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Nickens DG, Feng Z, Shen J, Gray SJ, Simmons R, Niu H, Bochman M. Cdc13 exhibits dynamic DNA strand exchange in the presence of telomeric DNA. Nucleic Acids Res 2024; 52:6317-6332. [PMID: 38613387 PMCID: PMC11194072 DOI: 10.1093/nar/gkae265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Telomerase is the enzyme that lengthens telomeres and is tightly regulated by a variety of means to maintain genome integrity. Several DNA helicases function at telomeres, and we previously found that the Saccharomyces cerevisiae helicases Hrq1 and Pif1 directly regulate telomerase. To extend these findings, we are investigating the interplay between helicases, single-stranded DNA (ssDNA) binding proteins (ssBPs), and telomerase. The yeast ssBPs Cdc13 and RPA differentially affect Hrq1 and Pif1 helicase activity, and experiments to measure helicase disruption of Cdc13/ssDNA complexes instead revealed that Cdc13 can exchange between substrates. Although other ssBPs display dynamic binding, this was unexpected with Cdc13 due to the reported in vitro stability of the Cdc13/telomeric ssDNA complex. We found that the DNA exchange by Cdc13 occurs rapidly at physiological temperatures, requires telomeric repeat sequence DNA, and is affected by ssDNA length. Cdc13 truncations revealed that the low-affinity binding site (OB1), which is distal from the high-affinity binding site (OB3), is required for this intermolecular dynamic DNA exchange (DDE). We hypothesize that DDE by Cdc13 is the basis for how Cdc13 'moves' at telomeres to alternate between modes where it regulates telomerase activity and assists in telomere replication.
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Affiliation(s)
- David G Nickens
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Zhitong Feng
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Jiangchuan Shen
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Spencer J Gray
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Robert H Simmons
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Hengyao Niu
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Matthew L Bochman
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
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2
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Iachettini S, Biroccio A, Zizza P. Therapeutic Use of G4-Ligands in Cancer: State-of-the-Art and Future Perspectives. Pharmaceuticals (Basel) 2024; 17:771. [PMID: 38931438 PMCID: PMC11206494 DOI: 10.3390/ph17060771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
G-quadruplexes (G4s) are guanine-rich non-canonical secondary structures of nucleic acids that were identified in vitro almost half a century ago. Starting from the early 1980s, these structures were also observed in eukaryotic cells, first at the telomeric level and later in regulatory regions of cancer-related genes, in regulatory RNAs and within specific cell compartments such as lysosomes, mitochondria, and ribosomes. Because of the involvement of these structures in a large number of biological processes and in the pathogenesis of several diseases, including cancer, the interest in G4 targeting has exponentially increased in the last few years, and a great number of novel G4 ligands have been developed. Notably, G4 ligands represent a large family of heterogeneous molecules that can exert their functions by recognizing, binding, and stabilizing G4 structures in multiple ways. Regarding anti-cancer activity, the efficacy of G4 ligands was originally attributed to the capability of these molecules to inhibit the activity of telomerase, an enzyme that elongates telomeres and promotes endless replication in cancer cells. Thereafter, novel mechanisms through which G4 ligands exert their antitumoral activities have been defined, including the induction of DNA damage, control of gene expression, and regulation of metabolic pathways, among others. Here, we provided a perspective on the structure and function of G4 ligands with particular emphasis on their potential role as antitumoral agents. In particular, we critically examined the problems associated with the clinical translation of these molecules, trying to highlight the main aspects that should be taken into account during the phases of drug design and development. Indeed, taking advantage of the successes and failures, and the more recent technological progresses in the field, it would be possible to hypothesize the development of these molecules in the future that would represent a valid option for those cancers still missing effective therapies.
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Affiliation(s)
| | | | - Pasquale Zizza
- Translational Oncology Research Unit, IRCCS—Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Roma, Italy; (S.I.); (A.B.)
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Gajarsky M, Stadlbauer P, Sponer J, Cucchiarini A, Dobrovolna M, Brazda V, Mergny JL, Trantirek L, Lenarcic Zivkovic M. DNA Quadruplex Structure with a Unique Cation Dependency. Angew Chem Int Ed Engl 2024; 63:e202313226. [PMID: 38143239 DOI: 10.1002/anie.202313226] [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: 09/06/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023]
Abstract
DNA quadruplex structures provide an additional layer of regulatory control in genome maintenance and gene expression and are widely used in nanotechnology. We report the discovery of an unprecedented tetrastranded structure formed from a native G-rich DNA sequence originating from the telomeric region of Caenorhabditis elegans. The structure is defined by multiple properties that distinguish it from all other known DNA quadruplexes. Most notably, the formation of a stable so-called KNa-quadruplex (KNaQ) requires concurrent coordination of K+ and Na+ ions at two distinct binding sites. This structure provides novel insight into G-rich DNA folding under ionic conditions relevant to eukaryotic cell physiology and the structural evolution of telomeric DNA. It highlights the differences between the structural organization of human and nematode telomeric DNA, which should be considered when using C. elegans as a model in telomere biology, particularly in drug screening applications. Additionally, the absence/presence of KNaQ motifs in the host/parasite introduces an intriguing possibility of exploiting the KNaQ fold as a plausible antiparasitic drug target. The structure's unique shape and ion dependency and the possibility of controlling its folding by using low-molecular-weight ligands can be used for the design or discovery of novel recognition DNA elements and sensors.
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Affiliation(s)
- Martin Gajarsky
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Current address: Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany
| | - Petr Stadlbauer
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Anne Cucchiarini
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Michaela Dobrovolna
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkynova 464, 61200, Brno, Czech Republic
| | - Vaclav Brazda
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkynova 464, 61200, Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Lukas Trantirek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Martina Lenarcic Zivkovic
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
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Wang X, Zheng D, Wang C, Xue D, Wang Q, Xia J. Harnessing intermolecular G-quadruplex-based spatial confinement effect for accelerated activation of CRISPR/Cas12a empowers ultra-sensitive detection of PML/RARA fusion genes. Anal Chim Acta 2024; 1287:342108. [PMID: 38182385 DOI: 10.1016/j.aca.2023.342108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/07/2024]
Abstract
Accurate detection and classification of the three isoforms of PML/RARA genomic fragments are crucial for predicting disease progression, stratifying risk, and administering precise drug therapies in acute promyelocytic leukemia (APL). In this study, we have developed a highly specific nucleic acid detection platform capable of quantifying the long isoform of the three main PML-RARA isoforms at a constant temperature. This platform integrates the strengths of the CRISPR/Cas12a nuclease-based method and the rolling circle amplification (RCA) technique. Notably, the RCA-assisted CRISPR/Cas12a trans-cleavage system incorporates a spatial confinement effect by utilizing intermolecular G-quadruplex structures. This innovative design effectively enhances the local concentration of CRISPR/Cas12a, thereby accelerating its cleaving efficiency towards reporter nucleic acids and enabling the detection of PML/RARA fusion gene expression through spectroscopy. The robust detection of PML/RARA fusion gene from human serum samples validates the reliability and potential of this platform in the screening, diagnosis, and prognosis of APL cases. Our findings present an approach that holds significant potential for the further development of the robust CRISPR/Cas sensor system, offering a rapid and adaptable paradigm for APL diagnosis.
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Affiliation(s)
- Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, 350000, PR China; NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian, 350000, PR China.
| | - Dan Zheng
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Chengyi Wang
- Department of Hematology & Oncology, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, Fujian, 350011, PR China
| | - Danni Xue
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Qi Wang
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Juan Xia
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China.
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Jedlička P, Tokan V, Kejnovská I, Hobza R, Kejnovský E. Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species. Mob DNA 2023; 14:3. [PMID: 37038191 PMCID: PMC10088271 DOI: 10.1186/s13100-023-00291-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Canonical telomeres (telomerase-synthetised) are readily forming G-quadruplexes (G4) on the G-rich strand. However, there are examples of non-canonical telomeres among eukaryotes where telomeric tandem repeats are invaded by specific retrotransposons. Drosophila melanogaster represents an extreme example with telomeres composed solely by three retrotransposons-Het-A, TAHRE and TART (HTT). Even though non-canonical telomeres often show strand biased G-distribution, the evidence for the G4-forming potential is limited. RESULTS Using circular dichroism spectroscopy and UV absorption melting assay we have verified in vitro G4-formation in the HTT elements of D. melanogaster. Namely 3 in Het-A, 8 in TART and 2 in TAHRE. All the G4s are asymmetrically distributed as in canonical telomeres. Bioinformatic analysis showed that asymmetric distribution of potential quadruplex sequences (PQS) is common in telomeric retrotransposons in other Drosophila species. Most of the PQS are located in the gag gene where PQS density correlates with higher DNA sequence conservation and codon selection favoring G4-forming potential. The importance of G4s in non-canonical telomeres is further supported by analysis of telomere-associated retrotransposons from various eukaryotic species including green algae, Diplomonadida, fungi, insects and vertebrates. Virtually all analyzed telomere-associated retrotransposons contained PQS, frequently with asymmetric strand distribution. Comparison with non-telomeric elements showed independent selection of PQS-rich elements from four distinct LINE clades. CONCLUSION Our findings of strand-biased G4-forming motifs in telomere-associated retrotransposons from various eukaryotic species support the G4-formation as one of the prerequisites for the recruitment of specific retrotransposons to chromosome ends and call for further experimental studies.
