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Song J, Yao L, Gooding AR, Thron V, Kasinath V, Cech TR. Diverse RNA Structures Induce PRC2 Dimerization and Inhibit Histone Methyltransferase Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610323. [PMID: 39257770 PMCID: PMC11383989 DOI: 10.1101/2024.08.29.610323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Methyltransferase PRC2 (Polycomb Repressive Complex 2) introduces histone H3K27 trimethylation, a repressive chromatin mark, to tune the differential expression of genes. PRC2 is precisely regulated by accessory proteins, histone post-translational modifications and, notably, RNA. Research on PRC2-associated RNA has mostly focused on the tight-binding G-quadruplex (G4) RNAs, which inhibit PRC2 enzymatic activity in vitro and in cells. Our recent cryo-EM structure provided a molecular mechanism for G4 RNA inactivating PRC2 via dimerization, but it remained unclear how diverse RNAs associate with and regulate PRC2. Here, we show that a single-stranded G-rich RNA and an atypical G4 structure called pUG-fold unexpectedly also mediate near-identical PRC2 dimerization resulting in inhibition of PRC2 methyltransferase activity. The conformational flexibility of arginine-rich loops within subunits EZH2 and AEBP2 of PRC2 can accommodate diverse RNA secondary structures, resulting in protein-RNA and protein-protein interfaces similar to those observed previously with G4 RNA. Furthermore, we address a recent report that failed to detect PRC2-associated RNAs in living cells by demonstrating the insensitivity of PRC2-RNA interaction to photochemical crosslinking. Our results support the significance of RNA-mediated PRC2 regulation by showing that this interaction is not limited to a single RNA secondary structure, consistent with the broad PRC2 transcriptome containing many G-tract RNAs incapable of folding into G4 structures.
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2
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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering. Org Biomol Chem 2024; 22:3025-3034. [PMID: 38530278 DOI: 10.1039/d4ob00279b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Clément Denhez
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR des Sciences Exactes et Naturelles, Reims, France
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, F-38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
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3
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Feng H, Lu XJ, Maji S, Liu L, Ustianenko D, Rudnick ND, Zhang C. Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes. Nat Commun 2024; 15:2279. [PMID: 38480694 PMCID: PMC10937933 DOI: 10.1038/s41467-024-46429-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different RNA-binding domains. Our work suggests protein-RNA photo-crosslinking is highly selective in the cellular environment, which can guide data interpretation and further technology development for UV-crosslinking-based assays.
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Affiliation(s)
- Huijuan Feng
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Suvrajit Maji
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Linxi Liu
- Department of Statistics, Columbia University, New York, NY, 10027, USA
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Noam D Rudnick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA.
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4
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Luo H, Zhang S, Zhong L. Ultraviolet germicidal irradiation: A prediction model to estimate UV-C-induced infectivity loss in single-strand RNA viruses. ENVIRONMENTAL RESEARCH 2024; 241:117704. [PMID: 37984783 DOI: 10.1016/j.envres.2023.117704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Ultraviolet germicidal irradiation (UVGI) disinfection technology is effective in inactivating microorganisms. However, its performance can vary against different microorganisms due to their diverse structural and genomic features. Thus, rapid predictions of UV (254 nm) inactivation kinetics are essential, particularly for highly infectious emerging pathogens, such as SARS-CoV-2, during the extemporary COVID-19 pandemic. In this study, aiming at single-strand RNA (ssRNA) viruses, an improved genomic model was introduced to predict the UV inactivation kinetics of viral genomes using genome sequence data. First, the overall virus infectivity loss in an aqueous matrix was estimated as the sum of damage to both the entire genome and the protein capsid. Then, the "UV rate constant ratio of aerosol and liquid" was used to convert the UV rate constant for viruses in a liquid-based matrix to an airborne state. The prediction model underwent both quantitative and qualitative validation using experimental data from this study and the literature. Finally, with the goal of mitigating potential airborne transmission of ssRNA viruses in indoor environments, this paper summarizes existing in-duct UVGI system designs and evaluates their germicidal performance. The prediction model may serve as a preliminary tool to assess the effectiveness of a UVGI system for emerging or unculturable viruses or to estimate the required UV dose when designing such a system.
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Affiliation(s)
- Hao Luo
- Department of Mechanical Engineering, University of Alberta, 9211-116 Street NW, Edmonton, Alberta, T6G 1H9, Canada
| | - Shuce Zhang
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - Lexuan Zhong
- Department of Mechanical Engineering, University of Alberta, 9211-116 Street NW, Edmonton, Alberta, T6G 1H9, Canada.
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5
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Espaldon A, Oguma K. Conformation-dependent UV inactivation efficiency of a conjugative, multi-drug resistant plasmid. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132324. [PMID: 37647660 DOI: 10.1016/j.jhazmat.2023.132324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
A conjugative, multi-drug-resistant plasmid was irradiated in-vivo and in-vitro with a 265-nm UV-light emitting diode (UV-LED) to investigate the gene inactivation efficiency of a plasmid deoxyribonucleic acid (pDNA) carrying DNA transfer and replication genes. The clinical-isolate 60 kb RP4 plasmid of the IncPα group containing the traG gene, was irradiated intracellularly in E. coli DH5α and extracellularly in a water medium at pH 8.5. Real-time quantitative polymerase chain reaction (RT-qPCR) measurements of the UV-fluence response gene inactivation rate constants revealed a decreasing pattern via a pseudo-1st-order inactivation kinetics in all forms examined. Our findings showed that the intracellular-supercoiled conformation, with k = 6.1 × 10-3 cm2/mJ, has the lowest UV susceptibility (lowest inactivation rate). UV absorbance measurements and a computational approach showed that the host's RNA provides the photo-shielding, demonstrating this high UV resistance. When UV exposure was measured in-vitro, the condensed DNA exhibited a self-shielding effect over supercoiled and denatured DNA due to the hypochromic-hyperchromic effects. This study has shown that large-sized conjugative plasmids with conformation-dependent UV/UV-LED-based gene inactivation play a significant role in preventing the spread of antibiotic resistance.
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Affiliation(s)
- Achilles Espaldon
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kumiko Oguma
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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6
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Ghasemi M, Debnath PC, Kim B, Pournoury M, Khazaeinezhad R, Hosseinzadeh Kassani S, Yeom DI, Oh K. Highly nonlinear optic nucleic acid thin-solid film to generate short pulse laser. Sci Rep 2023; 13:17494. [PMID: 37840076 PMCID: PMC10577146 DOI: 10.1038/s41598-023-44242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023] Open
Abstract
Using aqueous precursors, we report successfully fabricating thin-solid films of two nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). We investigated the potential of these films deposited on a fiber optic platform as all-fiber integrated saturable absorbers (SAs) for ultrafast nonlinear optics. RNA-SA performances were comparable to those of DNA-SA in terms of its nonlinear transmission, modulation depth, and saturation intensity. Upon insertion of these devices into an Erbium-doped fiber ring-laser cavity, both RNA and DNA SAs enabled efficient passive Q-switching operation. RNA-SA application further facilitated robust mode-locking and generated a transform-limited soliton pulse, exhibiting a pulse duration of 633 femtoseconds. A detailed analysis of these pulsed laser characteristics compared RNA and DNA fiber optic SAs with other nonlinear optic materials. The findings of this research establish the feasibility of utilizing RNA as a saturable absorber in ultrafast laser systems with an equal or higher potential as DNA, which presents novel possibilities for the nonlinear photonic applications of nucleic acid thin solid films.
