1
|
Xie C, Yang R, Wan X, Li H, Ge L, Li X, Zhao G. A High-Proton Conductivity All-Biomass Proton Exchange Membrane Enabled by Adenine and Thymine Modified Cellulose Nanofibers. Polymers (Basel) 2024; 16:1060. [PMID: 38674980 PMCID: PMC11054160 DOI: 10.3390/polym16081060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Nanocellulose fiber materials were considered promising biomaterials due to their excellent biodegradability, biocompatibility, high hydrophilicity, and cost-effectiveness. However, their low proton conductivity significantly limited their application as proton exchange membranes. The methods previously reported to increase their proton conductivity often introduced non-biodegradable groups and compounds, which resulted in the loss of the basic advantages of this natural polymer in terms of biodegradability. In this work, a green and sustainable strategy was developed to prepare cellulose-based proton exchange membranes that could simultaneously meet sustainability and high-performance criteria. Adenine and thymine were introduced onto the surface of tempo-oxidized nanocellulose fibers (TOCNF) to provide many transition sites for proton conduction. Once modified, the proton conductivity of the TOCNF membrane increased by 31.2 times compared to the original membrane, with a specific surface area that had risen from 6.1 m²/g to 86.5 m²/g. The wet strength also increased. This study paved a new path for the preparation of environmentally friendly membrane materials that could replace the commonly used non-degradable ones, highlighting the potential of nanocellulose fiber membrane materials in sustainable applications such as fuel cells, supercapacitors, and solid-state batteries.
Collapse
Affiliation(s)
- Chong Xie
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Runde Yang
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Xing Wan
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Haorong Li
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Liangyao Ge
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Xiaofeng Li
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China
| | - Guanglei Zhao
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| |
Collapse
|
2
|
Xie C, Yang R, Wan X, Li H, Ge L, Li X, Zhao G. A Novel Nanofiber Hydrogel Adhesive Based on Carboxymethyl Cellulose Modified by Adenine and Thymine. Polymers (Basel) 2024; 16:1008. [PMID: 38611265 PMCID: PMC11013687 DOI: 10.3390/polym16071008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Natural polymer-based adhesive hydrogels have garnered significant interest for their outstanding strength and versatile applications, in addition to being eco-friendly. However, the adhesive capabilities of purely natural products are suboptimal, which hampers their practical use. To address this, we engineered carboxymethyl cellulose (CMC) surfaces with complementary bases, adenine (A) and thymine (T), to facilitate the self-assembly of adhesive hydrogels (CMC-AT) with a nanofiber configuration. Impressively, the shear adhesive strength reached up to 6.49 MPa with a mere 2% adhesive concentration. Building upon this innovation, we conducted a comparative analysis of the shear adhesion properties between CMC and CMC-AT hydrogel adhesives when applied to delignified and non-delignified wood chips. We examined the interplay between the adhesives and the substrate, as well as the role of mechanical interlocking in overall adhesion performance. Our findings offer a fresh perspective on the development of new biodegradable polymer hydrogel adhesives.
Collapse
Affiliation(s)
- Chong Xie
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Runde Yang
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Xing Wan
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Haorong Li
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Liangyao Ge
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| | - Xiaofeng Li
- School of Food Science and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China
| | - Guanglei Zhao
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Engineering, South China University of Technology, Wushan Road, Guangzhou 510641, China; (C.X.); (R.Y.); (X.W.); (H.L.); (L.G.)
| |
Collapse
|
3
|
Zhou F, Mao J, Jin Z, Zhu L, Li X. Multi-omic analysis of precocious puberty girls: pathway changes and metabolite validation. Front Endocrinol (Lausanne) 2024; 15:1285666. [PMID: 38487340 PMCID: PMC10937432 DOI: 10.3389/fendo.2024.1285666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/15/2024] [Indexed: 03/17/2024] Open
Abstract
Objective Precocious puberty (PP) is a prevalent endocrine disorder affecting the physical and mental wellbeing of children. Identifying the triggering factors of PP has become a central issue. This study seeks to investigate the metabolomic and transcriptomic alterations in PP. Material and methods First, 37 school-aged girls diagnosed with PP and 25 age-matched prepubertal control girls were recruited, and the fecal samples were collected for non-targeted metabolomic analysis to screen for differentially expressed metabolites (DEMs). Subsequently, an animal model of PP was constructed by danazol administration to neonatal female rats, and both fecal non-targeted metabolomics and serum next-generation transcriptomic sequencing were performed to screen DEMs and differentially expressed genes (DEGs) in PP. Moreover, the DEM co-existing in clinical and animal models was administrated to PP rats to explore the role of the target metabolite in PP. Results A total of 24 DEMs in PP clinical samples and 180 DEMs and 425 DEGs in PP animal samples were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEMs and DEGs were enriched in disease-associated pathways, including fatty acid synthesis, glycerolipid metabolism, pyrimidine metabolism, steroid hormone biosynthesis, progesterone-mediated oocyte maturation, and gonadotropin-releasing hormone (GnRH) signaling pathway, forming a tight DEM-DEG pathway regulatory network. Further DEM validation demonstrated that thymine supplementation delayed the opening of the vagina and development of PP in model rats. Conclusion This study reveals that the metabolomic and transcriptomic changes, along with enriched pathways, are implicated in PP based on clinical and animal analyses. The findings may provide new strategies and research avenues for PP treatment.
Collapse
Affiliation(s)
- Fang Zhou
- Department of Pediatrics, Traditional Chinese Medicine Hospital of Zhuji, Zhuji, Zhejiang, China
| | - Jianhong Mao
- Department of Clinical Lab, Traditional Chinese Medicine Hospital of Zhuji, Zhuji, Zhejiang, China
| | - Zhenzhen Jin
- Department of Pediatrics, Traditional Chinese Medicine Hospital of Zhuji, Zhuji, Zhejiang, China
| | - Li Zhu
- Department of Pediatrics, Traditional Chinese Medicine Hospital of Zhuji, Zhuji, Zhejiang, China
| | - Xiaofang Li
- Department of Chinese Materia Medica, Traditional Chinese Medicine Hospital of Zhuji, Zhuji, Zhejiang, China
| |
Collapse
|
4
|
Komova NS, Serebrennikova KV, Berlina AN, Zherdev AV, Dzantiev BB. Sensitive Silver-Enhanced Microplate Apta-Enzyme Assay of Sb 3+ Ions in Drinking and Natural Waters. Molecules 2023; 28:6973. [PMID: 37836816 PMCID: PMC10574334 DOI: 10.3390/molecules28196973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
The toxic effects of antimony pose risks to human health. Therefore, simple analytical techniques for its widescale monitoring in water sources are in demand. In this study, a sensitive microplate apta-enzyme assay for Sb3+ detection was developed. The biotinylated aptamer A10 was hybridized with its complementary biotinylated oligonucleotide T10 and then immobilized on the surface of polysterene microplate wells. Streptavidin labeled with horseradish peroxidase (HRP) bound to the biotin of a complementary complex and transformed the 3,3',5,5'-tetramethylbenzidine substrate, generating an optical signal. Sb3+ presenting in the sample bounded to an A10 aptamer, thus releasing T10, preventing streptavidin-HRP binding and, as a result, reducing the optical signal. This effect allowed for the detection of Sb3+ with a working range from 0.09 to 2.3 µg/mL and detection limit of 42 ng/mL. It was established that the presence of Ag+ at the stage of A10/T10 complex formation promoted dehybridization of the aptamer A10 and the formation of the A10/Sb3+ complex. The working range of the Ag+-enhanced microplate apta-enzyme assay for Sb3+ was determined to be 8-135 ng/mL, with a detection limit of 1.9 ng/mL. The proposed enhanced approach demonstrated excellent selectivity against other cations/anions, and its practical applicability was confirmed through an analysis of drinking and spring water samples with recoveries of Sb3+ in the range of 109.0-126.2% and 99.6-106.1%, respectively.