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Affiliation(s)
- Pavel Jedlička
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Viktor Tokan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic.
| | - Iva Kejnovská
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Eduard Kejnovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic.
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6
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Bai D, Shan SW, Zhang X, Li Y, Xie J, Wu WQ. Comprehensive insights into the structures and dynamics of plant telomeric G-quadruplexes. Int J Biol Macromol 2023; 231:123281. [PMID: 36657543 DOI: 10.1016/j.ijbiomac.2023.123281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Telomeres, which are located at the ends of eukaryotic chromosomes, are crucial for genomic maintenance. Most telomeric DNA is composed of tandemly repeated guanine (G)-rich sequences, which form G-quadruplexes (G4s). The structures and dynamics of telomeric G4s are essential for telomere functioning and helpful for G4-based biosensing. However, they are far from being understood, especially for plants. In this contribution, the folding, environment-induced G4 dynamics, and protein-catalyzed unfolding of plant telomeric G4s were comprehensively studied. It was found that diverse plant telomeric sequences from land plants to green algae could fold into G4 structures. In addition, 5'-proximal ssDNA but not 3'-proximal ssDNA drove conversion of anti-parallel G4 structures to parallel structures, and both 5' and 3' ssDNA decreased the stability of G4s in dilute solution. Furthermore, molecular crowding promoted the formation of parallel structures for three-layer but not for two-layer G4s, and increased the stability of all selected G4s. Finally, AtRecQ2 helicase resolved the stable parallel structure of typical plant telomeric G4 in crowded solution, but ssDNA binding protein AtRPA did not. Furthermore, AtRecQ2 unwound the structure more efficiently in the presence of AtRPA. The results may expand our understanding on the structures and dynamics of plant telomeric G4s.
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Affiliation(s)
- Di Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Song-Wang Shan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yan Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jie Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wen-Qiang Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China.
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7
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Chen Z, Wang Y. A label- and enzyme-free fluorescence assay based on thioflavin T–induced G-quadruplexes for the detection of telomerase activity. JOURNAL OF CHEMICAL RESEARCH 2023. [DOI: 10.1177/17475198221139085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A label- and enzyme-free fluorescence assay based on thioflavin T–induced G-quadruplexes is developed to sensitively and specifically detect telomerase activity. Thioflavin T has a dual role as an efficient inducer and fluorescent probe, and the incorporation of thioflavin T into the thioflavin T–induced G-quadruplexes results in an intense fluorescence enhancement. In the presence of thioflavin T and K+, G-quadruplexes are formed by elongation of the telomerase substrate primer that is catalyzed by telomerase extracted from cancer cells. Thus, the telomerase activity in cancer cell extracts can be evaluated by measuring the thioflavin T fluorescence. More importantly, thioflavin T can specifically recognize and bind to G-quadruplexes, whereas it cannot recognize single- and double-stranded DNAs, which leads to the thioflavin T–based fluorescence assay exhibiting a reduced background and improved signal-to-noise ratio. As a result, the proposed assay has the linear range from 5 to 200 HeLa cells and the detection limit is 34 HeLa cells, which holds great potential for use in the detection of telomerase activity and the diagnosis of cancer.
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Affiliation(s)
- Zhe Chen
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, P.R. China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, P.R. China
| | - Yunxia Wang
- Department of Laboratory Science, Shanxi Medical University, Taiyuan, P.R. China
- The Sixth Hospital of Shanxi Medical University (General Hospital of Tisco), Taiyuan, P.R. China
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8
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Vinayagamurthy S, Bagri S, Mergny JL, Chowdhury S. Telomeres expand sphere of influence: emerging molecular impact of telomeres in non-telomeric functions. Trends Genet 2023; 39:59-73. [PMID: 36404192 PMCID: PMC7614491 DOI: 10.1016/j.tig.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022]
Abstract
Although the impact of telomeres on physiology stands well established, a question remains: how do telomeres impact cellular functions at a molecular level? This is because current understanding limits the influence of telomeres to adjacent subtelomeric regions despite the wide-ranging impact of telomeres. Emerging work in two distinct aspects offers opportunities to bridge this gap. First, telomere-binding factors were found with non-telomeric functions. Second, locally induced DNA secondary structures called G-quadruplexes are notably abundant in telomeres, and gene regulatory regions genome wide. Many telomeric factors bind to G-quadruplexes for non-telomeric functions. Here we discuss a more general model of how telomeres impact the non-telomeric genome - through factors that associate at telomeres and genome wide - and influence cell-intrinsic functions, particularly aging, cancer, and pluripotency.
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Affiliation(s)
- Soujanya Vinayagamurthy
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jean-Louis Mergny
- Institute of Biophysics of the CAS, v.v.i. Královopolská 135, 612 65 Brno, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India.
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Spiridonova VA, Naumova YO, Nikolaeva PA, Novikova TM, Kolomijtseva GY. Thermodynamics and Kinetics of Unfolding of Antiparallel G-Quadruplexes in Anti-Thrombin Aptamers. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1292-1300. [PMID: 36509716 DOI: 10.1134/s0006297922110086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The process of unfolding of G-quadruplex structure in the RE31 DNA-aptamer and in its complex with thrombin under the action of the fluorescently labeled complementary oligonucleotides of varying length with formation of double-helix structures has been studied. It has been suggested that G-quadruplex unfolding involves formation of an intermediate complex with an oligonucleotide. Thermodynamic parameters and kinetics of unfolding of the free aptamer and its complex with thrombin differ. Extension of the oligonucleotide sequence complementary to G-quadruplex by two nucleotides to cover the so-called "hinge region" had little impact on the conformational transition of G-quadruplex of the free aptamer. However, a pronounced effect has been observed for the aptamer-protein complex. Most likely these differences could be explained by the thrombin-induced conformational transition of the aptamer involving the hinge region.
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Affiliation(s)
- Vera A Spiridonova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yulia O Naumova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Polina A Nikolaeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tatiana M Novikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Galina Ya Kolomijtseva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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11
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Mustafa G, Gyawali P, Taylor JA, Maleki P, Nunez MV, Guntrum MC, Shiekh S, Balci H. A single molecule investigation of i-motif stability, folding intermediates, and potential as in-situ pH sensor. Front Mol Biosci 2022; 9:977113. [PMID: 36072435 PMCID: PMC9441956 DOI: 10.3389/fmolb.2022.977113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
We present a collection of single molecule work on the i-motif structure formed by the human telomeric sequence. Even though it was largely ignored in earlier years of its discovery due to its modest stability and requirement for low pH levels (pH < 6.5), the i-motif has been attracting more attention recently as both a physiologically relevant structure and as a potent pH sensor. In this manuscript, we establish single molecule Förster resonance energy transfer (smFRET) as a tool to study the i-motif over a broad pH and ionic conditions. We demonstrate pH and salt dependence of i-motif formation under steady state conditions and illustrate the intermediate states visited during i-motif folding in real time at the single molecule level. We also show the prominence of intermediate folding states and reversible folding/unfolding transitions. We present an example of using the i-motif as an in-situ pH sensor and use this sensor to establish the time scale for the pH drop in a commonly used oxygen scavenging system.
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12
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G-Quadruplex Formed by the Promoter Region of the hTERT Gene: Structure-Driven Effects on DNA Mismatch Repair Functions. Biomedicines 2022; 10:biomedicines10081871. [PMID: 36009419 PMCID: PMC9405553 DOI: 10.3390/biomedicines10081871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
G-quadruplexes (G4s) are a unique class of noncanonical DNAs that play a key role in cellular processes and neoplastic transformation. Herein, we focused on the promoter region of human TERT oncogene, whose product is responsible for the immortality of cancer cells. It has been shown by chemical probing and spectroscopic methods that synthetic 96-nt DNAs modeling the wild-type G-rich strand of the hTERT promoter and its variants with G>A point substitutions corresponding to somatic driver mutations fold into three stacked parallel G4s with sites of local G4 destabilization caused by G>A substitutions in the G4 motif. These models were used to elucidate how the hTERT multiG4 affects the binding affinity and functional responses of two key proteins, MutS and MutL, involved in the initial stage of DNA mismatch repair (MMR) in Escherichiacoli and Neisseriagonorrhoeae with different MMR mechanisms. We have shown for the first time that (i) point substitutions do not affect the effective binding of these proteins to the hTERT G4 structure, and (ii) the endonuclease activity of MutL from N. gonorrhoeae is significantly suppressed by the stable G4 scaffold. It is likely that some of the genomic instability associated with G4 may be related to the blockage of human intrinsic methyl-independent MMR attempting to operate near G4 structures.
