1
|
Paul R, Paul R, Dutta D, Dash J. pH-dependent complex formation with TAR RNA and DNA: application towards logic gates. Analyst 2024; 149:1976-1980. [PMID: 38465447 DOI: 10.1039/d4an00074a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.
Collapse
Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| |
Collapse
|
2
|
Kumari B, Huwaidi A, Robert G, Cloutier P, Bass AD, Sanche L, Wagner JR. Shape Resonances in DNA: Nucleobase Release, Reduction, and Dideoxynucleoside Products Induced by 1.3 to 2.3 eV Electrons. J Phys Chem B 2022; 126:5175-5184. [PMID: 35793462 DOI: 10.1021/acs.jpcb.2c01851] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the details of DNA damage caused by high-energy particles or photons is complicated by the multitude of reactive species, arising from the ionization and dissociation of H2O, DNA, and protein. In this work, oligonucleotides (ODNs) are irradiated with a beam of low-energy electrons of 1.3 to 2.3 eV, which can only induce damage via the decay of shape resonances into various dissociative electron attachment channels. Using LC-MS/MS analysis, the major products are the release of nonmodified nucleobases (NB; Cyt ≫ Thy ∼ Ade > Gua). Additional damage includes 5,6-dihydropyrimidines (dHT > dHU) and eight nucleosides with modified sugar moieties consisting of 2',3'- and 2',5'-dideoxynucleosides (ddG > ddA ∼ ddC > ddT). The distribution of products is remarkably different in a 16-mer ODN compared to that observed previously with thymidylyl-(3'-5')-thymidine. This difference is explained by electron delocalization occurring within a sufficiently long strand, the DEA theory of O'Malley, and recent time-dependent density functional theory calculations.
Collapse
Affiliation(s)
- Bhavini Kumari
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Alaa Huwaidi
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Gabriel Robert
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Pierre Cloutier
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Andrew D Bass
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| |
Collapse
|
3
|
Kumar A, Sevilla MD. Proton-Transfer Reactions in One-Electron-Oxidized G-Quadruplexes: A Density Functional Theory Study. J Phys Chem B 2022; 126:1483-1491. [PMID: 35152699 PMCID: PMC8881324 DOI: 10.1021/acs.jpcb.1c10529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, G-quadruplexes (Gq) formed in B-DNA as secondary structures are found to be important therapeutic targets and material for developing nanodevices. Gq are guanine-rich and thus susceptible to oxidative damage by producing short-lived intermediate radicals via proton-transfer reactions. Understanding the mechanisms of radical formation in Gq is of fundamental interest to understand the early stages of DNA damage. Herein, we used density functional theory including aqueous phase (ωB97XD-PCM/6-31++G**) and considered single layer of Gq [G-quartets (G4): association of four guanines in a cyclic Hoogsteen hydrogen-bonded arrangement (Scheme 1)] to unravel the mechanisms of formation of intermediates by calculating the relative Gibbs free energies and spin density distributions of one-electron-oxidized G4 and its various proton-transfer states: G•+, G(N1-H)•, G(N2-H')•, G(N2-H″)•, G(N1-H)•-(H+O6)G, and G(N2-H)•-(H+N7)G. The present calculation predicts the formation of G(N2-H)•-(H+N7)G, which is only ca. 0.8 kcal/mol higher in energy than the initially formed G•+. The formation of G(N2-H)•-(H+N7)G plays a key role in explaining the formation of 8-OG along with G(N1-H)• formation via tautomerization from G(N2-H)•, as proposed recently.
Collapse
Affiliation(s)
- Anil Kumar
- Corresponding Author: . Tel: +1 248 370 2327, . Tel: +1 248 370 2328
| | | |
Collapse
|
4
|
Rodrigues F, Georgelin T, Rigaud B, Zhuang G, Fonseca MG, Valtchev V, Jaber M. Deadlocks of adenine ribonucleotide synthesis: evaluation of adsorption and condensation reactions in a zeolite micropore space. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00837h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report on adenine, d-ribose, and monophosphate adsorption/co-adsorption into the synthetic analog of the zeolite mineral mordenite followed by drying at 50 °C and thermal activation at 150 °C under an argon atmosphere.
