51
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Yu Z, Fenk KD, Huang D, Sen S, Cowan JA. Rapid Telomere Reduction in Cancer Cells Induced by G-Quadruplex-Targeting Copper Complexes. J Med Chem 2019; 62:5040-5048. [DOI: 10.1021/acs.jmedchem.9b00215] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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52
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Tippana R, Chen MC, Demeshkina NA, Ferré-D'Amaré AR, Myong S. RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36. Nat Commun 2019; 10:1855. [PMID: 31015431 PMCID: PMC6478676 DOI: 10.1038/s41467-019-09802-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
DHX36 is a DEAH-box helicase that resolves parallel G-quadruplex structures formed in DNA and RNA. The recent co-crystal structure of DHX36 bound G4-DNA revealed an intimate contact, but did not address the role of ATP hydrolysis in G4 resolving activity. Here, we demonstrate that unlike on G4-DNA, DHX36 displays ATP-independent unfolding of G4-RNA followed by ATP-dependent refolding, generating a highly asymmetric pattern of activity. Interestingly, DHX36 refolds G4-RNA in several steps, reflecting the discrete steps in forming the G4 structure. We show that the ATP-dependent activity of DHX36 arises from the RNA tail rather than the G4. Mutations that perturb G4 contact result in quick dissociation of the protein from RNA upon ATP hydrolysis, while mutations that interfere with binding the RNA tail induce dysregulated activity. We propose that the ATP-dependent activity of DHX36 may be useful for dynamically resolving various G4-RNA structures in cells.
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Affiliation(s)
- Ramreddy Tippana
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Michael C Chen
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1TN, UK.,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Natalia A Demeshkina
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL, 61801, USA.
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53
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Zuffo M, Xie X, Granzhan A. Strength in Numbers: Development of a Fluorescence Sensor Array for Secondary Structures of DNA. Chemistry 2019; 25:1812-1818. [DOI: 10.1002/chem.201805422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Michela Zuffo
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
| | - Xiao Xie
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
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54
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Genome-wide analysis of regulatory G-quadruplexes affecting gene expression in human cytomegalovirus. PLoS Pathog 2018; 14:e1007334. [PMID: 30265731 PMCID: PMC6179306 DOI: 10.1371/journal.ppat.1007334] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/10/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022] Open
Abstract
G-quadruplex (G4), formed by repetitive guanosine-rich sequences, is known to play various key regulatory roles in cells. Herpesviruses containing a large double-stranded DNA genome show relatively higher density of G4-forming sequences in their genomes compared to human and mouse. However, it remains poorly understood whether all of these sequences form G4 and how they play a role in the virus life cycle. In this study, we performed genome-wide analyses of G4s present in the putative promoter or gene regulatory regions of a 235-kb human cytomegalovirus (HCMV) genome and investigated their roles in viral gene expression. We evaluated 36 putative G4-forming sequences associated with 20 genes for their ability to form G4 and for the stability of G4s in the presence or absence of G4-stabilizing ligands, by circular dichroism and melting temperature analyses. Most identified sequences formed a stable G4; 28 sequences formed parallel G4s, one formed an antiparallel G4, and four showed mixed conformations. However, when we assessed the effect of G4 on viral promoters by cloning the 20 putative viral promoter regions containing 36 G4-forming sequences into the luciferase reporter and monitoring the expression of luciferase reporter gene in the presence of G4-stabilizing chemicals, we found that only 9 genes were affected by G4 formation. These results revealed promoter context-dependent gene suppression by G4 formation. Mutational analysis of two potential regulatory G4s also demonstrated gene suppression by the sequence-specific G4 formation. Furthermore, the analysis of a mutant virus incapable of G4 formation in the UL35 promoter confirmed promoter regulation by G4 in the context of virus infection. Our analyses provide a platform for assessing G4 functions at the genomic level and demonstrate the properties of the HCMV G4s and their regulatory roles in viral gene expression.