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13
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Dobrovolná M, Bohálová N, Peška V, Wang J, Luo Y, Bartas M, Volná A, Mergny JL, Brázda V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. Int J Mol Sci 2022; 23:8482. [PMID: 35955617 PMCID: PMC9369095 DOI: 10.3390/ijms23158482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5'UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.
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Affiliation(s)
- Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
| | - Jiawei Wang
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Yu Luo
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, CEDEX, 91405 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
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14
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Abstract
We present single-molecule experimental and computational modeling studies investigating the accessibility of human telomeric overhangs of physiologically relevant lengths. We studied 25 different overhangs that contain 4-28 repeats of GGGTTA (G-Tract) sequence and accommodate one to seven tandem G-quadruplex (GQ) structures. Using the FRET-PAINT method, we probed the distribution of accessible sites via a short imager strand, which is complementary to a G-Tract and transiently binds to available sites. We report accessibility patterns that periodically change with overhang length and interpret these patterns in terms of the underlying folding landscape and folding frustration. Overhangs that have [4n]G-Tracts, (12, 16, 20…) demonstrate the broadest accessibility patterns where the peptide nucleic acid probe accesses G-Tracts throughout the overhang. On the other hand, constructs with [4n+2]G-Tracts, (14, 18, 22…) have narrower patterns where the neighborhood of the junction between single- and double-stranded telomeres is most accessible. We interpret these results as the folding frustration being higher in [4n]G-Tract constructs compared to [4n+2]G-Tract constructs. We also developed a computational model that tests the consistency of different folding stabilities and cooperativities between neighboring GQs with the observed accessibility patterns. Our experimental and computational studies suggest the neighborhood of the junction between single- and double-stranded telomeres is least stable and most accessible, which is significant as this is a potential site where the connection between POT1/TPP1 (bound to single-stranded telomere) and other shelterin proteins (localized on double-stranded telomere) is established.
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15
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Marquevielle J, De Rache A, Vialet B, Morvan E, Mergny JL, Amrane S. G-quadruplex structure of the C. elegans telomeric repeat: a two tetrads basket type conformation stabilized by a non-canonical C-T base-pair. Nucleic Acids Res 2022; 50:7134-7146. [PMID: 35736226 PMCID: PMC9262591 DOI: 10.1093/nar/gkac523] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
The Caenorhabditis elegans model has greatly contributed to the understanding of the role of G-quadruplexes in genomic instability. The GGCTTA repeats of the C. elegans telomeres resemble the GGGTTA repeats of the human telomeres. However, the comparison of telomeric sequences (Homo sapiens, Tetrahymena, Oxytricha, Bombyx mori and Giardia) revealed that small changes in these repeats can drastically change the topology of the folded G-quadruplex. In the present work we determined the structure adopted by the C. elegans telomeric sequence d[GG(CTTAGG)3]. The investigated C. elegans telomeric sequence is shown to fold into an intramolecular two G-tetrads basket type G-quadruplex structure that includes a C-T base pair in the diagonal loop. This work sheds light on the telomeric structure of the widely used C. elegans animal model.
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Affiliation(s)
- Julien Marquevielle
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Aurore De Rache
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
- Department of Chemistry, UNamur, 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Brune Vialet
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Jean-Louis Mergny
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Samir Amrane
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
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16
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Jonchhe S, Pandey S, Beneze C, Emura T, Sugiyama H, Endo M, Mao H. Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity. Nucleic Acids Res 2022; 50:697-703. [PMID: 35037040 PMCID: PMC8789071 DOI: 10.1093/nar/gkab1298] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/06/2021] [Accepted: 01/09/2022] [Indexed: 12/02/2022] Open
Abstract
Both ligand binding and nanocavity can increase the stability of a biomolecular structure. Using mechanical unfolding in optical tweezers, here we found that a DNA origami nanobowl drastically increased the stability of a human telomeric G-quadruplex bound with a pyridostatin (PDS) ligand. Such a stability change is equivalent to >4 orders of magnitude increase (upper limit) in binding affinity (Kd: 490 nM → 10 pM (lower limit)). Since confined space can assist the binding through a proximity effect between the ligand-receptor pair and a nanoconfinement effect that is mediated by water molecules, we named such a binding as mechanochemical binding. After minimizing the proximity effect by using PDS that can enter or leave the DNA nanobowl freely, we attributed the increased affinity to the nanoconfinement effect (22%) and the proximity effect (78%). This represents the first quantification to dissect the effects of proximity and nanoconfinement on binding events in nanocavities. We anticipate these DNA nanoassemblies can deliver both chemical (i.e. ligand) and mechanical (i.e. nanocavity) milieus to facilitate robust mechanochemical binding in various biological systems.
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Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Christian Beneze
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.,Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka 564-8680, Japan
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
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17
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Beseiso D, Chen EV, McCarthy SE, Martin KN, Gallagher EP, Miao J, Yatsunyk L. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2959-2972. [PMID: 35212369 PMCID: PMC8934647 DOI: 10.1093/nar/gkac091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3′-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5′-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.
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Affiliation(s)
- Dana Beseiso
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Erin V Chen
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Sawyer E McCarthy
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Kailey N Martin
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Elizabeth P Gallagher
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Joanne Miao
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
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18
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Cebrián R, Belmonte-Reche E, Pirota V, de Jong A, Morales JC, Freccero M, Doria F, Kuipers OP. G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action. J Med Chem 2021; 65:4752-4766. [PMID: 34928608 PMCID: PMC8958502 DOI: 10.1021/acs.jmedchem.1c01905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Guanidine DNA quadruplex
(G4-DNA) structures convey a distinctive
layer of epigenetic information that is critical for regulating key
biological activities and processes as transcription, replication,
and repair in living cells. The information regarding their role and
use as therapeutic drug targets in bacteria is still scarce. Here,
we tested the biological activity of a G4-DNA ligand library, based
on the naphthalene diimide (NDI) pharmacophore, against both Gram-positive
and Gram-negative bacteria. For the best compound identified, NDI-10, a different action mechanism was described for Gram-positive
or negative bacteria. This asymmetric activity profile could be related
to the different prevalence of putative G4-DNA structures in each
group, the influence that they can exert on gene expression, and the
different roles of the G4 structures in these bacteria, which seem
to promote transcription in Gram-positive bacteria and repress transcription
in Gram-negatives.
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Affiliation(s)
- Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Efres Belmonte-Reche
- Advanced (magnetic) Theranostic Nanostructures Lab, International Iberian Nanotechnology Laboratory, Nanomedicine unit, Avenida Mestre José Veiga, s/n 4715-310 Braga, Portugal
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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19
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Song X, Ding Q, Pu Y, Zhang J, Sun R, Yin L, Wei W, Liu S. Application of the Dimeric G-Quadruplex and toehold-mediated strand displacement reaction for fluorescence biosensing of ochratoxin A. Biosens Bioelectron 2021; 192:113537. [PMID: 34339903 DOI: 10.1016/j.bios.2021.113537] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 12/30/2022]
Abstract
Ochratoxin A (OTA) is one of the most toxic mycotoxins that exists in various agro-products and foods. Here, a non-label and enzyme-free fluorescence biosensor for highly specific detection of OTA has been developed by the combination of toehold-mediated strand displacement reaction (TMSD) and G-quadruplex dimer/ThT (G-dimer/ThT). The DNA duplex (aptamer-IP) is composed of the anti-OTA aptamer and a single stranded initiation probe (IP). In the presence of OTA, the attachment of target to aptamer leads to the liberation of the IP, which activates the cycle TMSD amplifications of two hairpin probes (H1 and H2) accompanied by the production of numerous H1-H2 assemblies. This double-stranded H1-H2 structure results in the proximity between the 5'-end overhang tail of H1 and the 3'-end stem of H2 to liberate the pre-blocked G-dimer sequence for lighting up ThT. In addition, the method displayed a stable fluorescence emission in the high-salt media. It was successfully applied to analyze OTA in real food samples. Hence, the constructed fluorescence biosensing platform might provide a new way for OTA and other toxin analysis detection.
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Affiliation(s)
- Xiaolei Song
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, PR China
| | - Qin Ding
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, PR China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, PR China.
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, PR China
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, PR China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, PR China
| | - Wei Wei
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, PR China; State Key Laboratory of Bioelectronics, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, PR China.
| | - Songqin Liu
- State Key Laboratory of Bioelectronics, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, PR China
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20
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Jin M, Li J, Chen Y, Zhao J, Zhang J, Zhang Z, Du P, Zhang L, Lu X. Near-Infrared Small Molecule as a Specific Fluorescent Probe for Ultrasensitive Recognition of Antiparallel Human Telomere G-Quadruplexes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32743-32752. [PMID: 34228441 DOI: 10.1021/acsami.1c07101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In the past 10 years, many fluorescent probes have been developed to recognize G-quadruplexes (G4s) since G4s play an important role in biological systems. However, the selectivity and sensitivity of existing probes for G4s limit their further applications. Herein, we design and synthesize a new probe (TOVJ) by introducing 9-vinyljulolidine into TO. The new probe exhibits almost no fluorescence in an aqueous solution. Upon interacting with G4s, especially the antiparallel G4s, the fluorescence intensity was greatly enhanced (maximum 2742-fold) with a large Stokes shift of 198 nm and the maximum emission peak at 694 nm (near-infrared region). TOVJ showed high sensitivity and selectivity to G4s over other DNA topologies (ssDNA/dsDNA), especially to antiparallel G4s. For antiparallel human telomere G4 detection, the limits of detection of Hum24 and 22AG Na+ were as low as 164 and 231 pM, respectively. This indicates that TOVJ is a highly sensitive fluorescence sensor that can be effectively used for antiparallel human telomere G4 detection. The result of live-cell imaging showed that TOVJ could enter live cells and locate in the mitochondria.