Collapse
Affiliation(s)
| | | | - Anna N. Berlina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (N.S.K.); (K.V.S.); (A.V.Z.); (B.B.D.)
| | | | | |
Collapse
|
5
|
Bordoni S, Tarroni R, Monari M, Cerini S, Battaglia F, Micheletti G, Boga C, Drius G. Ru-Controlled Thymine Tautomerization Frozen by a k 1(O)-, k 2(N,O)-Metallacycle: An Experimental and Theoretical Approach. Molecules 2023; 28:molecules28103983. [PMID: 37241724 DOI: 10.3390/molecules28103983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The reaction of mer-(Ru(H)2(CO)(PPh3)3) (1) with one equivalent of thymine acetic acid (THAcH) unexpectedly produces the macrocyclic dimer k1(O), k2(N,O)-(Ru(CO)(PPh3)2THAc)2 (4) and, concomitantly, the doubly coordinated species k1(O), k2(O,O)-(Ru(CO)(PPh3)2THAc) (5). The reaction promptly forms a complicated mixture of Ru-coordinated mononuclear species. With the aim of shedding some light in this context, two plausible reaction paths were proposed by attributing the isolated or spectroscopically intercepted intermediates on the basis of DFT-calculated energetic considerations. The cleavage of the sterically demanding equatorial phosphine in the mer-species releases enough energy to enable self-aggregation, producing the stable, symmetric 14-membered binuclear macrocycle of 4. The k1-acetate iminol (C=N-OH) unit of the mer-tautomer k1(O)-(Ru(CO)(PPh3)2(THAc)) (2) likely exhibits a stronger nucleophilic aptitude than the prevalent N(H)-C(O) amido species, thus accomplishing extra stabilization through concomitant k2(N,O)-thymine heteroleptic side-chelation. Furthermore, both the ESI-Ms and IR simulation spectra validated the related dimeric arrangement in solution, in agreement with the X-ray determination of the structure. The latter showed tautomerization to the iminol form. The 1H NMR spectra in chlorinated solvents of the kinetic mixture showed the simultaneous presence of 4 and the doubly coordinated 5, in rather similar amounts. THAcH added in excess preferentially reacts with 2 or trans-k2(O,O)-(RuH(CO)(PPh3)2THAc) (3) rather than attacking the starting Complex 1, promptly forming the species of 5. The proposed reaction paths were inferred by spectroscopically monitoring the intermediate species, for which the results were strongly dependent on the of conditions the reaction (stoichiometry, solvent polarity, time, and the concentration of the mixture). The selected mechanism proved to be more reliable, due to the final dimeric product stereochemistry.
Collapse
Affiliation(s)
- Silvia Bordoni
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (CIRI SDV), University of Bologna, 40126 Bologna, Italy
| | - Riccardo Tarroni
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Magda Monari
- Department of Chemistry 'Giacomo Ciamician', Alma Mater Studiorum, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Stefano Cerini
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Fabio Battaglia
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Gabriele Micheletti
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Carla Boga
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Giacomo Drius
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| |
Collapse
|
6
|
Haj Hasan A, Preet G, Milne BF, Ebel R, Jaspars M. Arabinofuranosyl Thymine Derivatives-Potential Candidates against Cowpox Virus: A Computational Screening Study. Int J Mol Sci 2023; 24:ijms24021751. [PMID: 36675269 PMCID: PMC9864678 DOI: 10.3390/ijms24021751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023] Open
Abstract
Cowpox is caused by a DNA virus known as the cowpox virus (CPXV) belonging to the Orthopoxvirus genus in the family Poxviridae. Cowpox is a zoonotic disease with the broadest host range among the known poxviruses. The natural reservoir hosts of CPXV are wild rodents. Recently, the cases of orthopoxviral infections have been increasing worldwide, and cowpox is considered the most common orthopoxviral infection in Europe. Cowpox is often a self-limiting disease, although cidofovir or anti-vaccinia gammaglobulin can be used in severe and disseminated cases of human cowpox. In this computational study, a molecular docking analysis of thymine- and arabinofuranosyl-thymine-related structures (1-21) on two cowpox-encoded proteins was performed with respect to the cidofovir standard and a 3D ligand-based pharmacophore model was generated. Three chemical structures (PubChem IDs: 123370001, 154137224, and 90413364) were identified as potential candidates for anti-cowpox agents. Further studies combining in vitro and in silico molecular dynamics simulations to test the stability of these promising compounds could effectively improve the future design of cowpox virus inhibitors, as molecular docking studies are not sufficient to consider a ligand a potential drug.
Collapse
Affiliation(s)
- Ahlam Haj Hasan
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Gagan Preet
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Bruce Forbes Milne
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
- CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
- Correspondence:
| |
Collapse
|
7
|
Ziganshina AY, Mansurova EE, Voloshina AD, Lyubina AP, Amerhanova SK, Shulaeva MM, Nizameev IR, Kadirov MK, Bakhtiozina LR, Semenov VE, Antipin IS. Thymine-Modified Nanocarrier for Doxorubicin Delivery in Glioblastoma Cells. Molecules 2023; 28:molecules28020551. [PMID: 36677608 PMCID: PMC9864328 DOI: 10.3390/molecules28020551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Brain tumor glioblastoma is one of the worst types of cancer. The blood-brain barrier prevents drugs from reaching brain cells and shields glioblastoma from treatment. The creation of nanocarriers to improve drug delivery and internalization effectiveness may be the solution to this issue. In this paper, we report on a new nanocarrier that was developed to deliver the anticancer drug doxorubicin to glioblastoma cells. The nanocarrier was obtained by nanoemulsion polymerization of diallyl disulfide with 1-allylthymine. Diallyl disulfide is a redox-sensitive molecule involved in redox cell activities, and thymine is a uracil derivative and one of the well-known bioactive compounds that can enhance the pharmacological activity of doxorubicin. Doxorubicin was successfully introduced into the nanocarrier with a load capacity of about 4.6%. Biological studies showed that the doxorubicin nanocarrier composition is far more cytotoxic to glioblastoma cells (T98G) than it is to cancer cells (M-HeLa) and healthy cells (Chang liver). The nanocarrier improves the penetration of doxorubicin into T98G cells and accelerates the cells' demise, as is evident from flow cytometry and fluorescence microscopy data. The obtained nanocarrier, in our opinion, is a promising candidate for further research in glioblastoma therapy.
Collapse
Affiliation(s)
- Albina Y. Ziganshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
- Correspondence:
| | - Elina E. Mansurova
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, Lobachevsky Str. 1/29, 420008 Kazan, Russia
| | - Alexandra D. Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Anna P. Lyubina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Syumbelya K. Amerhanova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Marina M. Shulaeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Irek R. Nizameev
- Department of Nanotechnologies in Electronics, Kazan National Research Technical University Named after A. N. Tupolev—KAI, 10, K. Marx Str., 420111 Kazan, Russia
| | - Marsil K. Kadirov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Leysan R. Bakhtiozina
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, Lobachevsky Str. 1/29, 420008 Kazan, Russia
| | - Vyacheslav E. Semenov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Igor S. Antipin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| |
Collapse
|
8
|
Wang Y, Dai C, Huang W, Ni T, Cao J, Pang J, Wei H, Wang C. Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π(+) Stacking Interactions in Thymine-[C(n)mim]Br (n = 2, 4, 6, 8, 10) Microhydrates. Molecules 2022; 27. [PMID: 36234781 DOI: 10.3390/molecules27196242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH2O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH2O-y[Cnmim]+-xBr−, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H2O-Br−-1, T-3H2O-[Cnmim]+-Br−-1, T-2H2O-[Cnmim]+-2Br−-1, and T-1H2O-2[Cnmim]+-2Br−-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[Cnmim]+) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br−) is front > top. The stability order for the different microhydrates is following T-5H2O-1 < T-4H2O-Br−-1 < T-3H2O-[Cnmim]+-Br−-1 < T-2H2O-[Cnmim]+-2Br−-1 < T-1H2O-2[Cnmim]+-2Br−-1. A good linear relationship between binding EB values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π+ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [Cnmim]+ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr− complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.
