1
|
Chawla M, Poater A, Oliva R, Cavallo L. Unveiling structural and energetic characterization of the emissive RNA alphabet anchored in the methylthieno[3,4- d]pyrimidine heterocycle core. Phys Chem Chem Phys 2024; 26:16358-16368. [PMID: 38805177 DOI: 10.1039/d3cp06136a] [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: 05/29/2024]
Abstract
This study presents a comprehensive theoretical exploration of the fluorescent non-natural emissive nucleobases- mthA, mthG, mthC, and mthU derived from the methylthieno[3,4-d]pyrimidine heterocycle. Our calculations, aligning with experimental findings, reveal that these non-natural bases exert minimal influence on the geometry of classical Watson-Crick base pairs within an RNA duplex, maintaining H-bonding akin to natural bases. In terms of energy, the impact of the modified bases, but for mthG, is also found to be little significant. We delved into an in-depth analysis of the photophysical properties of these non-natural bases. This investigation unveiled a correlation between their absorption/emission peaks and the substantial impact of the modification on the energy levels of the highest unoccupied molecular orbitals (HOMO) and the lowest unoccupied molecular orbital (LUMO). Notably, this alteration in energy levels resulted in a significant reduction of the HOMO-LUMO gap, from approximately 5.4-5.5 eV in the natural bases, to roughly 3.9-4.7 eV in the modified bases. This shift led to a consequential change in absorption and emission spectra towards longer wavelengths, elucidating their bathochromic shift.
Collapse
Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, KAUST Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Ma Aurèlia Capmany 69, Girona 17003, Catalonia, Spain
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, Naples, I-80143, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, KAUST Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
| |
Collapse
|
2
|
Tor Y. Isomorphic Fluorescent Nucleosides. Acc Chem Res 2024; 57:1325-1335. [PMID: 38613490 PMCID: PMC11079976 DOI: 10.1021/acs.accounts.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.
Collapse
Affiliation(s)
- Yitzhak Tor
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
3
|
Babar V, Sharma S, Shaikh AR, Oliva R, Chawla M, Cavallo L. Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS 2 and Janus MoSSe Monolayers. ACS APPLIED MATERIALS & INTERFACES 2024; 16:21427-21437. [PMID: 38634539 PMCID: PMC11071042 DOI: 10.1021/acsami.3c18400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA nucleobase detection, owing to their impressive surface-to-volume ratio. This study employs density functional theory with van der Waals corrections to methodically scrutinize the adsorption behavior and electronic band structure properties of a DNA system composed of eight hachimoji nucleotide letters adsorbed on both MoS2 and MoSSe monolayers. Through a comprehensive conformational search, we pinpoint the most favorable adsorption sites, quantifying their adsorption energies and charge transfer properties. The analysis of electronic band structure unveils the emergence of flat bands in close proximity to the Fermi level post-adsorption, a departure from the pristine MoS2 and MoSSe monolayers. Furthermore, leveraging the nonequilibrium Green's function approach, we compute the current-voltage characteristics, providing valuable insights into the electronic transport properties of the system. All hachimoji bases exhibit physisorption with a horizontal orientation on both monolayers. Notably, base G demonstrates high sensitivity on both substrates. The obtained current-voltage (I-V) characteristics, both without and with base adsorption on MoS2 and the Se side of MoSSe, affirm excellent sensing performance. This research significantly advances our understanding of potential DNA sensing platforms and their electronic characteristics, thereby propelling the endeavor for personalized medicine through enhanced DNA sequencing technologies.