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Affiliation(s)
- Ming Jin
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jing Li
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yang Chen
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jie Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jiahui Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Zhen Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Peiyao Du
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Libing Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Xiaoquan Lu
- Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, People's Republic of China
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21
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Chatain J, Blond A, Phan AT, Saintomé C, Alberti P. GGGCTA repeats can fold into hairpins poorly unfolded by replication protein A: a possible origin of the length-dependent instability of GGGCTA variant repeats in human telomeres. Nucleic Acids Res 2021; 49:7588-7601. [PMID: 34214172 PMCID: PMC8287962 DOI: 10.1093/nar/gkab518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/01/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022] Open
Abstract
Human telomeres are composed of GGGTTA repeats and interspersed with variant repeats. The GGGCTA variant motif was identified in the proximal regions of human telomeres about 10 years ago and was shown to display a length-dependent instability. In parallel, a structural study showed that four GGGCTA repeats folded into a non-canonical G-quadruplex (G4) comprising a Watson-Crick GCGC tetrad. It was proposed that this non-canonical G4 might be an additional obstacle for telomere replication. In the present study, we demonstrate that longer GGGCTA arrays fold into G4 and into hairpins. We also demonstrate that replication protein A (RPA) efficiently binds to GGGCTA repeats structured into G4 but poorly binds to GGGCTA repeats structured into hairpins. Our results (along with results obtained with a more stable variant motif) suggest that GGGCTA hairpins are at the origin of GGGCTA length-dependent instability. They also suggest, as working hypothesis, that failure of efficient binding of RPA to GGGCTA structured into hairpins might be involved in the mechanism of GGGCTA array instability. On the basis of our present and past studies about telomeric G4 and their interaction with RPA, we propose an original point of view about telomeric G4 and the evolution of telomeric motifs.
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Affiliation(s)
- Jean Chatain
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
| | - Alain Blond
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d’Histoire naturelle, CNRS, Paris 75005, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Carole Saintomé
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
- Sorbonne Université, UFR927, Paris 75005, France
| | - Patrizia Alberti
- Laboratoire Structure et Instabilité des Génomes (StrInG), Muséum national d’Histoire naturelle, CNRS, Inserm, Paris 75005, France
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22
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Peska V, Fajkus P, Bubeník M, Brázda V, Bohálová N, Dvořáček V, Fajkus J, Garcia S. Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae. Sci Rep 2021; 11:12784. [PMID: 34140564 PMCID: PMC8211666 DOI: 10.1038/s41598-021-92126-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023] Open
Abstract
Telomerase RNA (TR) carries the template for synthesis of telomere DNA and provides a scaffold for telomerase assembly. Fungal TRs are long and have been compared to higher eukaryotes, where they show considerable diversity within phylogenetically close groups. TRs of several Saccharomycetaceae were recently identified, however, many of these remained uncharacterised in the template region. Here we show that this is mainly due to high variability in telomere sequence. We predicted the telomere sequences using Tandem Repeats Finder and then we identified corresponding putative template regions in TR candidates. Remarkably long telomere units and the corresponding putative TRs were found in Tetrapisispora species. Notably, variable lengths of the annealing sequence of the template region (1–10 nt) were found. Consequently, species with the same telomere sequence may not harbour identical TR templates. Thus, TR sequence alone can be used to predict a template region and telomere sequence, but not to determine these exactly. A conserved feature of telomere sequences, tracts of adjacent Gs, led us to test the propensity of individual telomere sequences to form G4. The results show highly diverse values of G4-propensity, indicating the lack of ubiquitous conservation of this feature across Saccharomycetaceae.
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Affiliation(s)
- Vratislav Peska
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.
| | - Petr Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Michal Bubeník
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Vojtěch Dvořáček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic
| | - Jiří Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, 61265, Czech Republic.,Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, 62500, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain.
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23
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Douglas ME, Diffley JFX. Budding yeast Rap1, but not telomeric DNA, is inhibitory for multiple stages of DNA replication in vitro. Nucleic Acids Res 2021; 49:5671-5683. [PMID: 34048583 PMCID: PMC8191780 DOI: 10.1093/nar/gkab416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/27/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022] Open
Abstract
Telomeres are copied and reassembled each cell division cycle through a multistep process called telomere replication. Most telomeric DNA is duplicated semiconservatively during this process, but replication forks frequently pause or stall at telomeres in yeast, mouse and human cells, potentially causing chronic telomere shortening or loss in a single cell cycle. We have investigated the cause of this effect by examining the replication of telomeric templates in vitro. Using a reconstituted assay for eukaryotic DNA replication in which a complete eukaryotic replisome is assembled and activated with purified proteins, we show that budding yeast telomeric DNA is efficiently duplicated in vitro unless the telomere binding protein Rap1 is present. Rap1 acts as a roadblock that prevents replisome progression and leading strand synthesis, but also potently inhibits lagging strand telomere replication behind the fork. Both defects can be mitigated by the Pif1 helicase. Our results suggest that GC-rich sequences do not inhibit DNA replication per se, and that in the absence of accessory factors, telomere binding proteins can inhibit multiple, distinct steps in the replication process.
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Affiliation(s)
- Max E Douglas
- Telomere Biology Laboratory, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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24
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Zhao J, Zhai Q. A highly selective switch-on fluorescence sensor targeting telomeric dimeric G-quadruplex. Bioorg Med Chem Lett 2021; 40:127971. [PMID: 33753263 DOI: 10.1016/j.bmcl.2021.127971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/04/2021] [Accepted: 03/13/2021] [Indexed: 11/28/2022]
Abstract
The fluorescence probes with high selectivity and sensitivity for telomeric multimeric G-quadruplexes have attracted much attention. Nevertheless, few small molecules have exhibited telomeric multimeric G-quadruplexes recognition specificity. Thus, there is an urgent demand to develop specific fluorescence probes for telomeric multimeric G-quadruplexes. We reported herein the specific sensing of telomeric dimeric G-quadruplex TTA45 via a fluorescence light-up response using a commercially available triazine derivative HPTA-1 as a probe. HPTA-1 could discriminate the telomeric dimeric G-quadruplex TTA45 against other types of DNA structures accompanied by a drastic enhancement of the emission intensity without compromising the conformation and stability. Compared with most multimeric G-quadruplex recognition ligands, HPTA-1 had much simpler structure and lower molecular weight. The binding mechanism studies suggested that the distinct fluorescence response was caused by electrostatic and π-π stacking interactions of HPTA-1 with the pocket between two G-quadruplex units of telomeric dimeric G-quadruplex TTA45..
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Affiliation(s)
- Jingfang Zhao
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhai
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China.
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25
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Abstract
![]()
Clustered regularly
interspaced palindromic repeats (CRISPR) and
CRISPR-associated (Cas) proteins, particularly Cas9, have provided
unprecedented control on targeting and editing specific DNA sequences.
If the target sequences are prone to folding into noncanonical secondary
structures, such as G-quadruplex (GQ), the conformational states and
activity of the CRISPR–Cas9 complex may be influenced, but
the impact has not been assessed. Using single molecule FRET, we investigated
structural characteristics of the complex formed by CRISPR–Cas9
and target DNA, which contains a potentially GQ forming sequence (PQS)
in either the target or the nontarget strand (TS or NTS). We observed
different conformational states and dynamics depending on the stability
of the GQ and the position of PQS. When PQS was in NTS, we observed
evidence for GQ formation for both weak and stable GQs. This is consistent
with R-loop formation between TS and crRNA releasing NTS from Watson–Crick
pairing and facilitating secondary structure formation in it. When
PQS was in TS, R-loop formation was adequate to maintain a weak GQ
in the unfolded state but not a GQ with moderate or high stability.
The observed structural heterogeneity within the target dsDNA and
the R-loop strongly depended on whether the PQS was in TS or NTS.
We propose these variations in the complex structures to have functional
implications for Cas9 activity.