Collapse
|
9
|
Thongkam T, Apilux A, Tusai T, Parnklang T, Kladsomboon S. Thy-AuNP-AgNP Hybrid Systems for Colorimetric Determination of Copper (II) Ions Using UV-Vis Spectroscopy and Smartphone-Based Detection. Nanomaterials (Basel) 2022; 12. [PMID: 35564160 DOI: 10.3390/nano12091449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023]
Abstract
A colorimetric probe based on a hybrid sensing system of gold nanoparticles (AuNPs), silver nanoparticles (AgNPs), and thymine (Thy) was developed for easy and rapid detection of copper (II) ions (Cu2+) in solution. The underlying principle of this probe was the Cu2+-triggered aggregation of the nanoparticle components. Color change of the sensing solution (from red to purple) was clearly observed with naked eyes. The experimental parameters, including pH and concentration of tris buffer, thymine concentration and AgNP dilution ratios, were investigated and optimized. Once optimized, the limits of detection were found to be 1, 0.09 and 0.03 ppm for naked eyes, smartphone application and UV-vis spectrophotometer, respectively. Furthermore, determination of Cu2+ was accomplished within 15 min under ambient conditions. For quantitative analysis, the linearity of detection was observed through ranges of 0.09−0.5 and 0.03−0.5 ppm using smartphone application and UV-vis spectrophotometer, respectively, conforming to the World Health Organization guideline for detection of copper at concentrations < 2 ppm in water. This developed hybrid colorimetric probe exhibited preferential selectivity toward Cu2+, even when assessed in the presence of other metal ions (Al3+, Ca2+, Pb2+, Mn2+, Mg2+, Zn2+, Fe3+, Ni2+, Co2+, Hg2+ and Cd2+). The developed procedure was also successfully applied to quantification of Cu2+ in real water samples. The recovery and relative standard deviation (RSD) values from real water sample analysis were in the ranges of 70.14−103.59 and 3.21−17.63%, respectively. Our findings demonstrated a successful development and implementation of the Thy-AuNP-AgNP hybrid sensing system for rapid, simple and portable Cu2+ detection in water samples using a spectrophotometer or a smartphone-based device.
Collapse
|
10
|
Huix-Rotllant M. Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM. Molecules 2021; 26:6021. [PMID: 34641565 DOI: 10.3390/molecules26196021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S2 to S1. In the S1 state, it gets trapped for several picoseconds until returning to the ground-state S0. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S0/S1 intersection and have a negligible effect on the S1/S2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.
Collapse
|
11
|
Orts-Arroyo M, Ten-Esteve A, Ginés-Cárdenas S, Castro I, Martí-Bonmatí L, Martínez-Lillo J. A Gadolinium(III) Complex Based on the Thymine Nucleobase with Properties Suitable for Magnetic Resonance Imaging. Int J Mol Sci 2021; 22:4586. [PMID: 33925589 DOI: 10.3390/ijms22094586] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/19/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
The paramagnetic gadolinium(III) ion is used as contrast agent in magnetic resonance (MR) imaging to improve the lesion detection and characterization. It generates a signal by changing the relaxivity of protons from associated water molecules and creates a clearer physical distinction between the molecule and the surrounding tissues. New gadolinium-based contrast agents displaying larger relaxivity values and specifically targeted might provide higher resolution and better functional images. We have synthesized the gadolinium(III) complex of formula [Gd(thy)2(H2O)6](ClO4)3·2H2O (1) [thy = 5-methyl-1H-pyrimidine-2,4-dione or thymine], which is the first reported compound based on gadolinium and thymine nucleobase. 1 has been characterized through UV-vis, IR, SEM-EDAX, and single-crystal X-ray diffraction techniques, and its magnetic and relaxometric properties have been investigated by means of SQUID magnetometer and MR imaging phantom studies, respectively. On the basis of its high relaxivity values, this gadolinium(III) complex can be considered a suitable candidate for contrast-enhanced magnetic resonance imaging.
Collapse
|
12
|
Petera L, Mrazikova K, Nejdl L, Zemankova K, Vaculovicova M, Pastorek A, Civis S, Kubelik P, Heays A, Cassone G, Sponer J, Ferus M, Sponer J. Prebiotic Route to Thymine from Formamide-A Combined Experimental-Theoretical Study. Molecules 2021; 26:molecules26082248. [PMID: 33924594 PMCID: PMC8069957 DOI: 10.3390/molecules26082248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers.
Collapse
Affiliation(s)
- Lukáš Petera
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
| | - Lukas Nejdl
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ 61200 Brno, Czech Republic
- Correspondence: (L.N.); (M.F.); (J.S.)
| | - Kristyna Zemankova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ 61200 Brno, Czech Republic
| | - Adam Pastorek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Svatopluk Civis
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Petr Kubelik
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Alan Heays
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, Italian National Research Council (IPCF-CNR), Viale Ferdinando Stagno d’Alcontres 37, 98158 Messina, Italy;
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
- Correspondence: (L.N.); (M.F.); (J.S.)
| | - Judit Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
- Correspondence: (L.N.); (M.F.); (J.S.)
| |
Collapse
|
13
|
Wong XK, Yeong KY. From Nucleic Acids to Drug Discovery: Nucleobases as Emerging Templates for Drug Candidates. Curr Med Chem 2021; 28:7076-7121. [PMID: 33588718 DOI: 10.2174/0929867328666210215113828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 11/22/2022]
Abstract
Nucleobases represent key structural motif in biologically active molecules including synthetic and natural products. Molecular modifications made on nucleobases or their isolation from natural sources are being widely investigated for the development of drugs with improved potency for the treatment of different diseases, such as cancer, as well as viral and bacterial infections. This review article focuses on the nucleobase analogue drug developments of the past 20 years (2000-2020). Various pharmacological and medicinal aspects of nucleobases and their analogues are discussed. The current state and limitations are also highlighted.
Collapse
Affiliation(s)
- Xi Khai Wong
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Bukit Jalil, 57000, Kuala Lumpur. Malaysia
| | - Keng Yoon Yeong
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway, 47500, Selangor. Malaysia
| |
Collapse
|
14
|
Liu Y, Yang K, Jia Y, Shi J, Tong Z, Wang Z. Thymine Sensitizes Gram-Negative Pathogens to Antibiotic Killing. Front Microbiol 2021; 12:622798. [PMID: 33584625 PMCID: PMC7875874 DOI: 10.3389/fmicb.2021.622798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/04/2021] [Indexed: 12/27/2022] Open
Abstract
Diminished antibiotic susceptibility of bacterial pathogens is an increasingly serious threat to human and animal health. Alternative strategies are required to combat antibiotic refractory bacteria. Bacterial metabolic state has been shown to play a critical role in its susceptibility to antibiotic killing. However, the adjuvant potential of nucleotides in combination with antibiotics to kill Gram-negative pathogens remains unknown. Herein, we found that thymine potentiated ciprofloxacin killing against both sensitive and resistant-E. coli in a growth phase-independent manner. Similar promotion effects were also observed for other bactericidal antibiotics, including ampicillin and kanamycin, in the fight against four kinds of Gram-negative bacteria. The mechanisms underlying this finding were that exogenous thymine could upregulate bacterial metabolism including increased TCA cycle and respiration, which thereby promote the production of ATP and ROS. Subsequently, metabolically inactive bacteria were converted to active bacteria and restored its susceptibility to antibiotic killing. In Galleria mellonella infection model, thymine effectively improved ciprofloxacin activity against E. coli. Taken together, our results demonstrated that thymine potentiates bactericidal antibiotics activity against Gram-negative pathogens through activating bacterial metabolism, providing a universal strategy to overcome Gram-negative pathogens.