Collapse
Affiliation(s)
- Vasudeo Babar
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sitansh Sharma
- Department
of Research and Innovation, STEMskills Research
and Education Lab Private Limited, Faridabad, Haryana 121002, India
| | - Abdul Rajjak Shaikh
- Department
of Research and Innovation, STEMskills Research
and Education Lab Private Limited, Faridabad, Haryana 121002, India
| | - Romina Oliva
- Department
of Sciences and Technologies, University
Parthenope of Naples, Centro Direzionale Isola C4, 80143 Naples, Italy
| | - Mohit Chawla
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Physical
Sciences and Engineering Division, KAUST Catalysis Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
4
|
Beal R, Valverde D, Gonçalvez PFB, Borin AC. Photophysics of tz Adenine and tz Guanine fluorescent nucleobases embedded into DNA and RNA. J Comput Chem 2023; 44:2246-2255. [PMID: 37486177 DOI: 10.1002/jcc.27194] [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: 04/25/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
UV-VIS photoinduced events of tz A and tz G embedded into DNA and RNA are described by combining the Extended Multi-State Second-Order Perturbation Theory (XMS-CASPT2) and electrostatic embedding molecular mechanics methods (QM/MM). Our results point out that the S1 1 (ππ* La ) state is the bright state in both environments. After the photoexcitation to the S1 1 (ππ* La ) state, the electronic population evolves barrierless towards its minimum, from where the excess of energy can be dissipated by fluorescence. As the minimum energy crossing point structure between the ground and first bright states lies in a high-energy region, the direct internal conversion to the ground state is an unviable mechanism. Other spectroscopic properties (for instance, absorption and Stokes shifts) and comparisons with photochemical properties of canonical nucleobases are also provided.
Collapse
Affiliation(s)
- Roiney Beal
- Grupo de Química Teórica e Computacional, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Danillo Valverde
- Unité de Chimie Physique Théorique et Structurale, Namur Institute of Structured Matter, Université de Namur, Namur, Belgium
| | - Paulo F B Gonçalvez
- Grupo de Química Teórica e Computacional, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| |
Collapse
|
5
|
Nguyen TL, Samuel Leon Magdaleno J, Rajjak Shaikh A, Choowongkomon K, Li V, Lee Y, Kim H. Designing a multi-epitope candidate vaccine by employing immunoinformatics approaches to control African swine fever spread. J Biomol Struct Dyn 2023; 41:10214-10229. [PMID: 36510707 DOI: 10.1080/07391102.2022.2153922] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
The African swine fever virus has been circulating for decades and is highly infectious, often fatal to farmed and wild pigs. There is currently no approved vaccine or treatment for the disease, making prevention even more difficult. Therefore, vaccine development is necessary and urgent to limit the consequences of ASF and ensure the food chain and sustainability of the swine industry. This research study was conducted to design a multi-epitope vaccine for controlling veterinary diseases caused by the African swine fever virus. We employed the immunoinformatics approaches to reveal 37 epitopes from different viral proteins of ASFV. These epitopes were linked to adjuvants and linkers to form a full-fledged immunogenic vaccine construct. The tertiary structure of the final vaccine was predicted using a deep-learning approach. The molecular docking and molecular dynamics predicted stable interactions between the vaccine and immune receptor TLR5 of Sus scrofa (Pig). The MD simulation studies reflect that the calculated parameters like RMSD, RMSF, number of hydrogen bonds, and finally, the buried interface surface area for the complex remained stable throughout the simulation time. This analysis suggests the stability of interface interactions between the TLR5 and the multi-epitope vaccine construct. Further, the physiochemical analysis demonstrated that our designed vaccine construct was expected to have high stability and prolonged half-life time in mammalian cells. Traditional vaccine design experiments require significant time and financial input from the development stage to the final product. Studies like this can assist in accelerating vaccine development while minimizing the cost.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jorge Samuel Leon Magdaleno
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Vladimir Li
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Youngho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| |
Collapse
|
6
|
Gong A, Liu W, Lin Y, Huang L, Xie Z. Adaptive Laboratory Evolution Reveals the Selenium Efflux Process To Improve Selenium Tolerance Mediated by the Membrane Sulfite Pump in Saccharomyces cerevisiae. Microbiol Spectr 2023; 11:e0132623. [PMID: 37098949 PMCID: PMC10269739 DOI: 10.1128/spectrum.01326-23] [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: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/27/2023] Open
Abstract
Selenium (Se) is a micronutrient in most eukaryotes, and Se-enriched yeast is the most common selenium supplement. However, selenium metabolism and transport in yeast have remained unclear, greatly hindering the application of this element. To explore the latent selenium transport and metabolism mechanisms, we performed adaptive laboratory evolution under the selective pressure of sodium selenite and successfully obtained selenium-tolerant yeast strains. Mutations in the sulfite transporter gene ssu1 and its transcription factor gene fzf1 were found to be responsible for the tolerance generated in the evolved strains, and the selenium efflux process mediated by ssu1 was identified in this study. Moreover, we found that selenite is a competitive substrate for sulfite during the efflux process mediated by ssu1, and the expression of ssu1 is induced by selenite rather than sulfite. Based on the deletion of ssu1, we increased the intracellular selenomethionine content in Se-enriched yeast. This work confirms the existence of the selenium efflux process, and our findings may benefit the optimization of Se-enriched yeast production in the future. IMPORTANCE Selenium is an essential micronutrient for mammals, and its deficiency severely threatens human health. Yeast is the model organism for studying the biological role of selenium, and Se-enriched yeast is the most popular selenium supplement to solve Se deficiency. The cognition of selenium accumulation in yeast always focuses on the reduction process. Little is known about selenium transport, especially selenium efflux, which may play a crucial part in selenium metabolism. The significance of our research is in determining the selenium efflux process in Saccharomyces cerevisiae, which will greatly enhance our knowledge of selenium tolerance and transport, facilitating the production of Se-enriched yeast. Moreover, our research further advances the understanding of the relationship between selenium and sulfur in transport.