Collapse
Affiliation(s)
- Francisco Rodrigues
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
- State University of Paraíba, UEPB, Department of Chemistry, Campina Grande, Paraíba, Brazil
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, 45000 Orléans, France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482), 4 place jussieu, 75005 Paris, France
| | - Guanzheng Zhuang
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
| | | | - Valentin Valtchev
- Normandy University, Laboratoire Catalyse & Spectrochimie, ENSICAEN, 6 bl Maréchal Juin, 14050 Caen, France
| | - Maguy Jaber
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
- Institut Universitaire de France, France
| |
Collapse
|
5
|
Zhou W, Liu J. Reaction mechanism and dynamics for C8-hydroxylation of 9-methylguanine radical cation by water molecules. Phys Chem Chem Phys 2021; 23:24464-24477. [PMID: 34698322 DOI: 10.1039/d1cp03884b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In contrast to their spontaneous deprotonation in aqueous solution, reactions of guanine and guanosine radical cations with water in the gas phase are exclusively initiated by hydration of the radical cations as reported in recent work (Y. Sun et al., Phys. Chem. Chem. Phys., 2018, 20, 27510). As gas-phase hydration reactions closely mimic the actual scenario for guanine radical cations in double-stranded DNA, exploration of subsequent reactions within their water complexes can provide an insight into the resulting oxidative damage to nucleosides. Herein guided-ion beam mass spectrometry experiment and direct dynamics trajectory simulations were carried out to examine prototype complexes of the 9-methylguanine radical cation with one and two water ligands (i.e., 9MG˙+·(H2O)1-2) in the gas phase, wherein the complexes were activated by collisional activation in the experiment and by thermal excitation at high temperatures in the simulations. Guided by mass spectroscopic measurements, trajectory results and reaction potential energy surface, three reaction pathways were identified. The first two reaction pathways start with H-atom abstraction from water by the O6 and N7 atoms in 9MG˙+ and are referred to as HAO6 and HAN7, respectively. The primary products of HAO6 and HAN7 reactions, including [9MG + HO6]+/[9MG + HN7]+ and ˙OH, react further to either form [8OH-9MG + HO6]˙+ and [8OH-9MG + HN7]˙+via C8-hydroxylation or form radical cations of 6-enol-guanine (6-enol-G˙+) and 7H-guanine (7HG˙+) via SN2-type methanol elimination. The third reaction pathway corresponds to the formation of 8OH-9MG+ by H elimination from the complex, referred to as HE. Among these product channels, [8OH-9MG + HN7]˙+ has the most favorable formation probability, especially in the presence of additional water molecules. This product may serve as a preceding structure to the 8-oxo-7,8-dihydroguanine lesion in DNA and has implications for health effects of radiation exposure and radiation therapy.
Collapse
Affiliation(s)
- Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| |
Collapse
|
6
|
Santermans S, Schanovsky F, Gupta M, Hellings G, Heyns M, Van Roy W, Martens K. The Significance of Nonlinear Screening and the pH Interference Mechanism in Field-Effect Transistor Molecular Sensors. ACS Sens 2021; 6:1049-1056. [PMID: 33496586 DOI: 10.1021/acssensors.0c02285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrolyte screening is well known for its detrimental impact on the sensitivity of liquid-gated field-effect transistor (FET) molecular sensors and is mostly described by the linearized Debye-Hückel model. However, charged and pH-sensitive FET sensing surfaces can limit the FET molecular sensitivity beyond the Debye-Hückel screening formalism. Pre-existing surface charges can lead to the breakdown of Debye-Hückel screening and induce enhanced nonlinear Poisson-Boltzmann screening. Moreover, the charging of the pH-sensitive surface groups interferes with biomolecule sensing resulting in a pH interference mechanism. With analytical equations and TCAD simulations, we highlight that the Debye-Hückel approximation can underestimate screening and overestimate FET molecular sensitivity by more than an order of magnitude. Screening strengthens significantly beyond Debye-Hückel in the proximity of even moderately charged surfaces and biomolecule charge densities (≥1 × 1012 q/cm2). We experimentally show the strong impact of both nonlinear screening and the pH interference effect on charge-based biomolecular sensing using a model system based on the covalent binding of single-stranded DNA on silicon FET sensors. The DNA signal increases from 24 mV at pH 7 to 96 mV at pH 3 in 1.5 mM PBS for a DNA density of 7 × 1012 DNA/cm2. Our model quantitatively explains the signal's pH dependence with roughly equal nonlinear screening and pH interference contributions. This work shows the importance of reducing the net charge and the pH sensitivity of the sensing surface to improve molecular sensing. Therefore, tailoring the gate dielectric and functional layer of FET sensors is a promising route to strong silicon FET molecular sensitivity boosts.
Collapse
Affiliation(s)
- Sybren Santermans
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
- Department of Materials Engineering, University of Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
| | - Franz Schanovsky
- Global TCAD Solutions GmbH, Bösendorferstraße 1/12, 1010 Wien, Austria
| | - Mihir Gupta
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
- Department of Physics and Astronomy, University of Leuven, Celestijnenlaan 200d, 3001 Leuven, Belgium
| | | | - Marc Heyns
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
- Department of Materials Engineering, University of Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
| | | | | |
Collapse
|
7
|
Deng P, Chen J, Yao L, Zhang P, Zhou J. Thymine-modified chitosan with broad-spectrum antimicrobial activities for wound healing. Carbohydr Polym 2021; 257:117630. [PMID: 33541656 DOI: 10.1016/j.carbpol.2021.117630] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/22/2020] [Accepted: 01/06/2021] [Indexed: 12/30/2022]
Abstract
Avoiding wound infections is a major challenge in wound care management, and new materials are urgently needed to address these problems. Herein, four water-soluble thymine-modified chitosan (TC) derivatives with the degree of substitution (DS) ranging from 0.23 to 0.62 were synthesized and freeze-dried to obtain porous sponge dressings. TC derivatives had broad-spectrum antibacterial activities against gram-negative bacteria, gram-positive bacteria, fungi, drug-resistance bacteria, Pseudomonas aeruginosa and Acinetobacter baumannii. Especially, the antioxidant and antibacterial properties of TC derivatives increased with increasing DS. Furthermore, TC derivatives showed excellent biocompatibility and blood compatibility. TC sponges could significantly accelerate the wound healing process than gauze and chitosan sponge. The histological analysis and immunohistochemical staining showed that the wounds treated with TC sponges displayed fewer inflammatory cells, and faster regeneration of epithelial tissue, collagen deposition and new blood vessel formation speed. Therefore, TC sponges can shed new light for wound dressing design.