Collapse
Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Kangni Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yuqian Jia
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Jingru Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Ziwen Tong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| |
Collapse
|
15
|
Pagano E, Frank B, Jaggers J, Twite M, Urban TT, Klawitter J, Davidson J. Alterations in Metabolites Associated with Hypoxemia in Neonates and Infants with Congenital Heart Disease. CONGENIT HEART DIS 2020; 15:251-265. [PMID: 34413893 PMCID: PMC8372212 DOI: 10.32604/chd.2020.012219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Objectives: (1) To measure the global shift in the metabolome in hypoxemic versus non-hypoxemic infants with congenital heart disease; (2) To identify metabolites and metabolic pathways that are altered in hypoxemia. Study Design: Analysis of serum samples obtained prior to cardiopulmonary bypass from 82 infants ≤120 days old with congenital heart disease requiring surgery at Children’s Hospital Colorado. Infants were divided into groups based on pre-operative oxygen saturations: non-hypoxemic (>92%), mild hypoxemia (85–92%), and severe hypoxemia (<85%). Tandem mass spectrometry was used to analyze 165 targeted metabolites. Partial least squares discriminant analysis and t-tests were used to determine differences among metabolic profiles and individual metabolites respectively. Results: The broad metabolic fingerprint of neonates or older infants did not vary by degree of hypoxemia. There were 12 individual metabolites that differed between hypoxemic and non-hypoxemic neonates, including lower methylmalonic acid (p = 2.44 × 10−4), glutamate (p = 0.001), and hypoxanthine (p = 0.003), and higher thymine (p = 8.67 × 10−4) and myo-inositol (p = 0.014) seen in hypoxemic neonates. Individual metabolites did not vary significantly between older infants with or without hypoxemia. Conclusions: We did not find evidence supporting global metabolic changes associated with cyanotic congenital heart disease in neonates or older infants. However, specific metabolites did discriminate between hypoxemic and non-hypoxemic neonates. These include methylmalonic acid, as well as several metabolites known to change in hypoxia-reoxygenation states (hypoxanthine) and chronic hypoxemic states (glutamate, thymine, myo-inositol) and may represent specific metabolic changes triggered by hypoxemia among neonates with cyanotic congenital heart disease.
Collapse
Affiliation(s)
- Evan Pagano
- University of Colorado, Department of Pediatrics, Aurora, CO 80045, USA
| | - Benjamin Frank
- University of Colorado, Department of Pediatrics, Aurora, CO 80045, USA
| | - James Jaggers
- University of Colorado, Department of Surgery, Aurora, CO 80045, USA
| | - Mark Twite
- University of Colorado, Department of Anesthesiology, Aurora, CO 80045, USA
| | - Tracy T Urban
- Children's Hospital Colorado Research Institute, Aurora, CO 80045, USA
| | - Jelena Klawitter
- University of Colorado, Department of Surgery, Aurora, CO 80045, USA
| | - Jesse Davidson
- University of Colorado, Department of Pediatrics, Aurora, CO 80045, USA
| |
Collapse
|
16
|
Frańska M, Michalak A, Ławniczak Ł. Gas-phase hydration of Mg 2+ complexes with deprotonated uracil, thymine, uridine, and thymidine. J Mass Spectrom 2020; 55:e4504. [PMID: 31970857 DOI: 10.1002/jms.4504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
Abstract
The gas-phase hydration of Mg2+ complexes with deprotonated uracil (U), thymine (T), uridine (Ur , uracil riboside), and thymidine (Tdr , thymine deoxyriboside) was studied. The aim of the work was to analyze the hydration of product ions (eg, [2U-H+Mg]+ ) formed as a result of the collision induced dissociation of the respective parent ion (eg, [3Ur -H+Mg]+ ). The efficiency of gas-phase hydration of the ions [2U-H+Mg]+ and [2T-H+Mg]+ was similar. However, the efficiency of gas-phase hydration of the ion [U+Ur -H+Mg]+ was much higher than that of gas-phase hydration of the ion [T+Tdr -H+Mg]+ . On the basis of the mass spectra obtained and the performed molecular modelling, it was concluded that in the ion [T+Tdr -H+Mg]+ , we deal with a steric hindrance due to the presence of a sugar moiety, which affects water attachment. In the ion [U+Ur -H+Mg]+ , the position of the sugar moiety does not affect water attachment.
Collapse
Affiliation(s)
- Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Anna Michalak
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Łukasz Ławniczak
- Institute of Chemical Technology and Engineering, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| |
Collapse
|
17
|
Wang S, Ferrag C, Noroozifar M, Kerman K. Simultaneous Determination of Four DNA bases at Graphene Oxide/Multi-Walled Carbon Nanotube Nanocomposite-Modified Electrode. Micromachines (Basel) 2020; 11:mi11030294. [PMID: 32168840 PMCID: PMC7143941 DOI: 10.3390/mi11030294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/19/2022]
Abstract
In this study, we developed a modified glassy carbon electrode (GCE) with graphene oxide, multi-walled carbon nanotube hybrid nanocomposite in chitosan (GCE/GO-MWCNT-CHT) to achieve simultaneous detection of four nucleobases (i.e., guanine (G), adenine (A), thymine (T) and cytosine (C)) along with uric acid (UA) as an internal standard. The nanocomposite was characterized using TEM and FT-IR. The linearity ranges were up to 151.0, 78.0, 79.5, 227.5, and 162.5 µM with a detection limit of 0.15, 0.12, 0.44, 4.02, 4.0, and 3.30 µM for UA, G, A, T, and C, respectively. Compared to a bare GCE, the nanocomposite-modified GCE demonstrated a large enhancement (~36.6%) of the electrochemical active surface area. Through chronoamperometric studies, the diffusion coefficients (D), standard catalytic rate constant (Ks), and heterogenous rate constant (Kh) were calculated for the analytes. Moreover, the nanocomposite-modified electrode was used for simultaneous detection in human serum, human saliva, and artificial saliva samples with recovery values ranging from 95% to 105%.
Collapse
Affiliation(s)
- Shuting Wang
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada; (S.W.); (C.F.); (M.N.)
| | - Celia Ferrag
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada; (S.W.); (C.F.); (M.N.)
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Meissam Noroozifar
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada; (S.W.); (C.F.); (M.N.)
| | - Kagan Kerman
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada; (S.W.); (C.F.); (M.N.)
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
- Correspondence:
| |
Collapse
|
18
|
Sahakyan AB, Mahtey A, Kawasaki F, Balasubramanian S. A Spontaneous Ring-Opening Reaction Leads to a Repair-Resistant Thymine Oxidation Product in Genomic DNA. Chembiochem 2020; 21:320-323. [PMID: 31386787 DOI: 10.1002/cbic.201900484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Indexed: 11/09/2022]
Abstract
The alphabet of modified DNA bases goes beyond the conventional four letters, with biological roles being found for many such modifications. Herein, we describe the observation of a modified thymine base that arises from spontaneous N1 -C2 ring opening of the oxidation product 5-formyl uracil, after N3 deprotonation. We first observed this phenomenon in silico through ab initio calculations, followed by in vitro experiments to verify its formation at a mononucleoside level and in a synthetic DNA oligonucleotide context. We show that the new base modification (Trex , thymine ring expunged) can form under physiological conditions, and is resistant to the action of common repair machineries. Furthermore, we found cases of the natural existence of Trex while screening a number of human cell types and mESC (E14), thus suggesting potential biological relevance of this modification.
Collapse
Affiliation(s)
- Aleksandr B Sahakyan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Present address: MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DS, UK
| | - Areeb Mahtey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Fumiko Kawasaki
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Present address: RIKEN, Center for Advanced Intelligence Project, Tokyo, 103-0027, Japan
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cancer Research (UK), Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK
| |
Collapse
|
19
|
Abdallh M, He P, Hearn MTW, Simon GP, Saito K. Light-Switchable Self-Healing Dynamic Linear Polymers: Reversible Cycloaddition Reactions of Thymine-Containing Units. Chempluschem 2020; 84:333-337. [PMID: 31939219 DOI: 10.1002/cplu.201900079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/17/2019] [Indexed: 11/09/2022]
Abstract
A dynamic linear polymer was formed by the [2π+2π] reversible cycloaddition reaction of a thymine-based monomer under topochemical conditions and was used in self-healing applications. The reversible polymerisation of the thymine monomer was confirmed by UV and GPC analysis. Irradiation at 302 nm resulted in polymerisation of the monomer, and irradiation with wavelengths lower than 240 nm resulted in depolymerisation and the production of oligomeric units. This leads to a reduction in the glass transition temperature, and promoted healing of surface scratches due to the increased chain mobility. The self-healing ability of scratched samples was assessed based on the visual disappearance of the damage. In addition, the mechanical properties of the polymer before and after healing were found to be similar.