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Affiliation(s)
- Marjan Ghasemi
- Photonic Device Physics Laboratory, Department of Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 120-749, South Korea
| | - Pulak Chandra Debnath
- Department of Physics and Energy Systems Research, Ajou University, Suwon, 443-749, South Korea
| | - Byungjoo Kim
- Department of Laser and Electron Beam Technologies, Korea Institute of Machinery and Materials (KIMM), 156, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34103, Republic of Korea
| | - Marzieh Pournoury
- Department of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Reza Khazaeinezhad
- Beckman Laser Institute, University of California, Irvine, Irvine, CA, 92697, USA
| | | | - Dong-Il Yeom
- Department of Physics and Energy Systems Research, Ajou University, Suwon, 443-749, South Korea
| | - Kyunghwan Oh
- Photonic Device Physics Laboratory, Department of Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 120-749, South Korea.
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7
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Rodríguez-Muñiz GM, Fraga-Timiraos AB, Navarrete-Miguel M, Borrego-Sánchez A, Roca-Sanjuán D, Miranda MA, Lhiaubet-Vallet V. Reductive Photocycloreversion of Cyclobutane Dimers Triggered by Guanines. J Org Chem 2023. [PMID: 37437138 PMCID: PMC10367068 DOI: 10.1021/acs.joc.3c00930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The quest for simple systems achieving the photoreductive splitting of four-membered ring compounds is a matter of interest not only in organic chemistry but also in biochemistry to mimic the activity of DNA photorepair enzymes. In this context, 8-oxoguanine, the main oxidatively generated lesion of guanine, has been shown to act as an intrinsic photoreductant by transferring an electron to bipyrimidine lesions and provoking their cycloreversion. But, in spite of appropriate photoredox properties, the capacity of guanine to repair cyclobutane pyrimidine dimer is not clearly established. Here, dyads containing the cyclobutane thymine dimer and guanine or 8-oxoguanine are synthesized, and their photoreactivities are compared. In both cases, the splitting of the ring takes place, leading to the formation of thymine, with a quantum yield 3.5 times lower than that for the guanine derivative. This result is in agreement with the more favored thermodynamics determined for the oxidized lesion. In addition, quantum chemistry calculations and molecular dynamics simulations are carried out to rationalize the crucial aspects of the overall cyclobutane thymine dimer photoreductive repair triggered by the nucleobase and its main lesion.
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Affiliation(s)
- Gemma M Rodríguez-Muñiz
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain
| | - Ana B Fraga-Timiraos
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain
| | - Miriam Navarrete-Miguel
- Instituto de Ciencia Molecular, Universitat de València, P.O.Box 22085, 46071 València, Spain
| | - Ana Borrego-Sánchez
- Instituto de Ciencia Molecular, Universitat de València, P.O.Box 22085, 46071 València, Spain
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P.O.Box 22085, 46071 València, Spain
| | - Miguel A Miranda
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain
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8
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Velema WA, Lu Z. Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications. JACS AU 2023; 3:316-332. [PMID: 36873678 PMCID: PMC9975857 DOI: 10.1021/jacsau.2c00625] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.
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Affiliation(s)
- Willem A. Velema
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6500 HC, The Netherlands
| | - Zhipeng Lu
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
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9
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Lee W, Matsika S. Mechanistic Aspects of the Effect of Flanking Nucleotide Sequence on CPD Formation and CPD Self-Repair in DNA. J Phys Chem B 2023; 127:18-25. [PMID: 36574488 DOI: 10.1021/acs.jpcb.2c06680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A cyclobutane pyrimidine dimer (CPD) is a photolesion which is produced by a cycloaddition reaction between two stacked pyrimidine bases upon UV light absorption. Because of its harmful effect on important cellular processes involving DNA and especially its relevance to skin cancer, the mechanisms of how a CPD is formed or repaired have been studied extensively, and it has been demonstrated that flanking nucleotide sequences play a crucial role in CPD formation or self-repair. Understanding the mechanisms behind this sequence dependence of CPD formation or self-repair is of great importance because it can give us valuable information on which sequence will be vulnerable to this DNA photodamage. This Perspective focuses on the mechanisms of how flanking nucleotide sequences affect CPD formation or self-repair, especially highlighting the role of computational studies in this field.
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Affiliation(s)
- Wook Lee
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, Korea
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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10
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Milovanović B, Novak J, Etinski M, Domcke W, Došlić N. On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution. Phys Chem Chem Phys 2022; 24:14836-14845. [PMID: 35697028 DOI: 10.1039/d2cp00495j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.
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Affiliation(s)
| | - Jurica Novak
- Department of Biotechnology, University of Rijeka, HR-51000 Rijeka, Croatia.,Scientific and Educational Center "Biomedical Technologies" School of Medical Biology, South Ural State University, RU-454080, Chelyabinsk, Russia.,Center for Artificial Intelligence and Cybersecurity, University of Rijeka, 51000 Rijeka, Croatia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
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11
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RNAi as a Foliar Spray: Efficiency and Challenges to Field Applications. Int J Mol Sci 2022; 23:ijms23126639. [PMID: 35743077 PMCID: PMC9224206 DOI: 10.3390/ijms23126639] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/04/2023] Open
Abstract
RNA interference (RNAi) is a powerful tool that is being increasingly utilized for crop protection against viruses, fungal pathogens, and insect pests. The non-transgenic approach of spray-induced gene silencing (SIGS), which relies on spray application of double-stranded RNA (dsRNA) to induce RNAi, has come to prominence due to its safety and environmental benefits in addition to its wide host range and high target specificity. However, along with promising results in recent studies, several factors limiting SIGS RNAi efficiency have been recognized in insects and plants. While sprayed dsRNA on the plant surface can produce a robust RNAi response in some chewing insects, plant uptake and systemic movement of dsRNA is required for delivery to many other target organisms. For example, pests such as sucking insects require the presence of dsRNA in vascular tissues, while many fungal pathogens are predominately located in internal plant tissues. Investigating the mechanisms by which sprayed dsRNA enters and moves through plant tissues and understanding the barriers that may hinder this process are essential for developing efficient ways to deliver dsRNA into plant systems. In this review, we assess current knowledge of the plant foliar and cellular uptake of dsRNA molecules. We will also identify major barriers to uptake, including leaf morphological features as well as environmental factors, and address methods to overcome these barriers.
