225119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 05/12/2023]
Abstract
By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson-Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons' dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.
Collapse
Affiliation(s)
- Enrique Maciá
- Departamento de Física de Materiales, Facultad CC. Físicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| |
Collapse
|
19
|
Landi A, Capobianco A, Peluso A. Coherent Effects in Charge Transport in Molecular Wires: Toward a Unifying Picture of Long-Range Hole Transfer in DNA. J Phys Chem Lett 2020; 11:7769-7775. [PMID: 32830977 PMCID: PMC8154848 DOI: 10.1021/acs.jpclett.0c01996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the framework of a multistep mechanism in which environmental motion triggers comparatively faster elementary electron-transfer steps and stabilizes hole-transfer products, microscopic coherence is crucial for rationalizing the observed yield ratios of oxidative damage to DNA. Interference among probability amplitudes of indistinguishable electron-transfer paths is able to drastically change the final outcome of charge transport, even in DNA oligomers constituted by similar building blocks, and allows for reconciling apparently discordant experimental observations. Properly tailored DNA oligomers appear to be a promising workbench for studying tunneling in the presence of dissipation at the macroscopic level.
Collapse
|
20
|
Kaczmarek R, Ward S, Debnath D, Jacobs T, Stark AD, Korczyński D, Kumar A, Sevilla MD, Denisov SA, Shcherbakov V, Pernot P, Mostafavi M, Dembinski R, Adhikary A. One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate. Chemistry 2020; 26:9495-9505. [PMID: 32059063 PMCID: PMC7416487 DOI: 10.1002/chem.202000247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/09/2020] [Indexed: 12/26/2022]
Abstract
The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S- )=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G.+ -P(S- )=S. The ionization potential of G-P(S- )=S was calculated to be slightly lower than that of guanine in 5'-dGMP. Subsequent thermally activated hole transfer from G.+ to P(S- )=S led to dithiyl radical (P-2S. ) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S- )=S concentrations showed a bimolecular conversion of P-2S. to the σ2 -σ*1 -bonded dimer anion radical [-P-2S- . 2S-P-]- [ΔG (150 K, DFT)=-7.2 kcal mol-1 ]. However, [-P-2S- . 2S-P-]- formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=-1.4 kcal mol-1 ]. Neither P-2S. nor [-P-2S- . 2S-P-]- oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.
Collapse
Affiliation(s)
- Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Dipra Debnath
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Taisiya Jacobs
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Alexander D Stark
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Dariusz Korczyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Sergey A Denisov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Viacheslav Shcherbakov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Pascal Pernot
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay, 91405 Cedex, France
| | - Roman Dembinski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
| |
Collapse
|
21
|
Kumar A, Adhikary A, Sevilla MD, Close DM. One-electron oxidation of ds(5'-GGG-3') and ds(5'-G(8OG)G-3') and the nature of hole distribution: a density functional theory (DFT) study. Phys Chem Chem Phys 2020; 22:5078-5089. [PMID: 32073006 PMCID: PMC7058519 DOI: 10.1039/c9cp06244k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Of particular interest in radiation-induced charge transfer processes in DNA is the extent of hole localization immediately after ionization and subsequent relaxation. To address this, we considered double stranded oligomers containing guanine (G) and 8-oxoguanine (8OG), i.e., ds(5'-GGG-3') and ds(5'-G8OGG-3') in B-DNA conformation. Using DFT, we calculated a variety of properties, viz., vertical and adiabatic ionization potentials, spin density distributions in oxidized stacks, solvent and solute reorganization energies and one-electron oxidation potential (E0) in the aqueous phase. Calculations for the vertical state of the -GGG- cation radical showed that the spin was found mainly (67%) on the middle G. However, upon relaxation to the adiabatic -GGG- cation radical, the spin localized (96%) on the 5'-G, as observed in experiments. Hole localizations on the middle G and 3'-G were higher in energy by 0.5 kcal mol-1 and 0.4 kcal mol-1, respectively, than that of 5'-G. In the -G8OGG- cation radical, the spin localized only on the 8OG in both vertical and adiabatic states. The calculated vertical ionization potentials of -GGG- and -G8OGG- stacks were found to be lower than that of the vertical ionization potential of a single G in DNA. The calculated E0 values of -GGG- and -G8OGG- stacks are 1.15 and 0.90 V, respectively, which owing to stacking effects are substantially lower than the corresponding experimental E0 values of their monomers (1.49 and 1.18 V, respectively). SOMO to HOMO level switching is observed in these oxidized stacks. Consequently, our calculations predict that local double oxidations in DNA will form triplet diradical states, which are especially significant for high LET radiations.
Collapse
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA.
| | | | | | | |
Collapse
|