Collapse
Affiliation(s)
- Mustafa Abdallh
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Peter He
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Milton T W Hearn
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - George P Simon
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Kei Saito
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
20
|
Hasaneen N, Ebead A, Hassan M, Afifi H, Hunter H, Lee-Ruff E, El-Gohary NS, Maarouf AR, El-Emam AA. Synthesis of Cyclobutane Analogue 4: Preparation of Purine and Pyrimidine Carbocyclic Nucleoside Derivatives. Molecules 2019; 24:molecules24183235. [PMID: 31491981 PMCID: PMC6767184 DOI: 10.3390/molecules24183235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 11/29/2022] Open
Abstract
The coupling of 2-bromo-3-benzoyloxycyclobutanone with purine under basic conditions produces two regioisomers consisting of the N-7 and N-9 alkylated products in equal amounts in their racemic forms. The distribution of the isomers is consistent with the charge delocalization between the N-7 and N-9 positions of the purinyl anion. The structural assignments and relative stereochemistry of each regioisomer were based on 1 and 2D NMR techniques. The relative stereochemistry of the C-2 and C-3 substituents in each regioisomer was the trans orientation consistent with steric factors in the coupling step. The N-9 regioisomer was reduced with sodium borohydride to give the all trans cyclobutanol as the major product in a stereoselective manner. The alcohol was debenzoylated with sodium methoxide in a transesterification step to give the nucleoside analogue. The regioisomeric pyrimidine nucleosides were prepared by Vorbrüggen coupling of the 3-hydroxymethylcyclobutanone triflate with either thymine or uracil followed by stereoselective hydride addition. Regiospecificity of the coupling at the N-1 position was observed and stereoselective reduction to the trans-disubstituted cyclobutanol structure assignments was based on NMR data.
Collapse
Affiliation(s)
- Noha Hasaneen
- Department of Chemistry, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Abdelaziz Ebead
- Chemistry Department, Faculty of Science, Arish University, Arish, Egypt
| | - Murtaza Hassan
- Department of Chemistry, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Hanan Afifi
- Basic Science Department, Faculty of Industrial Education, Beni-Suef University, Beni-Suef, Egypt
| | - Howard Hunter
- Department of Chemistry, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Edward Lee-Ruff
- Department of Chemistry, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada.
| | - Nadia S El-Gohary
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Azza R Maarouf
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Ali A El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| |
Collapse
|
21
|
Zeng W, Zhang Y, Zheng W, Luo Q, Han J, Liu J, Zhao Y, Jia F, Wu K, Wang F. Discovery of Cisplatin Binding to Thymine and Cytosine on a Single-Stranded Oligodeoxynucleotide by High Resolution FT-ICR Mass Spectrometry. Molecules 2019; 24:E1852. [PMID: 31091778 DOI: 10.3390/molecules24101852] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
The clinically widely-used anticancer drug, cisplatin, binds strongly to DNA as a DNA-damaging agent. Herein, we investigated the interaction of cisplatin with a 15-mer single-stranded C,T-rich oligodeoxynucleotide, 5′-CCTT4CTT7G8C9T10TCTCC-3′ (ODN15), using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in conjunction with tandem mass spectrometry (top-down MS). Top-down MS analysis with collision-induced dissociation (CID) fragmentation of the mono-platinated and di-platinated ODN15 provided abundant and informative Pt-containing or Pt-free a/[a − B], w and internal fragments, allowing the unambiguous identification of T4, T7, C9, and T10 as the platination sites on the cisplatin-ODN15 adducts. These results revealed that, in addition to the well-established guanine site, the unexpected thermodynamic binding of cisplatin to cytosine and thymine bases was also evident at the oligonucleotide level. Furthermore, the binding models of cisplatin with cytosine and thymine bases were built as the Pt coordinated to cytosine-N(3) and thymine-N(3) with displacement of the proton or tautomerization of thymine. These findings contribute to a better understanding of the mechanism of action of cisplatin and its preference for gene loci when the drug binds to cellular DNA, and also demonstrate the great potential and superiority of FT-ICR MS in studying the interactions of metallodrugs with large biomolecules.
Collapse
|
22
|
Kong H, Zhang C, Sun Q, Yu X, Xie L, Wang L, Li L, Hu S, Ju H, He Y, Zhu J, Xu W. Nickel Adatoms Induced Tautomeric Dehydrogenation of Thymine Molecules on Au(111). ACS Nano 2018; 12:9033-9039. [PMID: 30130397 DOI: 10.1021/acsnano.8b02821] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tautomerization of nucleobases may induce base mismatches resulting in the abnormal disturbance of gene replication and expression, which has therefore attracted widespread interests in many disciplines. Metal atoms participating in a variety of important biological processes are found to be able to affect the nucleobase tautomerization as evidenced by many theoretical and spectroscopic studies. To get the real-space evidence and to unravel the underlying mechanism for the metal-induced tautomerization, especially from the keto form to the enol one, the interplay of high-resolution scanning tunneling microscopy imaging/manipulation and density functional theory (DFT) calculations has been employed. We present a process showing the Ni adatom-induced keto-enol tautomeric dehydrogenation of thymine molecules on Au(111). The key to making such a process feasible is the Ni atoms which greatly lower the energy barrier for the tautomerization from keto to enol form, which is rationalized by extensive DFT-based transition-state search calculations.
Collapse
Affiliation(s)
- Huihui Kong
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering , Nanjing University of Science and Technology , Xiaolingwei 200 , Nanjing 210094 , Jiangsu , P. R. China
| | - Chi Zhang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Qiang Sun
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Xin Yu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Lei Xie
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Likun Wang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Lei Li
- Ministry of Education Key Laboratory of Green Preparation and Application for Functional Materials, School of Materials Science and Engineering , Hubei University , Wuhan 430062 , P. R. China
| | - Shanwei Hu
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Huanxin Ju
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Yunbin He
- Ministry of Education Key Laboratory of Green Preparation and Application for Functional Materials, School of Materials Science and Engineering , Hubei University , Wuhan 430062 , P. R. China
| | - Junfa Zhu
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| |
Collapse
|
23
|
de Souza Oliveira M, de Santana ÁAD, Correa RS, Soares MBP, Batista AA, Bezerra DP. Ru(II)- Thymine Complex Causes Cell Growth Inhibition and Induction of Caspase-Mediated Apoptosis in Human Promyelocytic Leukemia HL-60 Cells. Int J Mol Sci 2018; 19:E1609. [PMID: 29848969 DOI: 10.3390/ijms19061609] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/15/2018] [Accepted: 05/02/2018] [Indexed: 01/01/2023] Open
Abstract
Ruthenium-based compounds represent a class of potential antineoplastic drugs. Recently, we designed, synthesized, and identified the Ru(II)-thymine complex [Ru(PPh3)2(Thy)(bipy)]PF6 (where PPh = triphenylphosphine, Thy = thymine and bipy = 2,2′-bipyridine) as a potent cytotoxic agent with the ability to bind to DNA and human and bovine serum albumins. In this study, the underlying cytotoxic mechanism of the [Ru(PPh3)2(Thy)(bipy)]PF6 complex was assessed. This complex displayed potent cytotoxicity in different cancer cell lines; the morphology that is associated with apoptotic cell death, increased internucleosomal DNA fragmentation without cell membrane permeability, loss of the mitochondrial transmembrane potential, increased phosphatidylserine externalization, and caspase-3 activation were observed in human promyelocytic leukemia HL-60 cells that were treated with the complex. Moreover, pretreatment of HL-60 cells with Z-VAD(OMe)-FMK, a pan-caspase inhibitor, partially reduced the apoptosis that was induced by the complex, indicating that the apoptotic cell death occurred through a caspase-mediated pathway. In conclusion, the [Ru(PPh3)2(Thy)(bipy)]PF6 complex displays potent cytotoxicity to different cancer cells and induces caspase-mediated apoptosis in HL-60 cells.