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12
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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. SN- and NS-puckered sugar conformers are precursors of the (6-4) photoproduct in thymine dinucleotide. Org Biomol Chem 2022; 20:2300-2307. [PMID: 35253821 DOI: 10.1039/d2ob00044j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some amount of furanose in a southern conformation, possibly in both, but certainly in one of the two adjacent nucleotides of a dipyrimidine site, is necessary for (6-4) photoproduct formation in oligonucleotides. To explore the necessity, role, and most favorable location of each South sugar conformer in the formation of the (6-4) adduct in the thymine dinucleotide TpT, the photochemical behavior of two synthetic analogues, in which the South sugar conformation is prohibited for one of their two sugars, has been examined. Herein, we experimentally demonstrate that the presence of one sugar presenting some amount of South puckering, at any of the extremities, is sufficient to trigger (6-4) adduct formation. Nonetheless, the photochemical behavior of the dinucleotide with a South-puckered conformation at the 5'-end, mimics more closely that of TpT. In addition, using the 5' North 3' South-dilocked dinucleotide, we demonstrate that the flexibility of the South pucker at the 3'-end has little influence on the (6-4) adduct formation.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Clément Denhez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
- MaSCA, P3M, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
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13
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Chan RCT, Ma C, Wong AKW, Chan CTL, Chow JCL, Kwok WM. Dual Time-Scale Proton Transfer and High-Energy, Long-Lived Excitons Unveiled by Broadband Ultrafast Time-Resolved Fluorescence in Adenine-Uracil RNA Duplexes. J Phys Chem Lett 2022; 13:302-311. [PMID: 34978832 DOI: 10.1021/acs.jpclett.1c03553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In contrast to the immense amount of research on electronically excited DNA, surprisingly little has been done about the excited states of RNA. Herein, we demonstrate an ultrafast broadband time-resolved fluorescence and fluorescence anisotropy study to probe directly the intrinsic fluorescence and overall dynamics of the fluorescence from a homopolymeric adenine·uracil RNA duplex adopting the A-form structure. The results unveiled complex deactivation through distinctive multichannels mediated by states of varied energy, a character of charge transfer, and a lifetime from sub-picosecond to nanoseconds. In particular, we observed an unprecedented kinetic isotopic effect and participation of unusual proton transfer from states in two discrete energies and time domains. We also identified a high-energy nanosecond emission that we attributed to its fluorescence anisotropy to long-lived weakly emissive excitons not reported in DNA. These distinguishing features originate from the stacking, pairing, and local hydration environment specific to the A-form conformation of the adenine·uracil double helix.
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Affiliation(s)
- Ruth Chau-Ting Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, 518071, Shenzhen, Guangdong, P. R. China
| | - Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, 518071, Shenzhen, Guangdong, P. R. China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Chris Tsz-Leung Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Joshua Chiu-Lok Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
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14
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Ghasemi M, Jeong H, Kim D, Kim B, Jang JI, Oh K. Linear and nonlinear optical properties of transfer ribonucleic acid (tRNA) thin solid films. RSC Adv 2022; 12:8661-8667. [PMID: 35424810 PMCID: PMC8984844 DOI: 10.1039/d1ra09412b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/14/2022] [Indexed: 12/03/2022] Open
Abstract
We successfully obtained transfer ribonucleic acid (tRNA) thin solid films (TSFs) using an aqueous solution precursor in an optimized deposition process. By varying the concentration of RNA and deposition process parameters, uniform solid layers of solid RNA with a thickness of 30 to 46 nm were fabricated consistently. Linear absorptions of RNA TSFs on quartz substrates were experimentally investigated in a wide spectral range covering UV–VIS–NIR to find high transparency for λ > 350 nm. We analyzed the linear refractive indices, n(λ) of tRNA TSFs on silicon substrates by using an ellipsometer in the 400 to 900 nm spectral range to find a linear correlation with the tRNA concentration in the aqueous solution. The thermo-optic coefficient (dn/dT) of the films was also measured to be in a range −4.21 × 10−4 to −5.81 × 10−4 °C−1 at 40 to 90 °C. We furthermore characterized nonlinear refractive index and nonlinear absorption of tRNA TSFs on quartz using a Z-scan method with a femtosecond laser at λ = 795 nm, which showed high potential as an efficient nonlinear optical material in the IR spectral range. Optical measurements of one of the vital biological molecules (RNA) in the human body.![]()
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Affiliation(s)
- Marjan Ghasemi
- Department of Physics, Photonic Device Physics Laboratory, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
| | - Hayoung Jeong
- Department of Physics, Photonic Device Physics Laboratory, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
- Center for Quantum Information, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea
| | - Donggyu Kim
- Department of Physics, Nonlinear Optical Material & Spectroscopy, Sogang University, 35 Baek-beom-ro, Seoul 04107, South Korea
| | - Byungjoo Kim
- Department of Physics, Photonic Device Physics Laboratory, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
- Center for Quantum Information, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea
| | - Joon Ik Jang
- Department of Physics, Nonlinear Optical Material & Spectroscopy, Sogang University, 35 Baek-beom-ro, Seoul 04107, South Korea
| | - Kyunghwan Oh
- Department of Physics, Photonic Device Physics Laboratory, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
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15
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Berdnikova DV. Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy. Chem Commun (Camb) 2021; 57:10819-10826. [PMID: 34585681 DOI: 10.1039/d1cc04241f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an emerging drug target that opens new perspectives in the treatment of viral and bacterial infections, cancer and a range of so far incurable genetic diseases. Among the various strategies towards the design and development of selective and efficient ligands for targeting and detection of therapeutically relevant RNA, photoswitchable RNA binders represent a very promising approach due to the possibility to control the ligand-RNA and protein-RNA interactions by light with high spatiotemporal resolution. However, the field of photoswitchable RNA binders still remains underexplored due to challenging design of lead structures that should combine high RNA binding selectivity with efficient photochemical performance. The aim of this highlight article is to describe the development of photoswitchable noncovalent RNA binders and to outline the current situation and perspectives of this emerging interdisciplinary field.
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Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
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16
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Cheng S, Ge Y, Lee Y, Yang X. Prediction of Photolysis Kinetics of Viral Genomes under UV 254 Irradiation to Estimate Virus Infectivity Loss. WATER RESEARCH 2021; 198:117165. [PMID: 33962243 DOI: 10.1016/j.watres.2021.117165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
UV254 irradiation disinfection is a commonly used method to inactivate pathogenic viruses in water and wastewater treatment. Model prediction method can serve as a pre-screening tool to quickly estimate the effectiveness of UV254 irradiation on emerging or unculturable viruses. In this study, an improved prediction model was applied to estimate UV254 photolysis kinetics of viral genomes (kpred, genome) based on the genome sequences and their photoreactivity and to correlate with the experimental virus infectivity loss kinetics (kexp, infectivity). The UV254 inactivation data of 102 viruses (including 2 dsRNA, 65 ssRNA, 33 dsDNA and 2 ssDNA viruses) were collected from the published experimental data with kexp, infectivity ranging from 0.016 to 3.49 cm2 mJ-1. The model had fairly good performance in predicting the virus susceptibility to UV254 irradiation except dsRNA viruses (Pearson's correlation coefficient = 0.64) and 70% of kpred, genome fell in the range of 1/2 to 2 times of kexp, infectivity. The positive deviation of the model often occurred for photoresistant viruses with low kexp, infectivity less than 0.20 cm2 mJ-1 (e.g., Adenovirus, Papovaviridae and Retroviridae). We also applied this model to predict the UV254 inactivation rate of SARS-CoV-2 (kpred, genome = 3.168 cm2 mJ-1) and a UV dose of 3 mJ cm-2 seemed to be able to achieve a 2-log removal by conservative calculation using 1/2kpred, genome value. This prediction method can be used as a prescreening tool to assess the effectiveness of UV254 irradiation for emerging/unculturable viruses in water or wastewater treatment.