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Affiliation(s)
- Hamza Balci
- Department of Physics, Kent State University, Kent, Ohio 44242, United States
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Viktorija Globyte
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft, 2629HZ, The Netherlands
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26
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Bonnell E, Pasquier E, Wellinger RJ. Telomere Replication: Solving Multiple End Replication Problems. Front Cell Dev Biol 2021; 9:668171. [PMID: 33869233 PMCID: PMC8047117 DOI: 10.3389/fcell.2021.668171] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/10/2021] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genomes are highly complex and divided into linear chromosomes that require end protection from unwarranted fusions, recombination, and degradation in order to maintain genomic stability. This is accomplished through the conserved specialized nucleoprotein structure of telomeres. Due to the repetitive nature of telomeric DNA, and the unusual terminal structure, namely a protruding single stranded 3' DNA end, completing telomeric DNA replication in a timely and efficient manner is a challenge. For example, the end replication problem causes a progressive shortening of telomeric DNA at each round of DNA replication, thus telomeres eventually lose their protective capacity. This phenomenon is counteracted by the recruitment and the activation at telomeres of the specialized reverse transcriptase telomerase. Despite the importance of telomerase in providing a mechanism for complete replication of telomeric ends, the majority of telomere replication is in fact carried out by the conventional DNA replication machinery. There is significant evidence demonstrating that progression of replication forks is hampered at chromosomal ends due to telomeric sequences prone to form secondary structures, tightly DNA-bound proteins, and the heterochromatic nature of telomeres. The telomeric loop (t-loop) formed by invasion of the 3'-end into telomeric duplex sequences may also impede the passage of replication fork. Replication fork stalling can lead to fork collapse and DNA breaks, a major cause of genomic instability triggered notably by unwanted repair events. Moreover, at chromosomal ends, unreplicated DNA distal to a stalled fork cannot be rescued by a fork coming from the opposite direction. This highlights the importance of the multiple mechanisms involved in overcoming fork progression obstacles at telomeres. Consequently, numerous factors participate in efficient telomeric DNA duplication by preventing replication fork stalling or promoting the restart of a stalled replication fork at telomeres. In this review, we will discuss difficulties associated with the passage of the replication fork through telomeres in both fission and budding yeasts as well as mammals, highlighting conserved mechanisms implicated in maintaining telomere integrity during replication, thus preserving a stable genome.
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Affiliation(s)
| | | | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, QC, Canada
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27
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Jing H, Fu W, Hu W, Xu S, Xu X, He M, Liu Y, Zhang N. NMR structural study on the self-trimerization of d(GTTAGG) into a dynamic trimolecular G-quadruplex assembly preferentially in Na+ solution with a moderate K+ tolerance. Nucleic Acids Res 2021; 49:2306-2316. [PMID: 33524157 PMCID: PMC7913680 DOI: 10.1093/nar/gkab028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/05/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
Vast G-quadruplexes (GQs) are primarily folded by one, two, or four G-rich oligomers, rarely with an exception. Here, we present the first NMR solution structure of a trimolecular GQ (tri-GQ) that is solely assembled by the self-trimerization of d(GTTAGG), preferentially in Na+ solution tolerant to an equal amount of K+ cation. Eight guanines from three asymmetrically folded strands of d(GTTAGG) are organized into a two-tetrad core, which features a broken G-column and two width-irregular grooves. Fast strand exchanges on a timescale of second at 17°C spontaneously occur between folded tri-GQ and unfolded single-strand of d(GTTAGG) that both species coexist in dynamic equilibrium. Thus, this tri-GQ is not just simply a static assembly but rather a dynamic assembly. Moreover, another minor tetra-GQ that has putatively tetrameric (2+2) antiparallel topology becomes noticeable only at an extremely high strand concentration above 18 mM. The major tri-GQ and minor tetra-GQ are considered to be mutually related, and their reversible interconversion pathways are proposed accordingly. The sequence d(GTTAGG) could be regarded as either a reading frame shifted single repeat of human telomeric DNA or a 1.5 repeat of Bombyx mori telomeric DNA. Overall, our findings provide new insight into GQs and expect more functional applications.
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Affiliation(s)
- Haitao Jing
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Wenqiang Fu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Suping Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Xiaojuan Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Miao He
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Yangzhong Liu
- University of Science and Technology of China, Hefei 230026, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China.,High Magnetic Field Laboratory of Anhui Province, Hefei 230031, China
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28
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Lee JW, Ong EBB. Genomic Instability and Cellular Senescence: Lessons From the Budding Yeast. Front Cell Dev Biol 2021; 8:619126. [PMID: 33511130 PMCID: PMC7835410 DOI: 10.3389/fcell.2020.619126] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/15/2020] [Indexed: 01/14/2023] Open
Abstract
Aging is a complex biological process that occurs in all living organisms. Aging is initiated by the gradual accumulation of biomolecular damage in cells leading to the loss of cellular function and ultimately death. Cellular senescence is one such pathway that leads to aging. The accumulation of nucleic acid damage and genetic alterations that activate permanent cell-cycle arrest triggers the process of senescence. Cellular senescence can result from telomere erosion and ribosomal DNA instability. In this review, we summarize the molecular mechanisms of telomere length homeostasis and ribosomal DNA stability, and describe how these mechanisms are linked to cellular senescence and longevity through lessons learned from budding yeast.
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Affiliation(s)
- Jee Whu Lee
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia.,USM-RIKEN International Centre for Aging Science (URICAS), Universiti Sains Malaysia, Penang, Malaysia
| | - Eugene Boon Beng Ong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia.,USM-RIKEN International Centre for Aging Science (URICAS), Universiti Sains Malaysia, Penang, Malaysia
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29
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Walunj MB, Srivatsan SG. Nucleic Acid Conformation Influences Postsynthetic Suzuki-Miyaura Labeling of Oligonucleotides. Bioconjug Chem 2020; 31:2513-2521. [PMID: 33089687 PMCID: PMC7611128 DOI: 10.1021/acs.bioconjchem.0c00466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemoselective transformations that work under physiological conditions have emerged as powerful tools to label nucleic acids in cell-free and cellular environments. However, detailed studies investigating the influence of nucleic acid conformation on the performance of such chemoselective nucleic labeling methods are less explored. Given that nucleic acids adopt complex structures, it is highly important to study the scope of the chemical modification method in the context of nucleic acid conformations. Here we report a systematic study on the effect of local conformation on the postsynthetic Suzuki-Miyaura functionalization of human telomeric (H-Telo) DNA repeat oligonucleotide (ON) sequences, which form multiple G-quadruplex (GQ) structures. 5-Iodo-2'-deoxyuridine (IdU)-modified H-Telo ONs were synthesized by the solid-phase method, and when subjected to Suzuki-Miyaura cross-coupling reaction, its efficiency was found to depend on the type of conformation and the position of IdU label in different loops of the GQ structure. IdU-labeled GQs gave better yields as compared to single-stranded random coil structures. However, the IdU-labeled duplex under different ionic conditions did not undergo the coupling reaction. Further, using this method, we directly installed an environment-sensitive fluorescent probe, which photophysically reported the formation as well as distinguished different GQ topologies of telomeric repeat. Collectively, this systematic study underscores the influence of nucleic acid conformation, which has to be taken into account when establishing postsynthetic chemoselective functionalization strategies.
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Affiliation(s)
- Manisha B. Walunj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Seergazhi G. Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, India
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30
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Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
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Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
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31
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Bryan TM. G-Quadruplexes at Telomeres: Friend or Foe? Molecules 2020; 25:molecules25163686. [PMID: 32823549 PMCID: PMC7464828 DOI: 10.3390/molecules25163686] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Telomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by either the enzyme telomerase or by recombination-based mechanisms. On the other hand, G-quadruplex formation in telomeric DNA, as elsewhere in the genome, can form an impediment to DNA replication and a source of genome instability. This review summarizes recent evidence for the in vivo existence of G-quadruplexes at telomeres, with a focus on human telomeres, and highlights some of the many unanswered questions regarding the location, form, and functions of these structures.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
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32
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Zhao J, Yang Z, Zhai Q, Wei D. Specific recognition of telomeric multimeric G-quadruplexes by a simple-structure quinoline derivative. Anal Chim Acta 2020; 1132:93-100. [PMID: 32980115 DOI: 10.1016/j.aca.2020.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 11/17/2022]
Abstract
The development of highly sensitive fluorescence probes for telomeric multimeric G-quadruplexes has attracted extensive attention. However, few probes reported have exhibited selectivity for telomeric multimeric G-quadruplexes. Thus, it is challenging to design fluorescence probes with high specificity and selectivity for telomeric multimeric G-quadruplexes. This study employed a commercially available quinoline derivative BEPQ-1 as an effective switch-on sensor for telomeric multimeric G-quadruplexes. The fluorescence intensity enhanced more than 20 folds upon the addition of telomeric multimeric G-quadruplexes. This probe exhibited good selectivity and sensitivity for telomeric multimeric G-quadruplexes. And the detection limit of BEPQ-1 for the telomeric multimeric G-quadruplex TTA45 was calculated to be 0.11 μM. The distinctive feature of BEPQ-1 is the simple structure and small size. In the light of binding mode, BEPQ-1 could even simultaneously bind to the end two G-quartets of the two adjacent G-quadruplex units in telomeric multimeric G-quadruplex by π-π stacking. To our knowledge, this is the first simple-structure fluorescence probe for telomeric multimeric G-quadruplex. This finding might provide a strategy to design specific probes for telomeric multimeric G-quadruplexes and contribute to understand the structures and functions of G-quadruplexes in the telomere region.