Collapse
|
24
|
Conti I, Martínez-Fernández L, Esposito L, Hofinger S, Nenov A, Garavelli M, Improta R. Multiple Electronic and Structural Factors Control Cyclobutane Pyrimidine Dimer and 6-4 Thymine-Thymine Photodimerization in a DNA Duplex. Chemistry 2017; 23:15177-15188. [PMID: 28809462 DOI: 10.1002/chem.201703237] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Indexed: 11/09/2022]
Abstract
The T-T photodimerization paths leading to the formation of cyclobutane pyrimidine dimer (CPD) and 6-4 pyrimidine pyrimidone (64-PP), the two main DNA photolesions, have been resolved for a T-T step in a DNA duplex by two complementary state-of-the-art quantum mechanical approaches: QM(CASPT2//CASSCF)/MM and TD-DFT/PCM. Based on the analysis of several different representative structures, we define a new-ensemble of cooperating geometrical and electronic factors (besides the distance between the reacting bonds) ruling T-T photodimerization in DNA. CPD is formed by a barrierless path on an exciton state delocalized over the two bases. Large interbase stacking and shift values, together with a small pseudorotation phase angle for T at the 3'-end, favor this reaction. The oxetane intermediate, leading to a 64-PP adduct, is formed on a singlet T→T charge-transfer state and is favored by a large interbase angle and slide values. A small energy barrier (<0.3 eV) is associated to this path, likely contributing to the smaller quantum yield observed for this process. Eventually, a clear directionality is always shown by the electronic excitation characterizing the singlet photoactive state driving the photodimerization process: an exciton that is more localized on T3 and a 5'-T→3'-T charge transfer for CPD and oxetane formation, respectively, thus calling for specific electronic constraints.
Collapse
Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale "T. Montanari", Università di Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | | | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Siegfried Hofinger
- TU Wien, Zentraler Informatikdienst, Wiedner Hauptstrasse 8-10, 1040, Wien, Austria.,Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49331-1295, USA
| | - Artur Nenov
- Dipartimento di Chimica Industriale "T. Montanari", Università di Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "T. Montanari", Università di Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy.,LIDYL, CEA, CNRS, Université Paris, Saclay, 91191, Gif-sur-Yvette, France
| |
Collapse
|
25
|
Šebesta F, Brela MZ, Diaz S, Miranda S, Murray JS, Gutiérrez-Oliva S, Toro-Labbé A, Michalak A, Burda JV. The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study. J Comput Chem 2017; 38:2680-2692. [PMID: 28925001 DOI: 10.1002/jcc.24911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/09/2017] [Accepted: 07/18/2017] [Indexed: 11/11/2022]
Abstract
This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+ , Zn2+ , and Hg2+ . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
| | - Mateusz Z Brela
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Silvia Diaz
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Sebastian Miranda
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, 70148
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Artur Michalak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
| |
Collapse
|
26
|
Abstract
The photoswitching of photosensitive bolaamphiphiles based on thymine was investigated. Topochemical principles were applied to create light-responsive supra-amphiphiles by the utilisation of dynamic covalent bonds created by the photo-dimerisation of a DNA base, thymine. In order to induce the photo-dimerisation of thymine, two bolaamphiphilic molecules were designed and synthesised to meet the required [2 π+2 π] photo-cycloaddition conditions. The amphiphiles were synthesised with different spacers and their photo-reversibility and morphologies were studied by using UV/Vis, NMR and infrared spectroscopy, rheometry, dynamic light scattering and transmission electron microscopy.
Collapse
Affiliation(s)
| | - Ben J Boyd
- Drug Delivery, Disposition and Dynamics and ARC Centre of Excellence, in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Kei Saito
- School of Chemistry, Monash University, Clayton, VIC, 3800, Australia
| |
Collapse
|
27
|
Yang H, Ye SB, Fu Y, Zhang W, Xie F, Gong L, Fang PP, Chen J, Tong Y. A Simple and Highly Sensitive Thymine Sensor for Mercury Ion Detection Based on Surface Enhanced Raman Spectroscopy and the Mechanism Study. Nanomaterials (Basel) 2017; 7:E192. [PMID: 28737720 DOI: 10.3390/nano7070192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 11/16/2022]
Abstract
Mercury ion (Hg2+) is recognized as one of the most toxic metal ions for the environment and for human health. Techniques utilized in the detection of Hg2+ are an important factor. Herein, a simple thymine was successfully employed as the surface enhanced Raman spectroscopy sensor for Hg2+ ion detection. The limit of detection (LOD) of the developed sensor is better than 0.1 nM (0.02 ppb). This sensor can also selectively distinguish Hg2+ ions over 7 types of alkali, heavy metal and transition-metal ions. Moreover, the LOD of the sensor can even achieve 1 ppb in practical application in the nature system, which is half the maximum allowable level (10 nM, 2 ppb) stipulated in the US Environmental Protection Agency standard. Further investigation of the thymine-Hg2+-thymine coordination mechanism provides a possible means of detecting other metal ions by replacing the metal ion-specific ligands. This work paves the way for the detection of toxic metal ions and environmental problems.
Collapse
|
28
|
Li P, Du S, Li Y, He J. Studies on the Two Thymine Residues in the Catalytic Core of 10-23 DNAzyme: The Impact on the Catalysis of Their 5-Substituted Functional Groups. Molecules 2017; 22:E1011. [PMID: 28640218 DOI: 10.3390/molecules22071011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In the 15-mer catalytic core of 10-23 DNAzyme, each residue contributes to the catalytic conformation differently. Here, the critically conserved T4 and the least conserved T8 were modified on their 5-position with hydroxyl, imidazolyl, and amino groups with a hydrogen-bonding ability. These external functional groups induced new interactions within the catalytic core, resulting in both negative and positive effects on the catalytic activity of 10-23 DNAzyme, and the different linkages could be used to modulate the effect of the functional groups. The conservation of T4 and T8 could be recognized at the level of the nucleobase, but at the level of the functional group, T4 is not completely conserved. Their 5-methyl groups could be modified for a better performance in terms of the DNAzyme.
Collapse
|
29
|
Abstract
Bioinspired strategies have drawn much attention for designing intelligent hydrogels with promising performance. Herein, we present a bioinspired adhesive hydrogel driven by adenine and thymine, which are the basic units of DNA. The adhesive hydrogel exhibited promising adhesive property for the surface of various solid materials, including muscle tissues, plastics, rubbers, glasses, metals, ceramics, carnelians, and woods. The maximum peeling strength of hydrogels was 330 N m-1 on aluminum, superior to that of PAAm hydrogels with 70 N m-1. The strong adhesive behavior remained more than 30 times repeated peeling tests. Moreover, the swelling behavior, morphological structure, mechanical strength, and peeling adhesive strength were also investigated and confirmed the formation and various characteristics of adhesive hydrogels driven by adenine and thymine. Thus, the biomimetic strategy to design promising adhesive hydrogels can provide various opportunities in tissue engineering, such as wound dressing, bioglues, and tissue adhesives.
Collapse
Affiliation(s)
- Xin Liu
- Polymeric and Soft Materials Laboratory, School of Chemical Engineering and Advanced Institute of Materials Science, Changchun University of Technology , Changchun 130012, China
| | - Qin Zhang
- Polymeric and Soft Materials Laboratory, School of Chemical Engineering and Advanced Institute of Materials Science, Changchun University of Technology , Changchun 130012, China
| | - Zijian Gao
- Polymeric and Soft Materials Laboratory, School of Chemical Engineering and Advanced Institute of Materials Science, Changchun University of Technology , Changchun 130012, China
| | - Ruibin Hou
- Polymeric and Soft Materials Laboratory, School of Chemical Engineering and Advanced Institute of Materials Science, Changchun University of Technology , Changchun 130012, China
| | - Guanghui Gao
- Polymeric and Soft Materials Laboratory, School of Chemical Engineering and Advanced Institute of Materials Science, Changchun University of Technology , Changchun 130012, China
| |
Collapse
|
30
|
Segarra-Martí J, Francés-Monerris A, Roca-Sanjuán D, Merchán M. Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2. Molecules 2016; 21:molecules21121666. [PMID: 27918489 PMCID: PMC6274573 DOI: 10.3390/molecules21121666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/16/2022] Open
Abstract
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.