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Affiliation(s)
- Shuangshuang Cheng
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuexian Ge
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Xin Yang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
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17
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Rockey NC, Henderson JB, Chin K, Raskin L, Wigginton KR. Predictive Modeling of Virus Inactivation by UV. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3322-3332. [PMID: 33576611 DOI: 10.1021/acs.est.0c07814] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
UV254 disinfection strategies are commonly applied to inactivate pathogenic viruses in water, food, air, and on surfaces. There is a need for methods that rapidly predict the kinetics of virus inactivation by UV254, particularly for emerging and difficult-to-culture viruses. We conducted a systematic literature review of inactivation rate constants for a wide range of viruses. Using these data and virus characteristics, we developed and evaluated linear and nonlinear models for predicting inactivation rate constants. Multiple linear regressions performed best for predicting the inactivation kinetics of (+) ssRNA and dsDNA viruses, with cross-validated root mean squared relative prediction errors similar to those associated with experimental rate constants. We tested the models by predicting and measuring inactivation rate constants of a (+) ssRNA mouse coronavirus and a dsDNA marine bacteriophage; the predicted rate constants were within 7% and 71% of the experimental rate constants, respectively, indicating that the prediction was more accurate for the (+) ssRNA virus than the dsDNA virus. Finally, we applied our models to predict the UV254 rate constants of several viruses for which high-quality UV254 inactivation data are not available. Our models will be valuable for predicting inactivation kinetics of emerging or difficult-to-culture viruses.
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Affiliation(s)
- Nicole C Rockey
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - James B Henderson
- Consulting for Statistics, Computing and Analytics Research, University of Michigan, Ann Arbor, MI 48109, United States
| | - Kaitlyn Chin
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Lutgarde Raskin
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Krista R Wigginton
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, United States
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18
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Greaves J, Stone D, Wu Z, Bibby K. Persistence of emerging viral fecal indicators in large-scale freshwater mesocosms. WATER RESEARCH X 2020; 9:100067. [PMID: 32995735 PMCID: PMC7516186 DOI: 10.1016/j.wroa.2020.100067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/30/2020] [Accepted: 09/02/2020] [Indexed: 05/18/2023]
Abstract
Fecal indicator bacteria (FIB) are typically used to monitor microbial water quality but are poor representatives of viruses due to different environmental fate. Viral fecal indicators have been proposed as alternatives to FIB; however, data evaluating the persistence of emerging viral fecal indicators under realistic environmental conditions is necessary to evaluate their potential application. In this study, we examined the persistence of five viral fecal indicators, including crAssphage and pepper mild mottle virus (PMMoV), and three bacterial fecal indicators (E. coli, enterococci and HF183/BacR287) in large-scale experimental ponds and freshwater mesocosms. Observed inactivation rate constants were highly variable and ranged from a minimum of -0.09 d-1 for PMMoV to a maximum of -3.5 d-1 for HF183/BacR287 in uncovered mesocosms. Overall, viral fecal indicators had slower inactivation than bacterial fecal indicators and PMMoV was inactivated more slowly than all other targets. These results demonstrate that bacterial fecal indicators inadequately represent viral fate following aging of sewage contaminated water due to differential persistence, and that currently used fecal indicator monitoring targets demonstrate highly variable persistence that should be considered during water quality monitoring and risk assessment.
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Affiliation(s)
- Justin Greaves
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN, 46556, USA
| | - Daniel Stone
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN, 46556, USA
| | - Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN, 46556, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, IN, 46556, USA
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19
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Bachman P, Fischer J, Song Z, Urbanczyk-Wochniak E, Watson G. Environmental Fate and Dissipation of Applied dsRNA in Soil, Aquatic Systems, and Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:21. [PMID: 32117368 PMCID: PMC7016216 DOI: 10.3389/fpls.2020.00021] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/10/2020] [Indexed: 05/10/2023]
Abstract
Two primary use patterns exist for dsRNA-based products for crop protection: in planta produced dsRNA such as in a genetically engineered (GE) crop; and topically applied dsRNA such as a spray application. To enable effective environmental risk assessments for these products, dsRNA must be successfully measured in relevant environmental compartments (soil, sediment, surface water) to provide information on potential exposure. This perspective reviews results from numerous environmental fate and degradation studies with topically applied unformulated dsRNAs to demonstrate the high lability of these molecules and low potential for persistence in the environment. Additionally, we report on results of a pilot study of topically applied dsRNA on soybean plants demonstrating similar rapid degradation under field conditions. Microbial degradation of nucleic acids in environmental compartments has been shown to be a key driver for this lack of persistence. In fact, the instability of dsRNA in the environment has posed a challenge for the development of commercial topically-applied products. Formulations or other approaches that mitigate environmental degradation may lead to development of commercially successful products but may change the known degradation kinetics of dsRNAs. The formulation of these products and the resultant impacts on the stability of the dsRNA in environmental compartments will need to be addressed using problem formulation and product formulation testing may be required on a case by case basis to ensure an effective risk assessment.
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Affiliation(s)
- Pamela Bachman
- Science Organization, The Climate Corporation, Creve Coeur, MO, United States
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, United States
| | - Joshua Fischer
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, United States
| | - Zihong Song
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, United States
| | | | - Greg Watson
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, United States
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20
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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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21
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Alnaser WE, Ghanem AZ, Alnaser NW, Alaraibi Q, Alshaikh F. The Null Effect of UVC Ceiling Light Exposure on SARS-CoV2. Health (London) 2020. [DOI: 10.4236/health.2020.1211108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Saha R, Chen IA. Effect of UV Radiation on Fluorescent RNA Aptamers' Functional and Templating Ability. Chembiochem 2019; 20:2609-2617. [PMID: 31125512 PMCID: PMC6899979 DOI: 10.1002/cbic.201900261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Indexed: 12/25/2022]
Abstract
Damage from ultraviolet (UV) radiation was likely to be an important selection pressure during the origin of life. RNA is believed to have been central to the origin of life and might form the basis for simple synthetic cells. Although photodamage of DNA has been extensively studied, photodamage is highly dependent on local molecular context, and damage to functional RNAs has been relatively under‐studied. We irradiated two fluorescent RNA aptamers and monitored the loss of activity, folding, and the kinetics of lesion accumulation. The loss of activity differed depending on the aptamer, with the Spinach2 aptamer retaining substantial activity after long exposure times. The binding pocket was particularly susceptible to damage, and melting of the duplex regions increased susceptibility; this is consistent with the view that duplex formation is protective. At the same time, susceptibility varied greatly depending on context, thus emphasizing the importance of studying many different RNAs to understand UV hardiness.