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55
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Cho H, Cho HS, Nam H, Jo H, Yoon J, Park C, Dang TVT, Kim E, Jeong J, Park S, Wallner ES, Youn H, Park J, Jeon J, Ryu H, Greb T, Choi K, Lee Y, Jang SK, Ban C, Hwang I. Translational control of phloem development by RNA G-quadruplex-JULGI determines plant sink strength. NATURE PLANTS 2018; 4:376-390. [PMID: 29808026 DOI: 10.1038/s41477-018-0157-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/19/2018] [Indexed: 05/24/2023]
Abstract
The emergence of a plant vascular system was a prerequisite for the colonization of land; however, it is unclear how the photosynthate transporting system was established during plant evolution. Here, we identify a novel translational regulatory module for phloem development involving the zinc-finger protein JULGI (JUL) and its targets, the 5' untranslated regions (UTRs) of the SUPPRESSOR OF MAX2 1-LIKE4/5 (SMXL4/5) mRNAs, which is exclusively conserved in vascular plants. JUL directly binds and induces an RNA G-quadruplex in the 5' UTR of SMXL4/5, which are key promoters of phloem differentiation. We show that RNA G-quadruplex formation suppresses SMXL4/5 translation and restricts phloem differentiation. In turn, JUL deficiency promotes phloem formation and strikingly increases sink strength per seed. We propose that the translational regulation by the JUL/5' UTR G-quadruplex module is a major determinant of phloem establishment, thereby determining carbon allocation to sink tissues, and that this mechanism was a key invention during the emergence of vascular plants.
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Affiliation(s)
- Hyunwoo Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hyun Seob Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Hoyoung Nam
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Joonseon Yoon
- Crop Seed Development Team, Seed Business Division, FarmHannong Co. Ltd., Daejeon, Korea
| | - Chanyoung Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Tuong Vi T Dang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Eunah Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Jongmin Jeong
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Soyoung Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Eva-Sophie Wallner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Hyungjun Youn
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Jongmin Park
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Jinseong Jeon
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, Korea
| | - Thomas Greb
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Kyuha Choi
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
| | - Yoontae Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Sung Key Jang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Korea.
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56
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Lee HT, Bose A, Lee CY, Opresko PL, Myong S. Molecular mechanisms by which oxidative DNA damage promotes telomerase activity. Nucleic Acids Res 2017; 45:11752-11765. [PMID: 28981887 PMCID: PMC5714237 DOI: 10.1093/nar/gkx789] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/14/2017] [Indexed: 11/13/2022] Open
Abstract
Telomeres are highly susceptible to oxidative DNA damage, which if left unrepaired can lead to dysregulation of telomere length homeostasis. Here we employed single molecule FRET, single molecule pull-down and biochemical analysis to investigate how the most common oxidative DNA lesions, 8-oxoguanine (8oxoG) and thymine glycol (Tg), regulate the structural properties of telomeric DNA and telomerase extension activity. In contrast to 8oxoG which disrupts the telomeric DNA structure, Tg exhibits substantially reduced perturbation of G-quadruplex folding. As a result, 8oxoG induces high accessibility, whereas Tg retains limited accessibility, of telomeric G-quadruplex DNA to complementary single stranded DNA and to telomere binding protein POT1. Surprisingly, the Tg lesion stimulates telomerase loading and activity to a similar degree as an 8oxoG lesion. We demonstrate that this unexpected stimulation arises from Tg-induced conformational alterations and dynamics in telomeric DNA. Despite impacting structure by different mechanisms, both 8oxoG and Tg enhance telomerase binding and extension activity to the same degree, potentially contributing to oncogenesis.
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Affiliation(s)
- Hui-Ting Lee
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Arindam Bose
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA 15261, USA
| | - Chun-Ying Lee
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health and UPMC Hillman Cancer Center, Pittsburgh, PA 15261, USA
| | - Sua Myong
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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57
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Feng G, Luo C, Yi H, Yuan L, Lin B, Luo X, Hu X, Wang H, Lei C, Nie Z, Yao S. DNA mimics of red fluorescent proteins (RFP) based on G-quadruplex-confined synthetic RFP chromophores. Nucleic Acids Res 2017; 45:10380-10392. [PMID: 28981852 PMCID: PMC5737560 DOI: 10.1093/nar/gkx803] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/26/2017] [Accepted: 08/31/2017] [Indexed: 12/29/2022] Open
Abstract
Red fluorescent proteins (RFPs) have emerged as valuable biological markers for biomolecule imaging in living systems. Developing artificial fluorogenic systems that mimic RFPs remains an unmet challenge. Here, we describe the design and synthesis of six new chromophores analogous to the chromophores in RFPs. We demonstrate, for the first time, that encapsulating RFP chromophore analogues in canonical DNA G-quadruplexes (G4) can activate bright fluorescence spanning red and far-red spectral regions (Em = 583-668 nm) that nearly match the entire RFP palette. Theoretical calculations and molecular dynamics simulations reveal that DNA G4 greatly restricts radiationless deactivation of chromophores induced by a twisted intramolecular charge transfer (TICT). These DNA mimics of RFP exhibit attractive photophysical properties comparable or superior to natural RFPs, including high quantum yield, large Stokes shifts, excellent anti-photobleaching properties, and two-photon fluorescence. Moreover, these RFP chromophore analogues are a novel and distinctive type of topology-selective G4 probe specific to parallel G4 conformation. The DNA mimics of RFP have been further exploited for imaging of target proteins. Using cancer-specific cell membrane biomarkers as targets, long-term real-time monitoring in single live cell and two-photon fluorescence imaging in tissue sections have been achieved without the need for genetic coding.