Collapse
Affiliation(s)
- Pengpeng Deng
- Hubei Engineering Center of Natural Polymers-based Medical Materials, Key Laboratory of Biomedical Polymers of Ministry of Education, and Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Juanjuan Chen
- Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Lichao Yao
- Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
| | - Pingan Zhang
- Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China.
| | - Jinping Zhou
- Hubei Engineering Center of Natural Polymers-based Medical Materials, Key Laboratory of Biomedical Polymers of Ministry of Education, and Department of Chemistry, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
8
|
Wei S, Zhang Z, Liu S, Wang Y. Theoretical insight into 7,8-dihydrogen-8-oxoguanine radical cation deprotonation. NEW J CHEM 2021. [DOI: 10.1039/d1nj01653a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The pKa values of reactive protons in 8-oxoG˙+ and potential energy profiles for 8-oxoG radical cation deprotonation reaction (N1–H and N7–H) were firstly calculated.
Collapse
Affiliation(s)
- Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Zhenhua Zhang
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
| | - Shijun Liu
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Yinghui Wang
- College of Science
- Chang’an University
- Xi’an 710064
- China
| |
Collapse
|
9
|
Iglesias E. Gold Nanoparticles as Colorimetric Sensors for the Detection of DNA Bases and Related Compounds. Molecules 2020; 25:molecules25122890. [PMID: 32586064 PMCID: PMC7356728 DOI: 10.3390/molecules25122890] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023] Open
Abstract
Results regarding interaction of colloidal gold solutions with nucleobases, including uracil (U), as well as its sulfur derivatives, 2-thiouracil (2TU) and 4-thiouracil (4TU), cytosine (C), adenine (A), and guanine (G), as well as urea and thiourea (TU), are reported. Anionic stabilized citrate gold nanoparticles (AuNPs) were synthesized by reducing the tetrachloroaurate (III) trihydrate with trisodium citrate. The surface plasmon resonance (SPR) band was used in the characterization of synthesized AuNPs, as well as transmission electron microscope (TEM) imaging, which was used in the characterization of dispersed and aggregated gold nanoparticles. Interactions of nucleobases with the gold surface was analyzed by following the plasmon absorbance band red shift of the AuNPs. The sulfur-containing compounds adsorbed to the nanoparticle surfaces by chemisorption-type interactions; with TU and 4TU, the process is accompanied by a sudden change in color; in contrast, 2TU forms stable functionalized gold nanoparticles. Urea and U do not adsorb to nanoparticle surfaces, but the other heterocyclic bases containing nitrogen interact effectively with the gold surface, causing the assembly of nanoparticles, even though the interparticle self-aggregation process was slower than that mediated by either TU or 4TU. The method is efficient in the colorimetric detection of nucleobases and derivatives at concentration levels on the order of 1 µM.
Collapse
Affiliation(s)
- Emilia Iglesias
- Departamento de Química. Facultad de Ciencias. Campus A Zapateira, Universidade A Coruña, 15008-La Coruña, Spain
| |
Collapse
|
10
|
Prediction of the tautomer stability and acidity of phenacylpyridines in aqueous solution. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2558-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
11
|
Zhou Q, Wang Y, Dai X, Yang C, Jie J, Su H. One-electron oxidation of TAT-motif triplex DNA and the ensuing Hoogsteen hydrogen-bonding dissociation. J Chem Phys 2020; 152:035101. [PMID: 31968979 DOI: 10.1063/1.5135769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One-electron oxidation of adenine (A) leads initially to the formation of adenine radical cation (A•+). Subsequent deprotonation of A•+ can provoke deoxyribonucleic acid (DNA) damage, which further causes senescence, cancer formation, and even cell death. However, compared with considerable reports on A•+ reactions in free deoxyadenosine (dA) and duplex DNA, studies in non-B-form DNA that play critical biological roles are rare at present. It is thus of vital importance to explore non-B-form DNA, among which the triplex is an emerging topic. Herein, we investigate the deprotonation behavior of A•+ in the TAT triplex with continuous A bases by time-resolved laser flash photolysis. The rate constants for the one-oxidation of triplex 8.4 × 108 M-1 s-1 and A•+ deprotonation 1.3 × 107 s-1 are obtained. The kinetic isotope effect of A•+ deprotonation in the TAT triplex is 1.8, which is characteristic of a direct release of the proton into the solvent similar to free base dA. It is thus elucidated that the A•+ proton bound with the third strand is most likely to be released into the solvent because of the weaker Hoogsteen H-bonding interaction and the presence of the highly mobile hydration waters within the third strand. Additionally, it is confirmed through Fourier transform infrared spectroscopy that the deprotonation of A•+ results in the dissociation of the third strand and disruption of the secondary structure of the triplex. These results provide valuable kinetic data and in-depth mechanistic insights for understanding the adenine oxidative DNA damage in the triplex.