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Affiliation(s)
- Ranajay Saha
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Irene A Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.,Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
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23
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Madronich S, Björn LO, McKenzie RL. Solar UV radiation and microbial life in the atmosphere. Photochem Photobiol Sci 2018; 17:1918-1931. [PMID: 29978175 DOI: 10.1039/c7pp00407a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Many microorganisms are alive while suspended in the atmosphere, and some seem to be metabolically active during their time there. One of the most important factors threatening their life and activity is solar ultraviolet (UV) radiation. Quantitative understanding of the spatial and temporal survival patterns in the atmosphere, and of the ultimate deposition of microbes to the surface, is limited by a number factors some of which are discussed here. These include consideration of appropriate spectral sensitivity functions for biological damage (e.g. inactivation), and the estimation of UV radiation impingent on a microorganism suspended in the atmosphere. We show that for several bacteria (E. coli, S. typhimurium, and P. acnes) the inactivation rates correlate well with irradiances weighted by the DNA damage spectrum in the UV-B spectral range, but when these organisms show significant UV-A (or visible) sensitivities, the correlations become clearly non-linear. The existence of these correlations enables the use of a single spectrum (here DNA damage) as a proxy for sensitivity spectra of other biological effects, but with some caution when the correlations are strongly non-linear. The radiative quantity relevant to the UV exposure of a suspended particle is the fluence rate at an altitude above ground, while down-welling irradiance at ground-level is the quantity most commonly measured or estimated in satellite-derived climatologies. Using a radiative transfer model that computes both quantities, we developed a simple parameterization to exploit the much larger irradiance data bases to estimate fluence rates, and present the first fluence-rate based climatology of DNA-damaging UV radiation in the atmosphere. The estimation of fluence rates in the presence of clouds remains a particularly challenging problem. Here we note that both reductions and enhancements in the UV radiation field are possible, depending mainly on cloud optical geometry and prevailing solar zenith angles. These complex effects need to be included in model simulations of the atmospheric life cycle of the organisms.
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24
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Qiao Z, Ye Y, Chang PH, Thirunarayanan D, Wigginton KR. Nucleic Acid Photolysis by UV 254 and the Impact of Virus Encapsidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:10408-10415. [PMID: 30106282 DOI: 10.1021/acs.est.8b02308] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Determining the influence of higher order structure on UVC photolysis will help inform predictions of nucleic acid fate and microorganism inactivation. We measured the direct UV254 photolysis kinetics of four model viral genomes composed of single-stranded and double-stranded RNA (ssRNA and dsRNA, respectively), as well as single-stranded and double-stranded DNA (ssDNA and dsDNA, respectively), in ultrapure water, in phosphate buffered saline (PBS), and encapsidated in their native virus particles. The photolysis rate constants of naked nucleic acids measured by qPCR (RT-qPCR for RNA) and normalized by the number of bases measured in a particular sequence exhibited the following trend: ssDNA > ssRNA ≈ dsDNA > dsRNA. In PBS, naked ssRNA bases reacted, on average, 24× faster than the dsRNA bases, whereas naked ssDNA bases reacted 4.3× faster than dsDNA bases. Endogenous indirect photolysis involving 1O2 and ·OH was ruled out as a major contributing factor in the reactions. A comparison of our measured rate constants with rate constants reported in the literature shows a general agreement among the nucleic acid UV254 direct photolysis kinetics. Our results underscore the high resistance of dsRNA to UVC photolysis and demonstrate the role that nucleic acid structure and solution chemistry play in photoreactivity.
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Affiliation(s)
- Zhong Qiao
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Yinyin Ye
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Pin Hsuan Chang
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Devibaghya Thirunarayanan
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
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25
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Alenko A, Fleming AM, Burrows CJ. Reverse Transcription Past Products of Guanine Oxidation in RNA Leads to Insertion of A and C opposite 8-Oxo-7,8-dihydroguanine and A and G opposite 5-Guanidinohydantoin and Spiroiminodihydantoin Diastereomers. Biochemistry 2017; 56:5053-5064. [PMID: 28845978 DOI: 10.1021/acs.biochem.7b00730] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reactive oxygen species, both endogenous and exogenous, can damage nucleobases of RNA and DNA. Among the nucleobases, guanine has the lowest redox potential, making it a major target of oxidation. Although RNA is more prone to oxidation than DNA is, oxidation of guanine in RNA has been studied to a significantly lesser extent. One of the reasons for this is that many tools that were previously developed to study oxidation of DNA cannot be used on RNA. In the study presented here, the lack of a method for seeking sites of modification in RNA where oxidation occurs is addressed. For this purpose, reverse transcription of RNA containing major products of guanine oxidation was used. Extension of a DNA primer annealed to an RNA template containing 8-oxo-7,8-dihydroguanine (OG), 5-guanidinohydantoin (Gh), or the R and S diastereomers of spiroiminodihydantoin (Sp) was studied under standing start conditions. SuperScript III reverse transcriptase is capable of bypassing these lesions in RNA inserting predominantly A opposite OG, predominantly G opposite Gh, and almost an equal mixture of A and G opposite the Sp diastereomers. These data should allow RNA sequencing of guanine oxidation products by following characteristic mutation signatures formed by the reverse transcriptase during primer elongation past G oxidation sites in the template RNA strand.
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Affiliation(s)
- Anton Alenko
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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26
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San Miguel K, Scott JG. The next generation of insecticides: dsRNA is stable as a foliar-applied insecticide. PEST MANAGEMENT SCIENCE 2016; 72:801-9. [PMID: 26097110 DOI: 10.1002/ps.4056] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/01/2015] [Accepted: 06/08/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND RNAi is a powerful tool used to study gene function. It also has been hypothesized to be a promising new method for control of insect pests on crops, although the perceived instability of dsRNA in the environment has constrained thinking about the options for this new type of pest control. RESULTS We confirmed that foliar application of Colorado potato beetle dsRNA actin is highly effective for control, demonstrated that treatment with actin-dsRNA protects potato plants for at least 28 days under greenhouse conditions and found that the dsRNA is not readily removed by water once dried on the leaves. CONCLUSION These new results suggest that foliar application of dsRNA could be a valuable control strategy for some pests. Technological aspects of spraying dsRNA that need to be considered in the future are discussed.
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Affiliation(s)
- Keri San Miguel
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Jeffrey G Scott
- Department of Entomology, Cornell University, Ithaca, NY, USA
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27
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Lee W, Matsika S. QM/MM studies reveal pathways leading to the quenching of the formation of thymine dimer photoproduct by flanking bases. Phys Chem Chem Phys 2016; 17:9927-35. [PMID: 25776223 DOI: 10.1039/c5cp00292c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is known that the formation of the photochemical product of thymine-thymine cyclobutane pyrimidine dimer (TT-CPD) formed upon UV excitation in DNA is significantly affected by the nature of the flanking bases, and that the oxidation potential of the flanking base correlates with the quenching of TT-CPD formation. However, the electronic details of this correlation have remained controversial. The quenching of thymine dimer formation exerted by flanking bases was suggested to be driven by both conformational and electronic effects. In the present study, we examine both of these effects using umbrella sampling and a quantum mechanical/molecular mechanical (QM/MM) approach for selected model systems. Our results demonstrate that a charge transfer (CT) state between the flanking base and the adjacent thymine base can provide a decay pathway for the population to escape from dimer formation, which eventually leads to the formation of an exciplex. The QM/MM vertical excitation energies also reveal that the oxidation potential of flanking bases correlates with the energy level of the CT state, thereby determining whether the CT state intersects with the state that can lead to dimer formation. The consistency between these results and experimentally obtained dimer formation rates implies that the quenching of dimer formation is mainly attributed to the decay pathway via the CT state. The present results further underline the importance of the electronic effects in quenching.