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Affiliation(s)
- Guangfu Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Chao Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Haibo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine laboratory, Hunan University, Changsha 410082, PR China
| | - Honghui Wang
- College of Biology, Hunan University, Changsha 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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58
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Jackowiak P, Hojka-Osinska A, Gasiorek K, Stelmaszczuk M, Gudanis D, Gdaniec Z, Figlerowicz M. Effects of G-quadruplex topology on translational inhibition by tRNA fragments in mammalian and plant systems in vitro. Int J Biochem Cell Biol 2017; 92:148-154. [PMID: 28989078 DOI: 10.1016/j.biocel.2017.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/05/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
Abstract
The folding of tRNA fragments (tRFs) into G-quadruplex structures and the implications of G-quadruplexes in translational inhibition have been studied mainly in mammalian systems. To increase our knowledge of these phenomena, we determined the influence of human and plant tRFs and model G-quadruplexes on translation in rabbit reticulocyte lysate and wheat germ extract. The efficiency of translational inhibition in the mammalian system was strongly associated with the type of G-quadruplex topology. In the plant system, the ability of a small RNA to adopt the G-quadruplex conformation was not sufficient to repress translation, indicating the importance of other structural determinants.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Hojka-Osinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Gasiorek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Michal Stelmaszczuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland.
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59
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Kwok CK, Merrick CJ. G-Quadruplexes: Prediction, Characterization, and Biological Application. Trends Biotechnol 2017; 35:997-1013. [PMID: 28755976 DOI: 10.1016/j.tibtech.2017.06.012] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 02/08/2023]
Abstract
Guanine (G)-rich sequences in nucleic acids can assemble into G-quadruplex structures that involve G-quartets linked by loop nucleotides. The structural and topological diversity of G-quadruplexes have attracted great attention for decades. Recent methodological advances have advanced the identification and characterization of G-quadruplexes in vivo as well as in vitro, and at a much higher resolution and throughput, which has greatly expanded our current understanding of G-quadruplex structure and function. Accumulating knowledge about the structural properties of G-quadruplexes has helped to design and develop a repertoire of molecular and chemical tools for biological applications. This review highlights how these exciting methods and findings have opened new doors to investigate the potential functions and applications of G-quadruplexes in basic and applied biosciences.
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Affiliation(s)
- Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
| | - Catherine J Merrick
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, UK.
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60
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Griffin WC, Gao J, Byrd AK, Chib S, Raney KD. A biochemical and biophysical model of G-quadruplex DNA recognition by positive coactivator of transcription 4. J Biol Chem 2017; 292:9567-9582. [PMID: 28416612 DOI: 10.1074/jbc.m117.776211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/14/2017] [Indexed: 12/22/2022] Open
Abstract
DNA sequences that are guanine-rich have received considerable attention because of their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4), which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA)-binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA. PC4 can bind alternative G4DNA topologies with a low nanomolar Kd value of ∼2 nm, similar to that observed for ssDNA. In consideration of the different structural features between G4DNA and ssDNA, these binding data indicated that PC4 can interact with G4DNA in a manner distinct from ssDNA. The stoichiometry of the PC4-G4 complex was 1:1 for PC4 dimer:G4 substrate. PC4 did not enhance the rate of folding of G4DNA, and formation of the PC4-G4DNA complex did not result in unfolding of the G4DNA structure. We assembled a G4DNA structure flanked by duplex DNA. We find that PC4 can interact with this G4DNA, as well as the complementary C-rich strand. Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dimer accommodates the DNA with one monomer on the G4 strand and the second monomer bound to the C-rich strand. Collectively, these data provide a novel mode of PC4 binding to a DNA secondary structure that remains within the framework of the model for binding to ssDNA. Additionally, consideration of the PC4-G4DNA interaction could provide insight into the biological functions of PC4, which remain incompletely understood.