Collapse
Affiliation(s)
- Ao Gong
- Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenyue Liu
- Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yelong Lin
- Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Laili Huang
- Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhixiong Xie
- Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China
- College of Life Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
7
|
Kaushik V, Jain P, Akhtar N, Joshi A, Gupta LR, Grewal RK, Oliva R, Shaikh AR, Cavallo L, Chawla M. Immunoinformatics-Aided Design and In Vivo Validation of a Peptide-Based Multiepitope Vaccine Targeting Canine Circovirus. ACS Pharmacol Transl Sci 2022. [DOI: 10.1021/acsptsci.2c00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Pankaj Jain
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Nahid Akhtar
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Amit Joshi
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Lovi Raj Gupta
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
8
|
Ribas-Massonis A, Cicujano M, Duran J, Besalú E, Poater A. Free-Radical Photopolymerization for Curing Products for Refinish Coatings Market. Polymers (Basel) 2022; 14:polym14142856. [PMID: 35890631 PMCID: PMC9324147 DOI: 10.3390/polym14142856] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023] Open
Abstract
Even though there are many photocurable compositions that are cured by cationic photopolymerization mechanisms, UV curing generally consists of the formation of cross-linking covalent bonds between a resin and monomers via a photoinitiated free radical polymerization reaction, obtaining a three-dimensional polymer network. One of its many applications is in the refinish coatings market, where putties, primers and clear coats can be cured faster and more efficiently than with traditional curing. All these products contain the same essential components, which are resin, monomers and photoinitiators, the latter being the source of free radicals. They may also include additives used to achieve a certain consistency, but always taking into account the avoidance of damage to the UV curing—for example, by removing light from the innermost layers. Surface curing also has its challenges since it can be easily inhibited by oxygen, although this can be solved by adding scavengers such as amines or thiols, able to react with the otherwise inactive peroxy radicals and continue the propagation of the polymerization reaction. In this review article, we cover a broad analysis from the organic point of view to the industrial applications of this line of research, with a wide current and future range of uses.
Collapse
Affiliation(s)
- Aina Ribas-Massonis
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Spain; (A.R.-M.); (J.D.); (E.B.)
| | - Magalí Cicujano
- Roberlo S.A., Ctra. N-II, km 706,5, Riudellots de la Selva, 17457 Girona, Spain;
| | - Josep Duran
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Spain; (A.R.-M.); (J.D.); (E.B.)
| | - Emili Besalú
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Spain; (A.R.-M.); (J.D.); (E.B.)
| | - Albert Poater
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Spain; (A.R.-M.); (J.D.); (E.B.)