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Affiliation(s)
- Jingfang Zhao
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ziyan Yang
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qianqian Zhai
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Dengguo Wei
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.
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33
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Jurikova K, Gajarsky M, Hajikazemi M, Nosek J, Prochazkova K, Paeschke K, Trantirek L, Tomaska L. Role of folding kinetics of secondary structures in telomeric G-overhangs in the regulation of telomere maintenance in Saccharomyces cerevisiae. J Biol Chem 2020; 295:8958-8971. [PMID: 32385108 PMCID: PMC7335780 DOI: 10.1074/jbc.ra120.012914] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
The ends of eukaryotic chromosomes typically contain a 3' ssDNA G-rich protrusion (G-overhang). This overhang must be protected against detrimental activities of nucleases and of the DNA damage response machinery and participates in the regulation of telomerase, a ribonucleoprotein complex that maintains telomere integrity. These functions are mediated by DNA-binding proteins, such as Cdc13 in Saccharomyces cerevisiae, and the propensity of G-rich sequences to form various non-B DNA structures. Using CD and NMR spectroscopies, we show here that G-overhangs of S. cerevisiae form distinct Hoogsteen pairing-based secondary structures, depending on their length. Whereas short telomeric oligonucleotides form a G-hairpin, their longer counterparts form parallel and/or antiparallel G-quadruplexes (G4s). Regardless of their topologies, non-B DNA structures exhibited impaired binding to Cdc13 in vitro as demonstrated by electrophoretic mobility shift assays. Importantly, whereas G4 structures formed relatively quickly, G-hairpins folded extremely slowly, indicating that short G-overhangs, which are typical for most of the cell cycle, are present predominantly as single-stranded oligonucleotides and are suitable substrates for Cdc13. Using ChIP, we show that the occurrence of G4 structures peaks at the late S phase, thus correlating with the accumulation of long G-overhangs. We present a model of how time- and length-dependent formation of non-B DNA structures at chromosomal termini participates in telomere maintenance.
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Affiliation(s)
- Katarina Jurikova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martin Gajarsky
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mona Hajikazemi
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarina Prochazkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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34
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Pal C, Chakraborty TK. Development of Minimal Diguanosinyl Motif toward RNA G-Quadruplex-Like Structures in Solution. Chembiochem 2020; 21:1837-1842. [PMID: 31995269 DOI: 10.1002/cbic.202000002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Indexed: 11/05/2022]
Abstract
Among the non-canonical structures of B-DNA, the G-quadruplex is of particular interest because of its well-defined conformation, high stability, and versatility. Herein we report our studies on the development of an amide-linked minimal diguanosinyl motif that forms a G-quadruplex-like structure in solution in the presence of potassium cations; various linear guanosine amino acid dimers were synthesized with linkers of different chain lengths to investigate the optimum flexibility required to form such structures.
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Affiliation(s)
- Chandan Pal
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Tushar Kanti Chakraborty
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
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35
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Functional Diversification of Replication Protein A Paralogs and Telomere Length Maintenance in Arabidopsis. Genetics 2020; 215:989-1002. [PMID: 32532801 DOI: 10.1534/genetics.120.303222] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 12/14/2022] Open
Abstract
Replication protein A (RPA) is essential for many facets of DNA metabolism. The RPA gene family expanded in Arabidopsis thaliana with five phylogenetically distinct RPA1 subunits (RPA1A-E), two RPA2 (RPA2A and B), and two RPA3 (RPA3A and B). RPA1 paralogs exhibit partial redundancy and functional specialization in DNA replication (RPA1B and RPA1D), repair (RPA1C and RPA1E), and meiotic recombination (RPA1A and RPA1C). Here, we show that RPA subunits also differentially impact telomere length set point. Loss of RPA1 resets bulk telomeres at a shorter length, with a functional hierarchy for replication group over repair and meiosis group RPA1 subunits. Plants lacking RPA2A, but not RPA2B, harbor short telomeres similar to the replication group. Telomere shortening does not correlate with decreased telomerase activity or deprotection of chromosome ends in rpa mutants. However, in vitro assays show that RPA1B2A3B unfolds telomeric G-quadruplexes known to inhibit replications fork progression. We also found that ATR deficiency can partially rescue short telomeres in rpa2a mutants, although plants exhibit defects in growth and development. Unexpectedly, the telomere shortening phenotype of rpa2a mutants is completely abolished in plants lacking the RTEL1 helicase. RTEL1 has been implicated in a variety of nucleic acid transactions, including suppression of homologous recombination. Thus, the lack of telomere shortening in rpa2a mutants upon RTEL1 deletion suggests that telomere replication defects incurred by loss of RPA may be bypassed by homologous recombination. Taken together, these findings provide new insight into how RPA cooperates with replication and recombination machinery to sustain telomeric DNA.
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36
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Tomáška Ľ, Nosek J. Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends. J Mol Evol 2020; 88:293-318. [PMID: 32157325 DOI: 10.1007/s00239-020-09935-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Biological entities are multicomponent systems where each part is directly or indirectly dependent on the others. In effect, a change in a single component might have a consequence on the functioning of its partners, thus affecting the fitness of the entire system. In this article, we provide a few examples of such complex biological systems, ranging from ant colonies to a population of amino acids within a single-polypeptide chain. Based on these examples, we discuss one of the central and still challenging questions in biology: how do such multicomponent consortia co-evolve? More specifically, we ask how telomeres, nucleo-protein complexes protecting the integrity of linear DNA chromosomes, originated from the ancestral organisms having circular genomes and thus not dealing with end-replication and end-protection problems. Using the examples of rapidly evolving topologies of mitochondrial genomes in eukaryotic microorganisms, we show what means of co-evolution were employed to accommodate various types of telomere-maintenance mechanisms in mitochondria. We also describe an unprecedented runaway evolution of telomeric repeats in nuclei of ascomycetous yeasts accompanied by co-evolution of telomere-associated proteins. We propose several scenarios derived from research on telomeres and supported by other studies from various fields of biology, while emphasizing that the relevant answers are still not in sight. It is this uncertainty and a lack of a detailed roadmap that makes the journey through the jungle of biological systems still exciting and worth undertaking.
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Affiliation(s)
- Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia
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Nuthanakanti A, Ahmed I, Khatik SY, Saikrishnan K, Srivatsan SG. Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe. Nucleic Acids Res 2020; 47:6059-6072. [PMID: 31106340 PMCID: PMC6614846 DOI: 10.1093/nar/gkz419] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2'-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ishtiyaq Ahmed
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- Correspondence may also be addressed to Kayarat Saikrishnan.
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- To whom correspondence should be addressed. Tel: +91 2025908086;
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Golenkina EA, Viryasova GM, Dolinnaya NG, Bannikova VA, Gaponova TV, Romanova YM, Sud’ina GF. The Potential of Telomeric G-quadruplexes Containing Modified Oligoguanosine Overhangs in Activation of Bacterial Phagocytosis and Leukotriene Synthesis in Human Neutrophils. Biomolecules 2020; 10:E249. [PMID: 32041263 PMCID: PMC7072695 DOI: 10.3390/biom10020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Human neutrophils are the first line of defense against bacterial and viral infections. They eliminate pathogens through phagocytosis, which activate the 5-lipoxygenase (5-LOX) pathway resulting in synthesis of leukotrienes. Using HPLC analysis, flow cytometry, and other biochemical methods, we studied the effect of synthetic oligodeoxyribonucleotides (ODNs) able to fold into G-quadruplex structures on the main functions of neutrophils. Designed ODNs contained four human telomere TTAGGG repeats (G4) including those with phosphorothioate oligoguanosines attached to the end(s) of G-quadruplex core. Just modified analogues of G4 was shown to more actively than parent ODN penetrate into cells, improve phagocytosis of Salmonella typhimurium bacteria, affect 5-LOX activation, the cytosol calcium ion level, and the oxidative status of neutrophils. As evident from CD and UV spectroscopy data, the presence of oligoguanosines flanking G4 sequence leads to dramatic changes in G-quadruplex topology. While G4 folds into a single antiparallel structure, two main folded forms have been identified in solutions of modified ODNs: antiparallel and dominant, more stable parallel. Thus, both the secondary structure of ODNs and their ability to penetrate into the cytoplasm of cells are important for the activation of neutrophil cellular effects. Our results offer new clues for understanding the role of G-quadruplex ligands in regulation of integral cellular processes and for creating the antimicrobial agents of a new generation.
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Affiliation(s)
- Ekaterina A. Golenkina
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow 119234, Russia; (E.A.G.); (G.M.V.)
| | - Galina M. Viryasova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow 119234, Russia; (E.A.G.); (G.M.V.)
| | - Nina G. Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow 119234, Russia; (N.G.D.); (V.A.B.)
| | - Valeria A. Bannikova
- Lomonosov Moscow State University, Department of Chemistry, Moscow 119234, Russia; (N.G.D.); (V.A.B.)
| | - Tatjana V. Gaponova
- National Research Center for Hematology, Russia Federation Ministry of Public Health, Moscow 125167, Russia;
| | - Yulia M. Romanova
- Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow 123098, Russia;
| | - Galina F. Sud’ina
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow 119234, Russia; (E.A.G.); (G.M.V.)