Collapse
Affiliation(s)
- Javier Segarra-Martí
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
- Present Address: Laboratoire de Chimie UMR 5182, École Normale Supérieure de Lyon, CNRS, Université de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France.
| | - Antonio Francés-Monerris
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Manuela Merchán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| |
Collapse
|
31
|
Stojanović L, Bai S, Nagesh J, Izmaylov AF, Crespo-Otero R, Lischka H, Barbatti M. New Insights into the State Trapping of UV-Excited Thymine. Molecules 2016; 21:E1603. [PMID: 27886099 PMCID: PMC6273395 DOI: 10.3390/molecules21111603] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 11/23/2022] Open
Abstract
After UV excitation, gas phase thymine returns to a ground state in 5 to 7 ps, showing multiple time constants. There is no consensus on the assignment of these processes, with a dispute between models claiming that thymine is trapped either in the first (S₁) or in the second (S₂) excited states. In the present study, a nonadiabatic dynamics simulation of thymine is performed on the basis of ADC(2) surfaces, to understand the role of dynamic electron correlation on the deactivation pathways. The results show that trapping in S₂ is strongly reduced in comparison to previous simulations considering only non-dynamic electron correlation on CASSCF surfaces. The reason for the difference is traced back to the energetic cost for formation of a CO π bond in S₂.
Collapse
Affiliation(s)
| | - Shuming Bai
- Aix Marseille Univ., CNRS, ICR, Marseille, France.
| | - Jayashree Nagesh
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Artur F Izmaylov
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Rachel Crespo-Otero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA.
| | | |
Collapse
|
32
|
Léon JC, Sinha I, Müller J. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes. Int J Mol Sci 2016; 17:554. [PMID: 27089326 PMCID: PMC4849010 DOI: 10.3390/ijms17040554] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase.
Collapse
Affiliation(s)
- J Christian Léon
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
| | - Indranil Sinha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
- NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
- NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
| |
Collapse
|
33
|
Afifi H, Ebead A, Pignatelli J, Lee-Ruff E. Synthesis of cyclobutane nucleosides 2-preparation of thymine and uracil analogues. Nucleosides Nucleotides Nucleic Acids 2015; 34:786-98. [PMID: 26397169 DOI: 10.1080/15257770.2015.1075551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
1-(2-Oxocyclobutyl-4-benzoyloxymethyl)-2,4(1H,3H)-pyrimidinedione and 1-(2-oxocyclobutyl-4-benzoyloxymethyl)-5-methyl-2,4(1H,3H)-pyrimidinedione can be prepared by reaction of uracil and thymine, respectively, with 3-benzoyloxymethyl-2-bromocyclobutanone. The N-alkylation gave both cis and trans isomers with the trans isomer predominating for uracil whereas the trans isomer was the only product which could be isolated for thymine. Both series were subjected to borohydride reduction followed by transesterification with methoxide giving the corresponding uracil and thymine nucleoside analogues. The uracil derivative 1-(2-oxocyclobutyl-4-benzoyloxymethyl)-2,4(1H,3H)-pyrimidinedione was irradiated in aqueous acetonitrile to generate isonucleoside analogues.
Collapse
Affiliation(s)
| | | | - Joseph Pignatelli
- c Department of Chemistry, York University , Toronto , Ontario , Canada
| | - Edward Lee-Ruff
- c Department of Chemistry, York University , Toronto , Ontario , Canada
| |
Collapse
|
34
|
Liu L, Pilles BM, Reiner AM, Gontcharov J, Zinth W. 2'-Methoxyacetophenone: An Efficient Photosensitizer for Cyclobutane Pyrimidine Dimer Formation. Chemphyschem 2015; 16:3483-7. [PMID: 26377612 DOI: 10.1002/cphc.201500582] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/20/2015] [Indexed: 01/08/2023]
Abstract
Stationary and time-resolved experiments show that 2'-methoxyacetophenone (2-M) is an interesting compound for the investigation of triplet states in thymine samples. Time-resolved emission experiments show that the fluorescence lifetime of 2-M is 660 ps. A similar time constant of 680 ps is found in transient IR experiments. The data indicate efficient intersystem crossing (≈97%) from the fluorescent singlet state to the triplet state. The lifetime of the triplet state of 2-M dissolved in D2O at room temperature and ambient oxygen concentration is 400 ns. 2-M has a strong absorption in the UV-A range and can photosensitize the triplet state of a thymidine dinucleotide with light at a wavelength of 320 nm. The experiments show that 2-M is well-suited for time-resolved experiments on the triplet-sensitizing process.
Collapse
Affiliation(s)
- Lizhe Liu
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany
| | - Bert M Pilles
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany
| | - Anne M Reiner
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany
| | - Julia Gontcharov
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany
| | - Wolfgang Zinth
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538, München, Germany.
| |
Collapse
|
35
|
Sridhar B, Nanubolu JB, Ravikumar K. Four cocrystals of thymine with phenolic coformers: influence of the coformer on hydrogen bonding. Acta Crystallogr C Struct Chem 2015; 71:602-9. [PMID: 26146400 DOI: 10.1107/s2053229615011614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/15/2015] [Indexed: 11/10/2022]
Abstract
Cocrystals are molecular solids composed of at least two types of neutral chemical species held together by noncovalent forces. Crystallization of thymine [systematic name: 5-methylpyrimidine-2,4(1H,3H)-dione] with four phenolic coformers resulted in cocrystal formation, viz. catechol (benzene-1,2-diol) giving thymine-catechol (1/1), C5H6N2O2·C6H6O2, (I), resorcinol (benzene-1,3-diol) giving thymine-resorcinol (2/1), 2C5H6N2O2·C6H6O2, (II), hydroquinone (benzene-1,4-diol) giving thymine-hydroquinone (2/1), 2C5H6N2O2·C6H6O2, (III), and pyrogallol (benzene-1,2,3-triol) giving thymine-pyrogallol (1/2), C5H6N2O2·2C6H6O3, (IV). The resorcinol molecule in (II) occupies a twofold axis, while the hydroquinone molecule in (III) is situated on a centre of inversion. Thymine-thymine base pairing is common across all four structures, albeit with different patterns. In (I)-(III), the base pair is propagated into an infinite one-dimensional ribbon, whereas it exists as a discrete dimeric unit in (IV). In (I)-(III), the two donor N atoms and one carbonyl acceptor O atom of thymine are involved in thymine-thymine base pairing and the remaining carbonyl O atom is hydrogen bonded to the coformer. In contrast, in (IV), just one donor N atom and one acceptor O atom are involved in base pairing, and the remaining donor N atom and acceptor O atom of thymine form hydrogen bonds to the coformer molecules. Thus, the utilization of the donor and acceptor atoms of thymine in the hydrogen bonding is influenced by the coformers.
Collapse
Affiliation(s)
- Balasubramanian Sridhar
- X-ray Crystallography Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Jagadeesh Babu Nanubolu
- X-ray Crystallography Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Krishnan Ravikumar
- X-ray Crystallography Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| |
Collapse
|
36
|
Chacon-Camacho OF, Buentello-Volante B, Velázquez-Montoya R, Ayala-Ramirez R, Zenteno JC. Homozygosity mapping identifies a GALK1 mutation as the cause of autosomal recessive congenital cataracts in 4 adult siblings. Gene 2014; 534:218-21. [PMID: 24211322 DOI: 10.1016/j.gene.2013.10.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/14/2013] [Accepted: 10/25/2013] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Monogenic congenital cataract is one of the most genetically heterogeneous ocular conditions with almost 30 different genes involved in its etiology. In adult patients, genotype-phenotype correlations are troubled by eye surgery during infancy and/or long-term ocular complications. Here, we describe the molecular diagnosis of GALK1 deficiency as the cause of autosomal recessive congenital cataract in a family from Costa Rica. METHODS Four affected siblings were included in the study. All of them underwent eye surgery during the first decade but medical records were not available. Congenital cataract was diagnosed by report. Molecular analysis included genome wide homozygosity mapping using a 250K SNP Affymetrix microarray followed by PCR amplification and direct nucleotide sequencing of candidate gene. RESULTS Genome wide homozygosity mapping revealed a 6Mb region of homozygosity shared by two affected siblings at 17q25. The GALK1 gene was included in this interval and direct sequencing of this gene revealed a homozygous c.1144C>T mutation (p.Q382) in all four affected subjects. CONCLUSIONS This work demonstrates the utility of homozygosity mapping in the retrospective diagnosis of a family with congenital cataracts in which ocular surgery at early age, the lack of medical records, and the presence of long term eye complications, impeded a clear clinical diagnosis during the initial phases of evaluation.