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Affiliation(s)
- Wook Lee
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA.
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28
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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29
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Günther C, Kind B, Reijns MAM, Berndt N, Martinez-Bueno M, Wolf C, Tüngler V, Chara O, Lee YA, Hübner N, Bicknell L, Blum S, Krug C, Schmidt F, Kretschmer S, Koss S, Astell KR, Ramantani G, Bauerfeind A, Morris DL, Cunninghame Graham DS, Bubeck D, Leitch A, Ralston SH, Blackburn EA, Gahr M, Witte T, Vyse TJ, Melchers I, Mangold E, Nöthen MM, Aringer M, Kuhn A, Lüthke K, Unger L, Bley A, Lorenzi A, Isaacs JD, Alexopoulou D, Conrad K, Dahl A, Roers A, Alarcon-Riquelme ME, Jackson AP, Lee-Kirsch MA. Defective removal of ribonucleotides from DNA promotes systemic autoimmunity. J Clin Invest 2014; 125:413-24. [PMID: 25500883 DOI: 10.1172/jci78001] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/09/2014] [Indexed: 01/22/2023] Open
Abstract
Genome integrity is continuously challenged by the DNA damage that arises during normal cell metabolism. Biallelic mutations in the genes encoding the genome surveillance enzyme ribonuclease H2 (RNase H2) cause Aicardi-Goutières syndrome (AGS), a pediatric disorder that shares features with the autoimmune disease systemic lupus erythematosus (SLE). Here we determined that heterozygous parents of AGS patients exhibit an intermediate autoimmune phenotype and demonstrated a genetic association between rare RNASEH2 sequence variants and SLE. Evaluation of patient cells revealed that SLE- and AGS-associated mutations impair RNase H2 function and result in accumulation of ribonucleotides in genomic DNA. The ensuing chronic low level of DNA damage triggered a DNA damage response characterized by constitutive p53 phosphorylation and senescence. Patient fibroblasts exhibited constitutive upregulation of IFN-stimulated genes and an enhanced type I IFN response to the immunostimulatory nucleic acid polyinosinic:polycytidylic acid and UV light irradiation, linking RNase H2 deficiency to potentiation of innate immune signaling. Moreover, UV-induced cyclobutane pyrimidine dimer formation was markedly enhanced in ribonucleotide-containing DNA, providing a mechanism for photosensitivity in RNase H2-associated SLE. Collectively, our findings implicate RNase H2 in the pathogenesis of SLE and suggest a role of DNA damage-associated pathways in the initiation of autoimmunity.
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30
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Hariharan M, Siegmund K, Saurel C, McCullagh M, Schatz GC, Lewis FD. Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 - 4) vs. (2 + 2) adducts. Photochem Photobiol Sci 2014; 13:266-71. [PMID: 24212351 DOI: 10.1039/c3pp50283j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photochemical reactions of eleven synthetic DNA hairpins possessing a single TT step either in a base-paired stem or in a hexanucleotide linker have been investigated. The major reaction products have been identified as the cis-syn (2 + 2) adduct and the (6 - 4) adduct on the basis of their spectroscopic properties including 1D and 2D NMR spectra, UV spectra and stability or instability to photochemical cleavage. Product quantum yields and ratios determined by HPLC analysis allow the behaviour of the eleven hairpins to be placed into three groups: Group I in which the (2 + 2) adduct is the major product, as is usually the case for DNA, Group II in which comparable amounts of (2 + 2) and (6 - 4) adducts are formed, and Group III in which the major product is the (6 - 4) adduct. The latter behaviour is without precedent in natural or synthetic DNA and appears to be related to the highly fluxional structures of the hairpin reactants. Molecular dynamics simulation of ground state conformations provides quantum yields and product ratios calculated using a single parameter model that are in reasonable agreement with most of the experimental results. Factors which may influence the observed product ratios are discussed.
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Affiliation(s)
- Mahesh Hariharan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA.
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31
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Law YK, Forties RA, Liu X, Poirier MG, Kohler B. Sequence-dependent thymine dimer formation and photoreversal rates in double-stranded DNA. Photochem Photobiol Sci 2014; 12:1431-9. [PMID: 23727985 DOI: 10.1039/c3pp50078k] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The kinetics of thymine-thymine cyclobutane pyrimidine dimer (TT-CPD) formation was studied at 23 thymine-thymine base steps in two 247-base pair DNA sequences irradiated at 254 nm. Damage was assayed site-specifically and simultaneously on both the forward and reverse strands by detecting emission from distinguishable fluorescent labels at the 5'-termini of fragments cleaved at CPD sites by T4 pyrimidine dimer glycosylase and separated by gel electrophoresis. The total DNA strand length of nearly 1000 bases made it possible to monitor damage at all 9 tetrads of the type XTTY, where X and Y are non-thymine bases. TT-CPD yields for different tetrads were found to vary by as much as an order of magnitude, but similar yields were observed at all instances of a given tetrad. Kinetic analysis of CPD formation at 23 distinct sites reveals that both the formation and reversal photoreactions depend sensitively on the identity of the nearest-neighbour bases on the 5' and the 3' side of a photoreactive TT base step. The lowest formation and reversal rates occur when two purine bases flank a TT step, while the highest formation and reversal rates are observed for tetrads with at least one flanking C. Overall, the results show that the probabilities of CPD formation and photoreversal depend principally on interactions with nearest-neighbour bases.
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Affiliation(s)
- Yu Kay Law
- Biophysics Program, The Ohio State University, Columbus, OH, USA
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32
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Kneuttinger AC, Kashiwazaki G, Prill S, Heil K, Müller M, Carell T. Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions. Photochem Photobiol 2013; 90:1-14. [PMID: 24354557 DOI: 10.1111/php.12197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022]
Abstract
Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Stefan Prill
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Korbinian Heil
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Markus Müller
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
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33
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Nair SG, Loppnow GR. Multiplexed, UVC-induced, sequence-dependent DNA damage detection. Photochem Photobiol 2013; 89:884-90. [PMID: 23441594 DOI: 10.1111/php.12066] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/22/2013] [Indexed: 12/12/2022]
Abstract
The exposure of DNA to ultraviolet (UV) radiation causes sequence-dependent damage. Thus, there is a need for an analytical technique that can detect damage in large numbers of DNA sequences simultaneously. In this study, we have designed an assay for UVC-induced DNA damage in multiple oligonucleotides simultaneously by using a 96-well plate and a novel automated sample mover. The UVC-induced DNA damage is measured using smart probes, analogs of molecular beacons in which guanosine nucleotides act as the fluorescence quencher. Our results show that the oligonucleotide damage constants obtained with this method are reproducible and similar to those obtained in cuvettes. The calibration curve for poly-dT shows good linearity (R(2) = 0.96), with limits of detection (LOD) and quantification (LOQ) equal to 55 and 183 nm, respectively. The results show that the damage kinetics upon irradiation is sensitive to the different types of photoproducts formed in the different sequences used; i.e. poly-A oligonucleotides containing guanine are damaged at a faster rate than poly-A oligonucleotides containing either thymine or cytosine. Thus, detecting DNA damage in a 96-well plate and quantifying the damage with smart probes are a simple, fast and inexpensive mix-and-read technique for multiplexed, sequence-specific DNA damage detection.