Collapse
Affiliation(s)
- Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Yinghui Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Xiaojuan Dai
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Chunfan Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| |
Collapse
|
12
|
Choi J, Tojo S, Ahn DS, Fujitsuka M, Miyamoto S, Kobayashi K, Ihee H, Majima T. Proton Transfer Accompanied by the Oxidation of Adenosine. Chemistry 2019; 25:7711-7718. [PMID: 30957282 DOI: 10.1002/chem.201900732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/03/2019] [Indexed: 11/07/2022]
Abstract
Despite numerous experimental and theoretical studies, the proton transfer accompanying the oxidation of 2'-deoxyadenosine 5'-monophosphate 2'-deoxyadenosine 5'-monophosphate (5'-dAMP, A) is still under debate. To address this issue, we have investigated the oxidation of A in acidic and neutral solutions by using transient absorption (TA) and time-resolved resonance Raman (TR3 ) spectroscopic methods in combination with pulse radiolysis. The steady-state Raman signal of A was significantly affected by the solution pH, but not by the concentration of adenosine (2-50 mm). More specifically, the A in acidic and neutral solutions exists in its protonated (AH+ (N1+H+ )) and neutral (A) forms, respectively. On the one hand, the TA spectral changes observed at neutral pH revealed that the radical cation (A.+ ) generated by pulse radiolysis is rapidly converted into A. (N6-H) through the loss of an imino proton from N6. In contrast, at acidic pH (<4), AH.2+ (N1+H+ ) generated by pulse radiolysis of AH+ (N1+H+ ) does not undergo the deprotonation process owing to the pKa value of AH.2+ (N1+H+ ), which is higher than the solution pH. Furthermore, the results presented in this study have demonstrated that A, AH+ (N1+H+ ), and their radical species exist as monomers in the concentration range of 2-50 mm. Compared with the Raman bands of AH+ (N1+H+ ), the TR3 bands of AH.2+ (N1+H+ ) are significantly down-shifted, indicating a decrease in the bond order of the pyrimidine and imidazole rings due to the resonance structure of AH.2+ (N1+H+ ). Meanwhile, A. (N6-H) does not show a Raman band corresponding to the pyrimidine+NH2 scissoring vibration due to diprotonation at the N6 position. These results support the final products generated by the oxidation of adenosine in acidic and neutral solutions being AH.2+ (N1+H+ ) and A. (N6-H), respectively.
Collapse
Affiliation(s)
- Jungkweon Choi
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Republic of Korea
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Sachiko Tojo
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Doo-Sik Ahn
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Republic of Korea
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Shunichi Miyamoto
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazuo Kobayashi
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Hyotcherl Ihee
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Republic of Korea
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| |
Collapse
|
13
|
Ma J, Marignier JL, Pernot P, Houée-Levin C, Kumar A, Sevilla MD, Adhikary A, Mostafavi M. Direct observation of the oxidation of DNA bases by phosphate radicals formed under radiation: a model of the backbone-to-base hole transfer. Phys Chem Chem Phys 2018; 20:14927-14937. [PMID: 29786710 DOI: 10.1039/c8cp00352a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In irradiated DNA, by the base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine. Phosphate radicals formed via ionization events in the DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier studies on irradiated hydrated DNA, on irradiated DNA-models in frozen aqueous solution and in neat dimethyl phosphate showed the formation of carbon-centered radicals and not phosphate radicals. Therefore, to model the backbone-to-base hole transfer process, we report picosecond pulse radiolysis studies of the reactions between H2PO4˙ with the DNA bases - G, A, T, and C in 6 M H3PO4 at 22 °C. The time-resolved observations show that in 6 M H3PO4, H2PO4˙ causes the one-electron oxidation of adenine, guanine and thymine, by forming the cation radicals via a single electron transfer (SET) process; however, the rate constant of the reaction of H2PO4˙ with cytosine is too low (<107 L mol-1 s-1) to be measured. The rates of these reactions are influenced by the protonation states and the reorganization energies of the base radicals and of the phosphate radical in 6 M H3PO4.
Collapse
Affiliation(s)
- Jun Ma
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France.