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Punt PM, Clever GH. Tailored Transition-Metal Coordination Environments in Imidazole-Modified DNA G-Quadruplexes. Chemistry 2019; 25:13987-13993. [PMID: 31468606 PMCID: PMC6899475 DOI: 10.1002/chem.201903445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/28/2019] [Indexed: 12/18/2022]
Abstract
Two types of imidazole ligands were introduced both at the end of tetramolecular and into the loop region of unimolecular DNA G‐quadruplexes. The modified oligonucleotides were shown to complex a range of different transition‐metal cations including NiII, CuII, ZnII and CoII, as indicated by UV/Vis absorption spectroscopy and ion mobility mass spectrometry. Molecular dynamics simulations were performed to obtain structural insight into the investigated systems. Variation of ligand number and position in the loop region of unimolecular sequences derived from the human telomer region (htel) allows for a controlled design of distinct coordination environments with fine‐tuned metal affinities. It is shown that CuII, which is typically square‐planar coordinated, has a higher affinity for systems offering four ligands, whereas NiII prefers G‐quadruplexes with six ligands. Likewise, the positioning of ligands in a square‐planar versus tetrahedral fashion affects binding affinities of CuII and ZnII cations, respectively. Gaining control over ligand arrangement patterns will spur the rational development of transition‐metal‐modified DNAzymes. Furthermore, this method is suited to combine different types of ligands, for example, those typically found in metalloenzymes, inside a single DNA architecture.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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40
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Belmonte-Reche E, Morales JC. G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool. NAR Genom Bioinform 2019; 2:lqz005. [PMID: 33575559 PMCID: PMC7671307 DOI: 10.1093/nargab/lqz005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/08/2019] [Accepted: 09/10/2019] [Indexed: 11/15/2022] Open
Abstract
We present G4-iM Grinder, a system for the localization, characterization and selection of potential G4s, i-Motifs and higher order structures. A robust and highly adaptable search engine identifies all structures that fit the user’s quadruplex definitions. Their biological relevance, in vitro formation probability and presence of known-to-form structures are then used as filters. The outcome is an efficient methodology that helps select the best candidates for a subsequent in vitro analysis or a macroscopic genomic quadruplex assessment. As proof of the analytical capabilities of G4-iM Grinder, the human genome was analyzed for potential G4s and i-Motifs. Many known-to-form structures were identified. New candidates were selected considering their score and appearance frequency. We also focused on locating Potential Higher Order Quadruplex Sequences (PHOQS). We developed a new methodology to predict the most probable subunits of these assemblies and applied it to a PHOQS candidate. Taking the human average density as reference, we examined the genomes of several etiological causes of disease. This first of its class comparative study found many organisms to be very dense in these potential quadruplexes. Many presented already known-to-form-G4s and i-Motifs. These findings suggest the potential quadruplexes have as therapeutic targets for these diseases that currently kill millions worldwide.
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Affiliation(s)
- Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain.,Life Sciences Department, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga, 4715-330 Braga, Portugal
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
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41
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Cogoi S, Ferino A, Miglietta G, Pedersen EB, Xodo LE. The regulatory G4 motif of the Kirsten ras (KRAS) gene is sensitive to guanine oxidation: implications on transcription. Nucleic Acids Res 2019; 46:661-676. [PMID: 29165690 PMCID: PMC5778462 DOI: 10.1093/nar/gkx1142] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/31/2017] [Indexed: 01/10/2023] Open
Abstract
KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleotides mimicking the KRAS G4-motif and found that 8-oxoG impacts folding and stability of the G-quadruplex. Dimethylsulphate-footprinting showed that the G-run carrying 8-oxoG is excluded from the G-tetrads and replaced by a redundant G-run in the KRAS G4-motif. Chromatin immunoprecipitation revealed that the base-excision repair protein OGG1 is recruited to the KRAS promoter when the level of 8-oxoG in the G4 region is raised by H2O2. Polyacrylamide gel electrophoresis evidenced that OGG1 removes 8-oxoG from the G4-motif in duplex, but when folded it binds to the G-quadruplex in a non-productive way. We also found that 8-oxoG enhances the recruitment to the KRAS promoter of MAZ and hnRNP A1, two nuclear factors essential for transcription. All this suggests that 8-oxoG in the promoter G4 region could have an epigenetic potential for the control of gene expression.
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Affiliation(s)
- Susanna Cogoi
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Annalisa Ferino
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | | | - Erik B Pedersen
- Nucleic Acid Center, Institute of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Luigi E Xodo
- Department of Medicine, University of Udine, 33100 Udine, Italy
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42
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Cheng M, Cheng Y, Hao J, Jia G, Zhou J, Mergny JL, Li C. Loop permutation affects the topology and stability of G-quadruplexes. Nucleic Acids Res 2019; 46:9264-9275. [PMID: 30184167 PMCID: PMC6182180 DOI: 10.1093/nar/gky757] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022] Open
Abstract
G-quadruplexes are unusual DNA and RNA secondary structures ubiquitous in a variety of organisms including vertebrates, plants, viruses and bacteria. The folding topology and stability of intramolecular G-quadruplexes are determined to a large extent by their loops. Loop permutation is defined as swapping two or three of these regions so that intramolecular G-quadruplexes only differ in the sequential order of their loops. Over the past two decades, both length and base composition of loops have been studied extensively, but a systematic study on the effect of loop permutation has been missing. In the present work, 99 sequences from 21 groups with different loop permutations were tested. To our surprise, both conformation and thermal stability are greatly dependent on loop permutation. Loop permutation actually matters as much as loop length and base composition on G-quadruplex folding, with effects on Tm as high as 17°C. Sequences containing a longer central loop have a high propensity to adopt a stable non-parallel topology. Conversely, sequences containing a short central loop tend to form a parallel topology of lower stability. In addition, over half of interrogated sequences were found in the genomes of diverse organisms, implicating their potential regulatory roles in the genome or as therapeutic targets. This study illustrates the structural roles of loops in G-quadruplex folding and should help to establish rules to predict the folding pattern and stability of G-quadruplexes.
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Affiliation(s)
- Mingpan Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yu Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingya Hao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,ARNA Laboratory, Inserm U1212, CNRS UMR5320, IECB, Université de Bordeaux, Pessac 33607, France.,Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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43
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Czech A, Konarev PV, Goebel I, Svergun DI, Wills PR, Ignatova Z. Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes. Sci Rep 2019; 9:2465. [PMID: 30792490 PMCID: PMC6384910 DOI: 10.1038/s41598-019-39213-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
Misfolding and aggregation of prion protein (PrP) causes neurodegenerative diseases like Creutzfeldt-Jakob disease (CJD) and scrapie. Besides the consensus that spontaneous conversion of normal cellular PrPC into misfolded and aggregating PrPSc is the central event in prion disease, an alternative hypothesis suggests the generation of pathological PrPSc by rare translational frameshifting events in the octa-repeat domain of the PrP mRNA. Ribosomal frameshifting most commonly relies on a slippery site and an adjacent stable RNA structure to stall translating ribosome. Hence, it is crucial to unravel the secondary structure of the octa-repeat domain of PrP mRNA. Each of the five octa-repeats contains a motif (GGCGGUGGUGGCUGGG) which alone in vitro forms a G-quadruplex. Since the propensity of mRNA to form secondary structure depends on the sequence context, we set to determine the structure of the complete octa-repeat region. We assessed the structure of full-length octa-repeat domain of PrP mRNA using dynamic light scattering (DLS), small angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy and selective 2'-hydroxyl acylation analysis by primer extension (SHAPE). Our data show that the PrP octa-repeat mRNA forms stable A-helical hairpins with no evidence of G-quadruplex structure even in the presence of G-quadruplex stabilizing agents.
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Affiliation(s)
- Andreas Czech
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany.
| | - Petr V Konarev
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
- National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ingrid Goebel
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg, Germany
| | - Peter R Wills
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology University of Hamburg, Hamburg, Germany
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44
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Saranathan N, Vivekanandan P. G-Quadruplexes: More Than Just a Kink in Microbial Genomes. Trends Microbiol 2019; 27:148-163. [PMID: 30224157 PMCID: PMC7127049 DOI: 10.1016/j.tim.2018.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/17/2018] [Accepted: 08/24/2018] [Indexed: 02/06/2023]
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. In this review we aim to provide an overview of the biological roles of G4s in microbial genomes with emphasis on recent discoveries. G4s are enriched and conserved in the regulatory regions of microbes, including bacteria, fungi, and viruses. Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. Recent studies on Epstein-Barr virus (EBV) shed light on the role of G4s within the microbial transcripts as cis-acting regulatory signals that modulate translation and facilitate immune evasion. Furthermore, G4s in microbial genomes have been linked to radioresistance, antigenic variation, recombination, and latency. G4s in microbial genomes represent novel therapeutic targets for antimicrobial therapy.