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Affiliation(s)
- Sindhu G Nair
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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34
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Madsen CS, Nielsen LJ, Pedersen NS, Lauritsen A, Nielsen P. Double-headed nucleotides in DNA-zipper structures; base–base interactions and UV-induced cross-coupling in the minor groove. RSC Adv 2013. [DOI: 10.1039/c3ra40857d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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35
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Patwardhan S, Tonzani S, Lewis FD, Siebbeles LDA, Schatz GC, Grozema FC. Effect of Structural Dynamics and Base Pair Sequence on the Nature of Excited States in DNA Hairpins. J Phys Chem B 2012; 116:11447-58. [DOI: 10.1021/jp307146u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Sameer Patwardhan
- Opto-Electronic Materials Section,
Department of Chemical Engineering, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The
Netherlands
- Department
of Chemistry, Center
for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Stefano Tonzani
- Department
of Chemistry, Center
for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Frederick D. Lewis
- Department
of Chemistry, Center
for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Laurens D. A. Siebbeles
- Opto-Electronic Materials Section,
Department of Chemical Engineering, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The
Netherlands
| | - George C. Schatz
- Department
of Chemistry, Center
for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Ferdinand C. Grozema
- Opto-Electronic Materials Section,
Department of Chemical Engineering, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The
Netherlands
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36
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Neelakandan PP, Pan Z, Hariharan M, Lewis FD. Facially-selective thymine-thymine photodimerization in TTT triads. Photochem Photobiol Sci 2012; 11:889-92. [PMID: 22580641 DOI: 10.1039/c2pp25089f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Irradiation of alkane-linked DNA hairpins possessing TTT steps with flanking purine bases yields products identified as the cis-syn (2 + 2) dimers formed between the central thymine and its 3'- and 5'-neighbors. Selective formation of the 3'-dimer is attributed to ground state conformational effects and electron transfer quenching by purine bases.
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Affiliation(s)
- Prakash P Neelakandan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA
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37
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Burgula LN, Radhakrishnan K, Kundu LM. Synthesis of modified uracil and cytosine nucleobases using a microwave-assisted method. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.03.056] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Pan Z, Chen J, Schreier WJ, Kohler B, Lewis FD. Thymine dimer photoreversal in purine-containing trinucleotides. J Phys Chem B 2011; 116:698-704. [PMID: 22103806 DOI: 10.1021/jp210575g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cyclobutane-pyrimidine dimer yields in UV-irradiated DNA are controlled by the equilibrium between forward and reverse photoreactions. Past studies have shown that dimer yields are suppressed at sites adjacent to a purine base, but the underlying causes are unclear. In order to investigate whether this suppression is the result of repair by electron transfer from a neighboring nucleobase, the yields and dynamics of the reverse reaction were studied using trinucleotides containing a cis-syn dimer (T<>T) flanked on the 5' or the 3' side by adenine or guanine. The probability of forming an excited state on T<>T or on the purine base was varied by tuning the irradiation wavelength between 240 and 280 nm. Cleavage quantum yields decrease by an order of magnitude over this wavelength range and are less than 1% at 280 nm, a wavelength that excites the purine base with more than 95% probability. Conditional quantum yields of cleavage for the trinucleotides given excitation of T<>T are similar in magnitude to the quantum yield of cleavage of unmodified T<>T. These results indicate that within experimental uncertainty all photoreversal in these single-stranded substrates is the result of direct electronic excitation of T<>T. Photolyase-like repair of T<>T due to electron transfer from an adjacent purine is negligible in these substrates. Instead, the observed variation in photoreversal quantum yields for adenine- versus guanine-flanked cis-syn dimer could be due to uncertainties in absorption cross sections or to a modest quenching effect by the purine on the excited state of T<>T. Pump-probe measurements reveal that the excited-state lifetimes of A or G in the dimer-containing trinucleotides are unperturbed by the neighboring dimer, indicating that electron transfer from purine base to T<>T is not competitive with rapid excited-state deactivation. Pump-probe measurements on unmodified T<>T in aqueous solution indicate that cleavage is most likely complete on a picosecond or subpicosecond time scale.
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Affiliation(s)
- Zhengzheng Pan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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39
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Pan Z, Hariharan M, Arkin JD, Jalilov AS, McCullagh M, Schatz GC, Lewis FD. Electron donor-acceptor interactions with flanking purines influence the efficiency of thymine photodimerization. J Am Chem Soc 2011; 133:20793-8. [PMID: 22032333 DOI: 10.1021/ja205460f] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Quantum yields for thymine photodimerization (Φ(TT)) have been determined for a series of short DNA single-strand and base-paired hairpin structures possessing a single thymine-thymine step with flanking purines. Values of Φ(TT) are strongly dependent upon the oxidation potential of the flanking purine, decreasing in the order: inosine > adenine > guanine > deazaguanine. The dependence of Φ(TT) on the ionization potential of the flanking purine is more pronounced when the purine of lower oxidation potential is located at the 5'- versus 3'-position in either a single strand or a hairpin. Molecular dynamics simulations for hairpin structures indicate that the TT step is π-stacked with both the 5' and 3' purine, but that there is little π-stacking with either purine in single-strand structures. The observation of moderately intense long-wavelength UV absorption features for hairpins having 5'-Z or G flanking purines suggests that excitation of ground state donor-acceptor complexes may account for more extensive quenching of dimerization by 5'- versus 3'-purines. The "purine effect" on Φ(TT) is attributed to a combination of ground state conformation, ground state electron donor-acceptor interactions, and excited state exciplex formation.
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Affiliation(s)
- Zhengzheng Pan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA
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40
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Chen Z, Liu Y, Zhou N, Zhang Q, Han K. Electrochemical study of thymine dimer based on DNA charge transfer. JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1134/s1061934811070045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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McCullagh M, Hariharan M, Lewis FD, Markovitsi D, Douki T, Schatz GC. Conformational Control of TT Dimerization in DNA Conjugates. A Molecular Dynamics Study. J Phys Chem B 2010; 114:5215-21. [DOI: 10.1021/jp100983t] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Mahesh Hariharan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Dimitra Markovitsi
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Thierry Douki
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60201
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42
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Glas AF, Schneider S, Maul MJ, Hennecke U, Carell T. Crystal structure of the T(6-4)C lesion in complex with a (6-4) DNA photolyase and repair of UV-induced (6-4) and Dewar photolesions. Chemistry 2009; 15:10387-96. [PMID: 19722240 DOI: 10.1002/chem.200901004] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
UV-light irradiation induces the formation of highly mutagenic lesions in DNA, such as cis-syn cyclobutane pyrimidine dimers (CPD photoproducts), pyrimidine(6-4)pyrimidone photoproducts ((6-4) photoproducts) and their Dewar valence isomers ((Dew) photoproducts). Here we describe the synthesis of defined DNA strands containing these lesions by direct irradiation. We show that all lesions are efficiently repaired except for the T(Dew)T lesion, which cannot be cleaved by the repair enzyme under our conditions. A crystal structure of a T(6-4)C lesion containing DNA duplex in complex with the (6-4) photolyase from Drosophila melanogaster provides insight into the molecular recognition event of a cytosine derived photolesion for the first time. In light of the previously postulated repair mechanism, which involves rearrangement of the (6-4) lesions into strained four-membered ring repair intermediates, it is surprising that the not rearranged T(6-4)C lesion is observed in the active site. The structure, therefore, provides additional support for the newly postulated repair mechanism that avoids this rearrangement step and argues for a direct electron injection into the lesion as the first step of the repair reaction performed by (6-4) DNA photolyases.