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Hartono YD, Xu Y, Karshikoff A, Nilsson L, Villa A. Modeling p K Shift in DNA Triplexes Containing Locked Nucleic Acids. J Chem Inf Model 2018. [PMID: 29537270 DOI: 10.1021/acs.jcim.7b00741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The protonation states for nucleic acid bases are difficult to assess experimentally. In the context of DNA triplex, the protonation state of cytidine in the third strand is particularly important, because it needs to be protonated in order to form Hoogsteen hydrogen bonds. A sugar modification, locked nucleic acid (LNA), is widely used in triplex forming oligonucleotides to target sites in the human genome. In this study, the parameters for LNA are developed in line with the CHARMM nucleic acid force field and validated toward the available structural experimental data. In conjunction, two computational methods were used to calculate the protonation state of the third strand cytidine in various DNA triplex environments: λ-dynamics and multiple pH regime. Both approaches predict p K of this cytidine shifted above physiological pH when cytidine is in the third strand in a triplex environment. Both methods show an upshift due to cytidine methylation, and a small downshift when the sugar configuration is locked. The predicted p K values for cytidine in DNA triplex environment can inform the design of better-binding oligonucleotides.
Collapse
Affiliation(s)
- Yossa Dwi Hartono
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden.,Division of Structural Biology and Biochemistry, School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - You Xu
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Andrey Karshikoff
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| |
Collapse
|
15
|
Martinez-Fernandez L, Improta R. Photoactivated proton coupled electron transfer in DNA: insights from quantum mechanical calculations. Faraday Discuss 2018; 207:199-216. [DOI: 10.1039/c7fd00195a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The energetics of the two main proton coupled electron transfer processes that could occur in DNA are determined by means of time dependent-DFT calculations, using the M052X functional and the polarizable continuum model to include solvent effect.
Collapse
Affiliation(s)
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche
- Istituto di Biostrutture e Bioimmagini
- 80136 Naples
- Italy
- LIDYL
| |
Collapse
|
16
|
Jie JL, Wang C, Zhao HM, Song D, Su HM. Experimental and Theoretical Study of Deprotonation of DNA Adenine Cation Radical. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1710198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jia-long Jie
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hong-mei Zhao
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Di Song
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hong-mei Su
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
17
|
Zheng L, Griesser M, Pratt DA, Greenberg MM. Aminyl Radical Generation via Tandem Norrish Type I Photocleavage, β-Fragmentation: Independent Generation and Reactivity of the 2'-Deoxyadenosin- N6-yl Radical. J Org Chem 2017; 82:3571-3580. [PMID: 28318253 DOI: 10.1021/acs.joc.7b00093] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Formal hydrogen atom abstraction from the nitrogen-hydrogen bonds in purine nucleosides produces reactive intermediates that are important in nucleic acid oxidation. Herein we describe an approach for the independent generation of the purine radical resulting from hydrogen atom abstraction from the N6-amine of 2'-deoxyadenosine (dA•). The method involves sequential Norrish Type I photocleavage of a ketone (7b) and β-fragmentation of the initially formed alkyl radical (8b) to form dA• and acetone. The formation of dA• was followed by laser flash photolysis, which yields a transient with λmax ≈ 340 nm and a broader weaker absorption centered at ∼560 nm. This transient grows in at ≥2 × 105 s-1; however, computations and reactivity data suggest that β-fragmentation occurs much faster, implying the consumption of dA• as it is formed. Continuous photolysis of 7b in the presence of ferrous ion or thiophenol produces good yields of dA, whereas less reactive thiols afford lower yields presumably due to a polarity mismatch. This tandem photochemical, β-fragmentation method promises to be useful for site-specific production of dA• in nucleic acid oligomers and/or polymers and also for the production of aminyl radicals, in general.
Collapse
Affiliation(s)
- Liwei Zheng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Markus Griesser
- Department of Chemistry & Biomolecular Sciences, University of Ottawa , 10 Marie Curie Pvt., Ottawa, Canada
| | - Derek A Pratt
- Department of Chemistry & Biomolecular Sciences, University of Ottawa , 10 Marie Curie Pvt., Ottawa, Canada
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| |
Collapse
|
18
|
Palagin D, Doye JPK. DNA-stabilized Ag-Au bimetallic clusters: the effects of alloying and embedding on optical properties. Phys Chem Chem Phys 2016; 18:22311-22. [PMID: 27459508 DOI: 10.1039/c6cp04352f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Global geometry optimization and time-dependent density functional theory calculations have been used to study the structural evolution and optical properties of AgnAun (n = 2-6) nanoalloys both as individual clusters and as clusters stabilized with the fragments of DNA of different size. We show that alloying can be used to control and tune the level of interaction between the metal atoms of the cluster and the organic fragments of the DNA ligands. For instance, gold and silver atoms are shown to exhibit synergistic effects in the process of charge transfer from the nucleobase to the cluster, with the silver atoms directly connected to the nitrogen atoms of cytosine increasing their positive partial charge, while their more electronegative neighbouring gold atoms host the excess negative charge. This allows the geometrical structures and optical absorption spectra of small bimetallic clusters to retain many of their main features upon aggregation with relatively large DNA fragments, such as a cytosine-based 9-nucleotide hairpin loop, which suggests a potential synthetic route to such hybrid metal-organic compounds, and opens up the possibility of bringing the unique tunable properties of bimetallic nanoalloys to biological applications.