Collapse
|
37
|
Kuang H, He H, Hou J, Xie Z, Jing X, Huang Y. Thymine modified amphiphilic biodegradable copolymers for photo-cross-linked micelles as stable drug carriers. Macromol Biosci 2013; 13:1593-600. [PMID: 23966335 DOI: 10.1002/mabi.201300254] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 06/24/2013] [Indexed: 11/10/2022]
Abstract
A photo-cross-linked micelle is synthesized via photodimerization of thymine moieties fabricated from amphiphilic block copolymers (mPEG-b-P(LA-co-MPT). The crosslinking behavior is monitored by UV-Vis spectra and (1) H NMR. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) showed that cross-linked micelles had smaller sizes than their uncross-linked precursors. In vitro studies reveal that cross-linking of the micelle cores results in a slow drug release and faster cellular uptake in comparison with uncross-linked ones in MCF-7 and Hela cells. Moreover, the paclitaxel (PTX)-loaded core-cross-linked micelles exhibit similar anticancer efficacy as free PTX. This work provides a convenient tool for designing a more stable structure in the blood circulation to realize a controlled drug delivery.
Collapse
Affiliation(s)
- Huihui Kuang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; Graduate School of Chinese Academy of Sciences, Beijing, 100049, China
| | | | | | | | | | | |
Collapse
|
38
|
Chacon-Camacho OF, Jitskii S, Buentello-Volante B, Quevedo-Martinez J, Zenteno JC. Exome sequencing identifies RDH12 compound heterozygous mutations in a family with severe retinitis pigmentosa. Gene 2013; 528:178-82. [PMID: 23900199 DOI: 10.1016/j.gene.2013.07.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/26/2013] [Accepted: 07/02/2013] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Retinitis pigmentosa (RP) is the most prevalent type of inherited retinal degeneration and one of the commonest causes of genetically determined visual dysfunction worldwide. To date, approximately 35 genes have been associated with nonsyndromic autosomal recessive RP (arRP), however the small contribution of each gene to the total prevalence of arRP and the lack of a clear genotype-phenotype correlation complicate the genetic analysis in affected patients. Next generation sequencing technologies are powerful and cost-effective methods for detecting causative mutations in both sporadic and familial RP cases. METHODS A Mexican family with 5 members affected from arRP was studied. All patients underwent a complete ophthalmologic examination. Molecular methods included genome-wide SNP homozygosity mapping, exome sequencing analysis, and Sanger-sequencing confirmation of causal mutations. RESULTS No regions of shared homozygosity among affected subjects were identified. Exome sequencing in a single patient allowed the detection of two missense mutations in the RDH12 gene: a c.446T>C transition predicting a novel p.L149P substitution, and a c.295C>A transversion predicting a previously reported p.L99I replacement. Sanger sequencing confirmed that all affected subjects carried both RDH12 mutations. CONCLUSIONS This study adds to the molecular spectrum of RDH12-related retinopathy and offers an additional example of the power of exome sequencing in the diagnosis of recessively inherited retinal degenerations.
Collapse
|
39
|
Abstract
The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
Collapse
Affiliation(s)
- James A Shapiro
- Dept. of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA. http://www.huffingtonpost.com/james-a-shapiro
| |
Collapse
|
40
|
de Martino M, Haitel A, Schatzl G, Klatte T. The protease activated receptor 1 gene variation IVSn -14 A>T is associated with distant metastasis and cancer specific survival in renal cell carcinoma. J Urol 2013; 190:1392-7. [PMID: 23517743 DOI: 10.1016/j.juro.2013.03.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2013] [Indexed: 12/17/2022]
Abstract
PURPOSE PAR-1 mediates angiogenesis and impacts the process of tumor growth and disease progression. We evaluated the associations of the gene variations PAR-1 IVSn -14 A>T (rs168753), -506 Ins/Del (rs11267092) and -1426 C>T (rs32934) with renal cell carcinoma pathology and cancer specific survival. MATERIALS AND METHODS DNA was extracted from the peripheral blood leukocytes of 236 consecutive patients with renal cell carcinoma. Genotyping was done using restriction fragment length polymorphism analysis of polymerase chain reaction amplicons and sequencing. RESULTS The IVSn -14 AA genotype was associated with a 3.13-fold increased risk of distant metastases (p = 0.015). In addition, cancer specific survival of patients with IVSn -14 AA was significantly worse than in those with AT/TT (HR 2.98, p = 0.019). The 1 and 4-year cancer specific survival rate for AA vs AT/TT was 89% vs 99% and 82% vs 92%, respectively. After adjusting for the stage, size, grade and necrosis (SSIGN) score on multivariable analysis, IVSn -14 AA was identified as an independent adverse prognostic factor (HR 2.72, p = 0.044). The variations -506 Ins/Del and -1426 C>T were not significantly associated with pathological factors or cancer specific survival. CONCLUSIONS Results suggest that the AA genotype of the PAR-1 variation IVSn -14 A>T is associated with an increased risk of metastasis and poorer prognosis of renal cell carcinoma. Therefore, assessing the individual risk based on genotypes may be a helpful adjunct to identify subgroups at high risk for a poor clinical outcome.
Collapse
|
41
|
Abstract
This study employs DFT (density functional theory) to investigate the formation of hydrazine-like (N-N) cross-linked structures between DNA base pair diradicals that are likely to result from the interaction of high linear energy transfer (LET) radiation, such as ion-beam radiation, with DNA. In our calculations, we generated the guanine (G), cytosine (C), adenine (A), and thymine (T) radicals by removing one hydrogen atom from an N-H bond involved in the normal base pairing. The radical species formed are those that naturally result from one-electron oxidation of the bases followed by deprotonation. N-N cross-links between G and C or A and T diradicals were studied using the BHandHLYP, B3LYP, M06, and M06-2X density functionals and 6-31G* basis set. From a comparison to several test cases performed with the G3B3 method, which gives thermodynamically reliable values, we found that calculations employing the BHandHLYP/6-31G* method predict the best estimates of bonding energies for hydrazine-like structures. Our study shows that the N-N cross-link formed between guanine radical and a neutral cytosine is endothermic in nature but can form metastable structures. However, the reactions between two DNA base radicals (diradical) to form several N-N cross-linked structures are found to be highly exothermic in nature. The N-N cross-links formed between various G-C, G-G, and C-C diradicals have binding energies in the range of ca. -54 to -68, -41 to -47, and -67 to -75 kcal/mol, respectively, whereas A-T, A-A, and T-T have binding energies of -80, -60, and -98 kcal/mol, respectively. In all purine-pyrimidine N-N cross-linked structures, the highest occupied molecular orbital (HOMO) is found to be localized on the purine moiety and the lowest unoccupied molecular orbital (LUMO) is on the pyrimidine moiety.
Collapse
Affiliation(s)
- Venkata Pottiboyina
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | | | | |
Collapse
|
42
|
Bose A, Dey D, Basu S. Laser flash photolysis and magnetic-field-effect studies on interaction of thymine and thymidine with menadione: role of sugar in controlling reaction pattern. Sci Technol Adv Mater 2008; 9:024205. [PMID: 27877956 PMCID: PMC5099713 DOI: 10.1088/1468-6996/9/2/024205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 05/20/2008] [Accepted: 12/17/2007] [Indexed: 06/06/2023]
Abstract
The magnetic field effect (MFE) in conjunction with laser flash photolysis has been used for the study of the interaction of one of the small drug like quinone molecules, 2-methyl, 1,4-naphthoquinone, commonly known as menadione (MQ), with one of the DNA bases, thymine (THN), and its corresponding nucleoside, thymidine (THDN), in acetonitrile (ACN) and sodium dodecylsulfate (SDS) micelles. It has been observed that THN undergoes electron transfer (ET) and hydrogen (H) abstraction with MQ, while THDN undergoes only H abstraction in both the media. However, our earlier studies showed that a purine base, adenine (ADN), and its nucleoside, 2'-deoxyadenosine (ADS), undergo ET in ACN and H abstraction in SDS. Here we have attempted to explain the differences in the reactions of these DNA bases with MQ. We also reveal the crucial role of a sugar unit in altering the behavior of purine and pyrimidine bases with respect to ET and H abstraction.
Collapse
Affiliation(s)
| | | | - Samita Basu
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata – 700 064, India
| |
Collapse
|