- Correspondence:
| |
Collapse
|
9
|
Poater J, Heitkämper J, Poater A, Maraval V, Chauvin R. Zwitterionic Aromaticity on Azulene Extrapolated to
carbo
‐Azulene. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jordi Poater
- Departament de Química Inorgànica i Orgànica & IQTCUB Universitat de Barcelona 08028 Barcelona Spain
- ICREA 08010 Barcelona Spain
| | - Juliane Heitkämper
- Universität Stuttgart Institut für Theoretische Chemie Pfaffenwaldring 55 70569 Stuttgart Germany
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, c/ Mª Aurèlia Capmany 69 17003 Girona, Catalonia Spain
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, c/ Mª Aurèlia Capmany 69 17003 Girona, Catalonia Spain
| | - Valérie Maraval
- LCC-CNRS University of Toulouse 205 route de Narbonne 31077 Toulouse France
| | - Remi Chauvin
- LCC-CNRS University of Toulouse 205 route de Narbonne 31077 Toulouse France
| |
Collapse
|
10
|
Parshotam S, Joy M, Rossano-Tapia M, Mora-Gomez VA, Brown A. The thermochemical, structural, and spectroscopic analyses of the tautomers of sulfur and selenium modified emissive nucleobases. CAN J CHEM 2021. [DOI: 10.1139/cjc-2020-0294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, density functional theory (DFT) and time dependent density functional theory (TD-DFT) are used to investigate the stabilities and spectral properties [IR, UV–vis, and two-photon absorption (2PA)] of two sets of modified RNA nucleobase tautomers. The modifications introduce either a sulfur or selenium atom to form an isothiazolo[4,3-d]pyrimidine or isoselenazolo[4,3-d]pyrimidine heterocyclic core, respectively. The relative stabilities of both sets of modified tautomers determined with B3LYP/6-31++G(d,p) reveal that in water (with a polarizable continuum model), the 6-keto-2-amino tautomer of guanine and the rare 4-imino-2-keto tautomer of cytosine may be present at significant populations, whereas the 6-enol-2-amino tautomer of guanine is more common in the gas phase. The identification of these modified tautomers is possible due to the natural differences in their vibrational modes and hence IR spectra. Furthermore, the photophysical properties of both these sets of modified tautomers indicate that excitation and emission energies are shifted relative to their more abundant form in both one photon absorption and emission and 2PA spectra, as determined at the B3LYP/6-31++G(d,p) and CAM-B3LYP/aug-cc-pVDZ levels of theory, respectively. Even though the 2PA cross sections in water for all of the species are small (0.3–2.3 GM), the modified cytosine tautomer shows promise, as its cross section is larger than the more dominant form. The spectral separation between the dominant form and the tautomers of isoselenazole and isothiazole modified cytosine and guanine are relatively similar, suggesting both modifications could be useful in elucidating the tautomers from their more abundant counterparts.
Collapse
Affiliation(s)
- Shyam Parshotam
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Megan Joy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Maria Rossano-Tapia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - V. A. Mora-Gomez
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| |
Collapse
|
11
|
Iqbal N, Yaqoob M, Javed M, Abbasi M, Iqbal J, Iqbal MA. Synthesis in combination with Biological and Computational evaluations of selenium-N-Heterocyclic Carbene compounds. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2020.113135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
12
|
Chawla M, Gorle S, Shaikh AR, Oliva R, Cavallo L. Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study. Comput Struct Biotechnol J 2021; 19:1312-1324. [PMID: 33738080 PMCID: PMC7940798 DOI: 10.1016/j.csbj.2021.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 01/14/2023] Open
Abstract
The non-natural ethynylmethylpyridone C-nucleoside (W), a thymidine (T) analogue that can be incorporated in oligonucleotides by automated synthesis, has recently been reported to form a high fidelity base pair with adenosine (A) and to be well accommodated in B-DNA duplexes. The enhanced binding affinity for A of W, as compared to T, makes it an ideal modification for biotechnological applications, such as efficient probe hybridization for the parallel detection of multiple DNA strands. In order to complement the experimental study and rationalize the impact of the non-natural W nucleoside on the structure, stability and dynamics of DNA structures, we performed quantum mechanics (QM) calculations along with molecular dynamics (MD) simulations. Consistently with the experimental study, our QM calculations show that the A:W base pair has an increased stability as compared to the natural A:T pair, due to an additional CH-π interaction. Furthermore, we show that mispairing between W and guanine (G) causes a distortion in the planarity of the base pair, thus explaining the destabilization of DNA duplexes featuring a G:W pair. MD simulations show that incorporation of single or multiple consecutive A:W pairs in DNA duplexes causes minor changes to the intra- and inter-base geometrical parameters, while a moderate widening/shrinking of the major/minor groove of the duplexes is observed. QM calculations applied to selected stacks from the MD simulations also show an increased stacking energy for W, over T, with the neighboring bases.