Collapse
Affiliation(s)
- Dennis Palagin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| |
Collapse
|
19
|
Close DM, Wardman P. Calculations of the Energetics of Oxidation of Aqueous Nucleosides and the Effects of Prototropic Equilibria. J Phys Chem A 2016; 120:4043-8. [PMID: 27219530 DOI: 10.1021/acs.jpca.6b02653] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently the calculated standard reduction potentials of the radical-cations of N-methyl substituted DNA bases have been reported that agree fairly well with the experimental results. However, there are issues reflecting the fact that the experimental results usually relate to the couple E(o)(Nuc(•),H(+)/NucH(+)), whereas the calculated results are for the E(o)(Nuc(•+)/Nuc) couple. To calculate the midpoint reduction potential at pH 7 (Em7), it is important to have accurate acid dissociation constants (pKs) for both ground-state bases and their radicals, and the effects of uncertainty in some of these values (e.g., that of the adenosine radical) must be considered. Calculations of the pKs of the radicals of the nucleic acid bases (as nucleosides) have been performed to explore the effects the various pKs have on calculating the values of Em7 and to see what improvements can be made with the accuracy of the calculations.
Collapse
Affiliation(s)
- David M Close
- Department of Physics, East Tennessee State University , Johnson City, Tennessee 37614, United States
| | - Peter Wardman
- Gray Cancer Institute, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford , Oxford OX3 7DQ, United Kingdom
| |
Collapse
|
20
|
Sevilla MD, Becker D, Kumar A, Adhikary A. Gamma and Ion-Beam Irradiation of DNA: Free Radical Mechanisms, Electron Effects, and Radiation Chemical Track Structure. Radiat Phys Chem Oxf Engl 1993 2016; 128:60-74. [PMID: 27695205 DOI: 10.1016/j.radphyschem.2016.04.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The focus of our laboratory's investigation is to study the direct-type DNA damage mechanisms resulting from γ-ray and ion-beam radiation-induced free radical processes in DNA which lead to molecular damage important to cellular survival. This work compares the results of low LET (γ-) and high LET (ion-beam) radiation to develop a chemical track structure model for ion-beam radiation damage to DNA. Recent studies on protonation states of cytosine cation radicals in the N1-substituted cytosine derivatives in their ground state and 5-methylcytosine cation radicals in ground as well as in excited state are described. Our results exhibit a radical signature of excitations in 5-methylcytosine cation radical. Moreover, our recent theoretical studies elucidate the role of electron-induced reactions (low energy electrons (LEE), presolvated electrons (epre-), and aqueous (or, solvated) electrons (eaq-)). Finally DFT calculations of the ionization potentials of various sugar radicals show the relative reactivity of these species.
Collapse
Affiliation(s)
- Michael D Sevilla
- Department of Chemistry, Oakland University, Rochester, MI - 48309, USA
| | - David Becker
- Department of Chemistry, Oakland University, Rochester, MI - 48309, USA
| | - Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI - 48309, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, MI - 48309, USA
| |
Collapse
|
21
|
Wang S, Zhang C, Zhao P, Bu Y. Efficient and Substantial DNA Lesions From Near 0 eV Electron-Induced Decay of the O4-Hydrogenated Thymine Nucleotides: A DFT Study. J Phys Chem B 2015; 119:13971-9. [PMID: 26441346 DOI: 10.1021/acs.jpcb.5b06195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Possible electron-induced ruptures of C3'-O3', C5'-O5', and N1-C1' bonds in O4-hydrogenated 2'-deoxythymidine-3'-monophosphate (3'-dT(O4H)MPH) and 2'-deoxythymidine-5'-monophosphate (5'-dT(O4H)MPH) are investigated using density functional theory calculations, and efficient pathways are proposed. Electron attachment causes remarkable structural relaxation in the thymine C6 site. A concerted process of intramolecular proton transfer (IPT) from the C2' site of 2'-deoxyribose to the C6 site and the C3'-O3' bond rupture is observed in [3'-dT(O4H)MPH](-). A low activation barrier (9.32 kcal/mol) indicates that this pathway is the most efficient one as compared to other known pathways leading to backbone breaks of a single strand DNA at the non-3'-end thymine, which prevents the N1-C1' bond cleavage in [3'-dT(O4H)MPH](-). However, essentially spontaneous N1-C1' bond cleavage following similar IPT is predicted in [5'-dT(O4H)MPH](-). A moderate activation barrier (13.02 kcal/mol) for the rate-controlling IPT step suggests that base release from the N1-C1' cleavage arises readily at the 3'-end of single strand DNA with the strand ended by a thymine. The C5'-O5' bond has only an insignificant change in the IPT process. Solvent effects are found to increase slightly the energy requirements for either bond ruptures (11.23 kcal/mol (C3'-O3') vs 16.18 kcal/mol (N1-C1')), but not change their relative efficiencies.