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Affiliation(s)
- Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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45
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Viryasova GM, Dolinnaya NG, Golenkina EA, Gaponova TV, Viryasov MB, Romanova YM, Sud'ina GF. G-quadruplex-forming oligodeoxyribonucleotides activate leukotriene synthesis in human neutrophils. J Biomol Struct Dyn 2019; 37:3649-3659. [PMID: 30238827 DOI: 10.1080/07391102.2018.1523748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Human polymorphonuclear leukocytes (PMNLs, neutrophils) play a major role in the immune response to bacterial and fungal infections and eliminate pathogens through phagocytosis. During phagocytosis of microorganisms, the 5-lipoxygenase (5-LOX) pathway is activated resulting in generation of leukotrienes, which mediate host defense. In this study, a library of oligodeoxyribonucleotides (ODNs) with varying numbers of human telomeric repeats (d(TTAGGG)n) and their analogues with phosphorothioate internucleotide linkages and single-nucleotide substitutions was designed. These ODNs with the potential to fold into G-quadruplex structures were studied from structural and functional perspectives. We showed that exogenous G-quadruplex-forming ODNs significantly enhanced 5-LOX metabolite formation in human neutrophils exposed to Salmonella Typhimurium bacteria. However, the activation of leukotriene synthesis was completely lost when G-quadruplex formation was prevented by substitution of guanosine with 7-deazaguanosine or adenosine residues at several positions. To our knowledge, this study is the first to demonstrate that G-quadruplex structures are potent regulators of 5-LOX product synthesis in human neutrophils in the presence of targets of phagocytosis. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Galina M Viryasova
- a Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , Moscow , Russia
| | - Nina G Dolinnaya
- b Department of Chemistry , Lomonosov Moscow State University , Moscow , Russia
| | - Ekaterina A Golenkina
- a Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , Moscow , Russia
| | - Tatjana V Gaponova
- c FGBU Hematology Research Centre , Russia Federation Ministry of Public Health , Moscow , Russia
| | - Mikhail B Viryasov
- b Department of Chemistry , Lomonosov Moscow State University , Moscow , Russia
| | - Yulia M Romanova
- d Gamaleya National Research Centre of Epidemiology and Microbiology , Moscow , Russia.,e Department of Unfectology and Virology, Sechenov First Moscow State Medical University , Moscow , Russia
| | - Galina F Sud'ina
- a Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , Moscow , Russia
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46
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Yeasmin Khusbu F, Zhou X, Chen H, Ma C, Wang K. Thioflavin T as a fluorescence probe for biosensing applications. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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47
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Sabale P, Ambi UB, Srivatsan SG. Clickable PNA Probes for Imaging Human Telomeres and Poly(A) RNAs. ACS OMEGA 2018; 3:15343-15352. [PMID: 30556003 PMCID: PMC6289544 DOI: 10.1021/acsomega.8b02550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/31/2018] [Indexed: 05/10/2023]
Abstract
The ability to bind strongly to complementary nucleic acid sequences, invade complex nucleic acid structures, and resist degradation by cellular enzymes has made peptide nucleic acid (PNA) oligomers as very useful hybridization probes in molecular diagnosis. For such applications, the PNA oligomers have to be labeled with appropriate reporters as they lack intrinsic labels that can be used in biophysical assays. Although solid-phase synthesis is commonly used to attach reporters onto PNA, development of milder and modular labeling methods will provide access to PNA oligomers labeled with a wider range of biophysical tags. Here, we describe the establishment of a postsynthetic modification strategy based on bioorthogonal chemical reactions in functionalizing PNA oligomers in solution with a variety of tags. A toolbox composed of alkyne- and azide-modified monomers were site-specifically incorporated into PNA oligomers and postsynthetically click-functionalized with various tags, ranging from sugar, amino acid, biotin, to fluorophores, by using copper(I)-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, and Staudinger ligation reactions. As a proof of utility of this method, fluorescent PNA hybridization probes were developed and used in imaging human telomeres in chromosomes and poly(A) RNAs in cells. Taken together, this simple approach of generating a wide range of functional PNA oligomers will expand the use of PNA in molecular diagnosis.
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48
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Smith-Carpenter JE, Taylor JS. Photocrosslinking of G-Quadruplex-Forming Sequences found in Human Promoters. Photochem Photobiol 2018; 95:252-266. [PMID: 30084501 DOI: 10.1111/php.12991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/05/2018] [Indexed: 01/28/2023]
Abstract
While is it well known that human telomeric DNA sequences can adopt G-quadruplex structures, some promoters sequences have also been found to form G-quadruplexes, and over 40% of promoters contain putative G-quadruplex-forming sequences. Because UV light has been shown to crosslink human telomeric G-quadruplexes by cyclobutane pyrimidine dimer (CPD) formation between T's on adjacent loops, UV light might also be able to photocrosslink G-quadruplexes in promoters. To investigate this possibility, 15 potentially UV-crosslinkable G-quadruplex-forming sequences found in a search of human DNA promoters were UVB irradiated in vitro, and three were confirmed to have formed nonadjacent CPDs by mass spectrometry. In addition to nonadjacent T=T CPDs found in human telomeric DNA, a nonadjacent T=U CPD was discovered that presumably arose from deamination of a nonadjacent T=C CPD. Analysis of the three sequences by circular dichroism, melting temperature analysis and chemical footprinting confirmed the presence of G-quadruplexes that could explain the formation of the nonadjacent CPDs. The formation of nonadjacent CPDs from the sequences in vitro suggests that they might be useful probes for the presence of non-B DNA structures, such as G-quadruplexes, in vivo, and if they were to form in vivo, might also have significant biological consequences.
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Zahin M, Dean WL, Ghim SJ, Joh J, Gray RD, Khanal S, Bossart GD, Mignucci-Giannoni AA, Rouchka EC, Jenson AB, Trent JO, Chaires JB, Chariker JH. Identification of G-quadruplex forming sequences in three manatee papillomaviruses. PLoS One 2018; 13:e0195625. [PMID: 29630682 PMCID: PMC5891072 DOI: 10.1371/journal.pone.0195625] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/25/2018] [Indexed: 11/30/2022] Open
Abstract
The Florida manatee (Trichechus manatus latirotris) is a threatened aquatic mammal in United States coastal waters. Over the past decade, the appearance of papillomavirus-induced lesions and viral papillomatosis in manatees has been a concern for those involved in the management and rehabilitation of this species. To date, three manatee papillomaviruses (TmPVs) have been identified in Florida manatees, one forming cutaneous lesions (TmPV1) and two forming genital lesions (TmPV3 and TmPV4). We identified DNA sequences with the potential to form G-quadruplex structures (G4) across the three genomes. G4 were located on both DNA strands and across coding and non-coding regions on all TmPVs, offering multiple targets for viral control. Although G4 have been identified in several viral genomes, including human PVs, most research has focused on canonical structures comprised of three G-tetrads. In contrast, the vast majority of sequences we identified would allow the formation of non-canonical structures with only two G-tetrads. Our biophysical analysis confirmed the formation of G4 with parallel topology in three such sequences from the E2 region. Two of the structures appear comprised of multiple stacked two G-tetrad structures, perhaps serving to increase structural stability. Computational analysis demonstrated enrichment of G4 sequences on all TmPVs on the reverse strand in the E2/E4 region and on both strands in the L2 region. Several G4 sequences occurred at similar regional locations on all PVs, most notably on the reverse strand in the E2 region. In other cases, G4 were identified at similar regional locations only on PVs forming genital lesions. On all TmPVs, G4 sequences were located in the non-coding region near putative E2 binding sites. Together, these findings suggest that G4 are possible regulatory elements in TmPVs.
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Affiliation(s)
- Maryam Zahin
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - William L. Dean
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Shin-je Ghim
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Joongho Joh
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Robert D. Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Sujita Khanal
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Gregory D. Bossart
- Georgia Aquarium, Atlanta, Georgia, United States of America
- Division of Comparative Pathology, Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | | | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Duthie Center for Engineering, Louisville, Kentucky, United States of America
- KBRIN Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
| | - Alfred B. Jenson
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - John O. Trent
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Julia H. Chariker
- KBRIN Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, Kentucky, United States of America
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Cozzoli L, Gjonaj L, Stuart MCA, Poolman B, Roelfes G. Responsive DNA G-quadruplex micelles. Chem Commun (Camb) 2018; 54:260-263. [PMID: 29231221 DOI: 10.1039/c7cc07899d] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A novel and versatile design of DNA-lipid conjugates is presented. The assembly of the DNA headgroups into G-quadruplex structures is essential for the formation of micelles and their stability. By hybridization with a complementary oligonucleotide the micelles were destabilized, resulting in cargo release. In combination with a hairpin DNA aptamer as complementary strand, the release is obtained selectively by the presence of ATP.
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Affiliation(s)
- Liliana Cozzoli
- Stratingh Institute for Chemistry, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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