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Affiliation(s)
- Andreas F Glas
- Department for Chemistry and Biochemistry, Ludwig-Maximilians University, Butenandtstr. 5-13, 81377 Munich, Germany
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43
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Maul MJ, Barends TRM, Glas AF, Cryle MJ, Domratcheva T, Schneider S, Schlichting I, Carell T. Crystal structure and mechanism of a DNA (6-4) photolyase. Angew Chem Int Ed Engl 2009; 47:10076-80. [PMID: 18956392 DOI: 10.1002/anie.200804268] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Melanie J Maul
- Centre for Integrative Protein Science, Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
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44
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Maul M, Barends T, Glas A, Cryle M, Domratcheva T, Schneider S, Schlichting I, Carell T. Röntgenkristallstruktur und Mechanismus der DNA-(6-4)-Photolyase. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200804268] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Hariharan M, Lewis FD. Context-dependent photodimerization in isolated thymine-thymine steps in DNA. J Am Chem Soc 2008; 130:11870-1. [PMID: 18702486 DOI: 10.1021/ja804950j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The effect of 280 nm irradiation on a family of synthetic DNA hairpins possessing an alkane linker connecting a six-base pair stem having a single T-T step located at different positions within the hairpin has been investigated. A single adduct assigned to the product of 2+2 dimerization is obtained except in the case of a T-T step located adjacent to the linker, in which case both 2+2 and 6-4 adducts are obtained. The efficiency of dimerization is similar for three hairpins having a T-T step located within the duplex interior. Lower efficiency is observed for a T-T step located at the open end of the hairpin and in T overhangs, whereas higher efficiency is observed for the T-T step adjacent to the linker and in a single T bulge. The context-dependence of dimerization efficiency is discussed.
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Affiliation(s)
- Mahesh Hariharan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA
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46
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Crespo-Hernández CE, de la Harpe K, Kohler B. Ground-state recovery following UV excitation is much slower in G x C-DNA duplexes and hairpins than in mononucleotides. J Am Chem Soc 2008; 130:10844-5. [PMID: 18646753 DOI: 10.1021/ja802183s] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Excited states in double-stranded oligonucleotides containing G.C base pairs were studied by femtosecond transient absorption spectroscopy. Relaxation to the electronic ground state occurs about 10 times more slowly in the duplexes and hairpins studied on average than in the individual mononucleotides of G and C. Detection of long-lived excited states in G.C oligonucleotides complements the earlier observation of slow ground-state recovery in A.T DNA, showing that excited states with picosecond lifetimes are formed in DNAs containing either kind of base pair. The results show further that Watson-Crick G.C base pairs in these base-paired and base-stacked duplexes do not enable subpicosecond relaxation to the electronic ground state. A model is proposed in which fluorescent exciton states decay rapidly and irreversibly to dark exciplex states. This model explains the seemingly contradictory observations of femtosecond fluorescence and slower, picosecond recovery of the ground-state population.
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47
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Matallana-Surget S, Meador JA, Joux F, Douki T. Effect of the GC content of DNA on the distribution of UVB-induced bipyrimidine photoproducts. Photochem Photobiol Sci 2008; 7:794-801. [PMID: 18597027 DOI: 10.1039/b719929e] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solar UV radiation is a major mutagen that damages DNA through the formation of dimeric photoproducts between adjacent thymine and cytosine bases. A major effect of the GC content of the genome is thus anticipated, in particular in prokaryotes where this parameter significantly varies among species. We quantified the formation of UV-induced photolesions within both isolated and cellular DNA of bacteria of different GC content. First, we could unambiguously show the favored formation of cytosine-containing photoproducts with increasing GC content (from 28 to 72%) in isolated DNA. Thymine-thymine cyclobutane dimer was a minor lesion at high GC content. This trend was confirmed by an accurate and quantitative analysis of the photochemical data based on the exact dinucleotide frequencies of the studied genomes. The observation of the effect of the genome composition on the distribution of photoproducts was then confirmed in living cells, using two marine bacteria exhibiting different GC content. Because cytosine-containing photoproducts are highly mutagenic, it may be predicted that species with genomes exhibiting a high GC content are more susceptible to UV-induced mutagenesis.
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Affiliation(s)
- Sabine Matallana-Surget
- UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Biologique de Banyuls, Observatoire Océanologique, F-66651, Banyuls/mer, France
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48
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Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species. Proc Natl Acad Sci U S A 2008; 105:2806-11. [PMID: 18287075 DOI: 10.1073/pnas.0708244105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA-binding alpha/beta-type small acid-soluble proteins (SASPs) are a major factor in the resistance and long-term survival of spores of Bacillus species by protecting spore DNA against damage due to desiccation, heat, toxic chemicals, enzymes, and UV radiation. We now report the crystal structure at 2.1 A resolution of an alpha/beta-type SASP bound to a 10-bp DNA duplex. In the complex, the alpha/beta-type SASP adopt a helix-turn-helix motif, interact with DNA through minor groove contacts, bind to approximately 6 bp of DNA as a dimer, and the DNA is in an A-B type conformation. The structure of the complex provides important insights into the molecular details of both DNA and alpha/beta-type SASP protection in the complex and thus also in spores.
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49
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Xie H, Xia F, Cao Z. Density Functional Study toward Understanding Dehydrogenation of the Adenine−Thymine Base Pair and Its Anion. J Phys Chem A 2007; 111:4384-90. [PMID: 17474725 DOI: 10.1021/jp0686137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The dehydrogenated radicals and anions of Watson-Crick adenine-thymine (A-T) base pair have been investigated by the B3LYP/DZP++ approach. Calculations show that the dehydrogenated radicals and anions have relatively high stabilities compared with the single base adenine and thymine. The electron attachment to the A-T base pair and its derivatives significantly modifies the hydrogen bond interactions and results in remarkable structural changes. As for the dehydrogenated A-T radicals, they have relatively high electron affinities and different dehydrogenation properties with respect to their constituent elements. The relatively low-cost hydrogen eliminations correspond to the (N9)-H (adenine) and (N1)-H (thymine) bonds cleavage. Both dehydrogenation processes have Gibbs free energies of reaction DeltaG degrees of 13.4 and 17.2 kcal mol-1, respectively. The solvent water exhibits significant effect on electron attachment and dehydrogenation properties of the A-T base pair and its derivatives. In the dehydrogenating process, the anionic A-T fragment gradually changes its electronic configuration from pi* to sigma* state, like the single bases adenine and thymine.
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Affiliation(s)
- Hujun Xie
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
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Lee G, Rabbi M, Clark RL, Marszalek PE. Nanomechanical fingerprints of UV damage to DNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2007; 3:809-13. [PMID: 17393552 DOI: 10.1002/smll.200600592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Gwangrog Lee
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
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