Collapse
Affiliation(s)
- Shoushan Wang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
| | - Changzhe Zhang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
| | - Peiwen Zhao
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
| |
Collapse
|
22
|
Adhikary A, Kumar A, Bishop CT, Wiegand TJ, Hindi RM, Adhikary A, Sevilla MD. π-Radical to σ-Radical Tautomerization in One-Electron-Oxidized 1-Methylcytosine and Its Analogs. J Phys Chem B 2015; 119:11496-505. [PMID: 26237072 DOI: 10.1021/acs.jpcb.5b05162] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this work, iminyl σ-radical formation in several one-electron-oxidized cytosine analogs, including 1-MeC, cidofovir, 2'-deoxycytidine (dCyd), and 2'-deoxycytidine 5'-monophosphate (5'-dCMP), were investigated in homogeneous, aqueous (D2O or H2O) glassy solutions at low temperatures by employing electron spin resonance (ESR) spectroscopy. Upon employing density functional theory (DFT) (DFT/B3LYP/6-31G* method), the calculated hyperfine coupling constant (HFCC) values of iminyl σ-radical agree quite well with the experimentally observed ones, thus confirming its assignment. ESR and DFT studies show that the cytosine iminyl σ-radical is a tautomer of the deprotonated cytosine π-cation radical [cytosine π-aminyl radical, C(N4-H)(•)]. Employing 1-MeC samples at various pHs ranging from ca. 8 to 11, ESR studies show that the tautomeric equilibrium between C(N4-H)(•) and the iminyl σ-radical at low temperature is too slow to be established without added base. ESR and DFT studies agree that, in the iminyl σ-radical, the unpaired spin is localized on the exocyclic nitrogen (N4) in an in-plane pure p-orbital. This gives rise to an anisotropic nitrogen hyperfine coupling (Azz = 40 G) from N4 and a near isotropic β-nitrogen coupling of 9.7 G from the cytosine ring nitrogen at N3. Iminyl σ-radical should exist in its N3-protonated form, as the N3-protonated iminyl σ-radical is stabilized in solution by over 30 kcal/mol (ΔG = -32 kcal/mol) over its conjugate base, the N3-deprotonated form. This is the first observation of an isotropic β-hyperfine ring nitrogen coupling in an N-centered DNA radical. Our theoretical calculations predict that the cytosine iminyl σ-radical can be formed in double-stranded DNA by a radiation-induced ionization-deprotonation process that is only 10 kcal/mol above the lowest energy path.
Collapse
Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Casandra T Bishop
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Tyler J Wiegand
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ragda M Hindi
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ananya Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| |
Collapse
|
23
|
Bucher DB, Pilles BM, Carell T, Zinth W. Dewar Lesion Formation in Single- and Double-Stranded DNA is Quenched by Neighboring Bases. J Phys Chem B 2015; 119:8685-92. [DOI: 10.1021/acs.jpcb.5b04694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Dominik B. Bucher
- BioMolecular
Optics and Center for Integrated Protein Science, Ludwig-Maximilians- Universität München Oettingenstrasse 67, 80538 München, Germany
- Center
for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | - Bert M. Pilles
- BioMolecular
Optics and Center for Integrated Protein Science, Ludwig-Maximilians- Universität München Oettingenstrasse 67, 80538 München, Germany
| | - Thomas Carell
- Center
for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | - Wolfgang Zinth
- BioMolecular
Optics and Center for Integrated Protein Science, Ludwig-Maximilians- Universität München Oettingenstrasse 67, 80538 München, Germany
| |
Collapse
|
24
|
Halder A, Halder S, Bhattacharyya D, Mitra A. Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study. Phys Chem Chem Phys 2015; 16:18383-96. [PMID: 25070186 DOI: 10.1039/c4cp02541e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protonated nucleobases have significant roles in facilitating catalytic functions of RNA, and in stabilizing different structural motifs. Reported pKa values of nucleobase protonation suggest that the population of neutral nucleobases is 10(3)-10(4) times higher than that of protonated nucleobases under physiological conditions (pH ∼ 7.4). Therefore, a molecular level understanding of various putative roles of protonated nucleobases cannot be achieved without addressing the question of how their occurrence propensities and stabilities are related to the free energy costs associated with the process of protonation under physiological conditions. With water as the proton donor, we use advanced QM methods to evaluate the site specific protonation propensities of nucleobases in terms of their associated free energy changes (ΔGprot). Quantitative follow up on the energetics of base pair formation and database search for evaluating their occurrence frequencies, reveal a lack of correlation between base pair stability and occurrence propensities on the one hand, and ease of protonation on the other. For example, although N7 protonated adenine (ΔGprot = 40.0 kcal mol(-1)) is found to participate in stable base pairing, base pairs involving N7 protonated guanine (ΔGprot = 36.8 kcal mol(-1)), on geometry optimization, converge to a minima where guanine transfers its extra proton to its partner base. Such observations, along with examples of weak base pairs involving N3 protonation of cytosine (ΔGprot = 37.0 kcal mol(-1)) are rationalized by analysing the protonation induced charge redistributions which are found to significantly influence, both positively and negatively, the hydrogen bonding potentials of different functional sites of individual nucleobases. Protonation induced charge redistribution is also found to strongly influence (i) the aromatic character of the rings of the participating bases and (ii) hydrogen bonding potential of the free edges of the protonated base pair. Comprehensive analysis of a non-redundant RNA crystal structure dataset further reveals that, while availability of stabilization possibilities determine the feasibility of occurrence of protonated bases, their occurrence context and specific functional roles are important factors determining their occurrence propensities.