Collapse
Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abdul Rajjak Shaikh
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
13
|
Flamme M, Röthlisberger P, Levi-Acobas F, Chawla M, Oliva R, Cavallo L, Gasser G, Marlière P, Herdewijn P, Hollenstein M. Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate. ACS Chem Biol 2020; 15:2872-2884. [PMID: 33090769 DOI: 10.1021/acschembio.0c00396] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.
Collapse
Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l’École de Médecine, 75006 Paris, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| |
Collapse
|
14
|
Kalra K, Gorle S, Cavallo L, Oliva R, Chawla M. Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs. Nucleic Acids Res 2020; 48:5825-5838. [PMID: 32392301 PMCID: PMC7293021 DOI: 10.1093/nar/gkaa345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 01/15/2023] Open
Abstract
We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1-3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-π interaction as compared to the OH-π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-π or the OH-π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.
Collapse
Affiliation(s)
- Kanav Kalra
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
15
|
Đorđević IS, Popadić M, Sarvan M, Petković-Benazzouz M, Janjić GV. Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:122-136. [PMID: 32831247 DOI: 10.1107/s2052520619016287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/03/2019] [Indexed: 06/11/2023]
Abstract
Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C-H...Se and C-H...S interactions (∼80%), notably less numerous are structures with Se...Se and S...S interactions (∼5%), and Se...π and S...π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C-H...Se (∼-0.8 kcal mol-1) and C-H...S interactions are weaker than the most stable parallel interaction (∼-3.3 kcal mol-1) and electrostatic interactions of σ/π type (∼-2.6 kcal mol-1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O-H...Se (∼-4.4 kcal mol-1) and N-H...Se interactions (∼-2.2 kcal mol-1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.
Collapse
Affiliation(s)
- Ivana S Đorđević
- SI Institute of Chemistry, Technology and Metallurgy, National Institute, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Marko Popadić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia
| | - Mirjana Sarvan
- Faculty of Physics, University of Belgrade, Studentski trg 12, Belgrade, Serbia
| | | | - Goran V Janjić
- SI Institute of Chemistry, Technology and Metallurgy, National Institute, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| |
Collapse
|
16
|
Chawla M, Minenkov Y, Vu KB, Oliva R, Cavallo L. Structural and Energetic Impact of Non-natural 7-Deaza-8-azaguanine, 7-Deaza-8-azaisoguanine, and Their 7-Substituted Derivatives on Hydrogen-Bond Pairing with Cytosine and Isocytosine. Chembiochem 2019; 20:2262-2270. [PMID: 30983115 DOI: 10.1002/cbic.201900245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Indexed: 12/12/2022]
Abstract
The impact of 7-deaza-8-azaguanine (DAG) and 7-deaza-8-azaisoguanine (DAiG) modifications on the geometry and stability of the G:C Watson-Crick (cWW) base pair and the G:iC and iG:C reverse Watson-Crick (tWW) base pairs has been characterized theoretically. In addition, the effect on the same base pairs of seven C7-substituted DAG and DAiG derivatives, some of which have been previously experimentally characterized, has been investigated. Calculations indicate that all of these modifications have a negligible impact on the geometry of the above base pairs, and that modification of the heterocycle skeleton has a small impact on the base-pair interaction energies. Instead, base-pair interaction energies are dependent on the nature of the C7 substituent. For the 7-substituted DAG-C cWW systems, a linear correlation between the base-pair interaction energy and the Hammett constant of the 7-substituent is found, with higher interaction energies corresponding to more electron-withdrawing substituents. Therefore, the explored modifications are expected to be accommodated in both parallel and antiparallel nucleic acid duplexes without perturbing their geometry, while the strength of a base pair (and duplex) featuring a DAG modification can, in principle, be tuned by incorporating different substituents at the C7 position.
Collapse
Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - Khanh B Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ho Chi Minh City, Vietnam
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
| |
Collapse
|
17
|
Richmond CJ, Escayola S, Poater A. Axial Ligand Effects of Ru-BDA Complexes in the O-O Bond Formation via the I2M Bimolecular Mechanism in Water Oxidation Catalysis. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201801450] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Craig J. Richmond
- Level 5; RMIT Europe Media-TIC Building; c/ Roc Boronat, 117 08018 Barcelona Catalonia Spain
| | - Sílvia Escayola
- Institut de Química Computacional i Catàlisi and Departament de Química; Universitat de Girona; c/ Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química; Universitat de Girona; c/ Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| |
Collapse
|