Collapse
Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India.
| | | | | | | |
Collapse
|
25
|
Thapa B, Schlegel HB. Calculations of pKa's and redox potentials of nucleobases with explicit waters and polarizable continuum solvation. J Phys Chem A 2014; 119:5134-44. [PMID: 25291241 DOI: 10.1021/jp5088866] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The SMD implicit solvation model augmented with one and four explicit water molecules was used to calculate pKa's and redox potentials of N-methyl-substituted nucleic acid bases guanine, adenine, cytosine, thymine, and uracil. Calculations were carried out with the B3LYP/6-31+G(d,p) level of theory. The same numbers of water molecules were hydrogen bonded to the neutral, protonated, and deprotonated nucleobases in their unoxidized and oxidized forms. The improvement in pKa1 involving neutrals and cations was modest. By contrast, the improvement in pKa2 involving neutrals and anions was quite significant, reducing the mean absolute error from 4.6 pKa units with no waters, to 2.6 with one water and 1.7 with four waters. For the oxidation of nucleobases, adding explicit waters did little to improve E(X(•),H(+)/XH), possibly because both species in the redox couple are neutral molecules at pH 7.
Collapse
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| |
Collapse
|
26
|
Kumar A, Sevilla MD. Proton transfer induced SOMO-to-HOMO level switching in one-electron oxidized A-T and G-C base pairs: a density functional theory study. J Phys Chem B 2014; 118:5453-8. [PMID: 24798145 PMCID: PMC4032191 DOI: 10.1021/jp5028004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In the present study,
we show that for one-electron oxidized A-T
or G-C base pairs the singly occupied molecular orbital (SOMO) is
located on A or G and is lower in energy than the doubly occupied
highest-occupied molecular orbital (HOMO) localized to the pyrimidines,
T or C. This directs second ionizations to the pyrimidine bases resulting
in triplet state diradical dications, (A•+-T•+) and (G•+-C•+). On interbase proton transfer, the SOMO and HOMO levels switch
and the second oxidation is redirected to G and A. For G-C, the doubly
oxidized singlet G(-H)+-C(H+) is more stable
than its triplet (G•+-C•+); however,
for A-T, the triplet (A•+-T•+)
lies lowest in energy. The study demonstrates that double ionization
of the A-T base pair results in a triplet dication diradical, which
is more stable than the proton-transferred triplet or singlet species;
whereas, double ionization of the G-C base pair, the proton transferred
doubly oxidized singlet, G(-H)+-C(H+), is more
stable and has both oxidations on guanine. In DNA, with both A-T and G-C, multiple oxidations would transfer
to the guanine base alone.
Collapse
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | | |
Collapse
|
27
|
Kumar A, Sevilla MD. π- vs σ-radical states of one-electron-oxidized DNA/RNA bases: a density functional theory study. J Phys Chem B 2013; 117:11623-32. [PMID: 24000793 DOI: 10.1021/jp407897n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As a result of their inherent planarity, DNA base radicals generated by one-electron oxidation/reduction or bond cleavage form π- or σ-radicals. While most DNA base systems form π-radicals, there are a number of nucleobase analogues such as one-electron-oxidized 6-azauraci1, 6-azacytosine, and 2-thiothymine or one-electron reduced 5-bromouracil that form more reactive σ-radicals. Elucidating the availability of these states within DNA, base radical electronic structure is important to the understanding of the reactivity of DNA base radicals in different environments. In this work, we address this question by the calculation of the relative energies of π- and σ-radical states in DNA/RNA bases and their analogues. We used density functional theory B3LYP/6-31++G** method to optimize the geometries of π- and σ-radicals in Cs symmetry (i.e., planar) in the gas phase and in solution using the polarized continuum model (PCM). The calculations predict that σ- and π-radical states in one-electron-oxidized bases of thymine, T(N3-H)(•), and uracil, U(N3-H)(•), are very close in energy; i.e., the π-radical is only ca. 4 kcal/mol more stable than the σ-radical. For the one-electron-oxidized radicals of cytosine, C(•+), C(N4-H)(•), adenine, A(•+), A(N6-H)(•), and guanine, G(•+), G(N2-H)(•), G(N1-H)(•), the π-radicals are ca. 16-41 kcal/mol more stable than their corresponding σ-radicals. Inclusion of solvent (PCM) is found to stabilize the π- over σ-radical of each of the systems. U(N3-H)(•) with three discrete water molecules in the gas phase is found to form a three-electron σ bond between the N3 atom of uracil and the O atom of a water molecule, but on inclusion of full solvation and discrete hydration, the π-radical remains most stable.
Collapse
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | | |
Collapse
|