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Affiliation(s)
- Wezley C Griffin
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
| | - Jun Gao
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
| | - Alicia K Byrd
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
| | - Shubeena Chib
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
| | - Kevin D Raney
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7101
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61
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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62
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Maleki P, Budhathoki JB, Roy WA, Balci H. A practical guide to studying G-quadruplex structures using single-molecule FRET. Mol Genet Genomics 2017; 292:483-498. [PMID: 28150040 DOI: 10.1007/s00438-017-1288-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/05/2017] [Indexed: 11/26/2022]
Abstract
In this article, we summarize the knowledge and best practices learned from bulk and single-molecule measurements to address some of the frequently experienced difficulties in single-molecule Förster resonance energy transfer (smFRET) measurements on G-quadruplex (GQ) structures. The number of studies that use smFRET to investigate the structure, function, dynamics, and interactions of GQ structures has grown significantly in the last few years, with new applications already in sight. However, a number of challenges need to be overcome before reliable and reproducible smFRET data can be obtained in measurements that include GQ. The annealing and storage conditions, the location of fluorophores on the DNA construct, and the ionic conditions of the experiment are some of the factors that are of critical importance for the outcome of measurements, and many of these manifest themselves in unique ways in smFRET assays. By reviewing these aspects and providing a summary of best practices, we aim to provide a practical guide that will help in successfully designing and performing smFRET studies on GQ structures.
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Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | | | - William A Roy
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH, 44242, USA.
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63
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Maleki P, Ma Y, Iida K, Nagasawa K, Balci H. A single molecule study of a fluorescently labeled telomestatin derivative and G-quadruplex interactions. Nucleic Acids Res 2016; 45:288-295. [PMID: 27899628 PMCID: PMC5224478 DOI: 10.1093/nar/gkw1090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/10/2016] [Accepted: 10/25/2016] [Indexed: 02/03/2023] Open
Abstract
The potential use of G-quadruplex (GQ) stabilizing small molecules as anti-cancer drugs has created a flurry of activity on various aspects of these molecules. Telomestatin and oxazole telomestatin derivatives (OTD) are some of the most prominent of such molecules, yet the underlying dynamics of their interactions with GQ and the extent of heterogeneities in these interactions are not known. We performed single molecule measurements to study binding kinetics, rotational freedom, and dwell time distributions of a Cy5-labeled OTD (L1Cy5–7OTD) as it interacted with several different GQ structures. Our measurements show that L1Cy5–7OTD dwells on more stable GQ for longer times and binds to such GQ with higher frequency. The dwell times showed a broad distribution, but were longer than a minute for a significant fraction of molecules (characteristic dwell time τ = 192 ± 15 s and τ = 98 ± 15 s for the more and less stable GQ, respectively). In addition, L1Cy5–7OTD might be able to bind to GQ in at least two different primary orientations and occasionally transition between these orientations. The dwell time in one of these orientations was significantly longer than that in the other one, suggesting different stabilities for different binding orientations.
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Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH 44240, USA
| | - Yue Ma
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Keisuke Iida
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44240, USA
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Qiu S, Zhao F, Zenasni O, Li J, Shih WC. Nanoporous Gold Disks Functionalized with Stabilized G-Quadruplex Moieties for Sensing Small Molecules. ACS APPLIED MATERIALS & INTERFACES 2016; 8:29968-29976. [PMID: 27622472 DOI: 10.1021/acsami.6b09767] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We report label-free small molecule sensing on nanoporous gold disks functionalized with stabilized Guanine-quadruplex (G4) moieties using surface-enhanced Raman spectroscopy (SERS). By utilizing the unique G4 topological structure, target molecules can be selectively captured onto nanoporous gold (NPG) disk surfaces via π-π stacking and electrostatic attractions. Together with high-density plasmonic "hot spots" of NPG disks, the captured molecules produce a remarkable SERS signal. Our strategy represents the first example of the detection of foreign molecules conjugated to nondouble helical DNA nanostructures using SERS while providing a new technique for studying the formation and evolution of G4 moieties. The molecular specificity of G4 is known to be controlled by its unit sequence. Without losing generality, we have selected d(GGT)7GG sequence for the sensing of malachite green (MG), a known carcinogen frequently abused illegally in aquaculture. The newly developed technique achieved a lowest detectable concentration at an impressive 50 pM, two orders of magnitude lower than the European Union (EU) regulatory requirement, with high specificity against potential interferents. To demonstrate the translational potential of this technology, we achieved a lowest detectable concentration of 5.0 nM, meeting the EU regulatory requirement, using a portable probe based detection system.
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Affiliation(s)
- Suyan Qiu
- Institute for Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences , Nanchang, Jiangxi 330200, P. R. China
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Single-molecule imaging reveals a common mechanism shared by G-quadruplex-resolving helicases. Proc Natl Acad Sci U S A 2016; 113:8448-53. [PMID: 27407146 DOI: 10.1073/pnas.1603724113] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
G-quadruplex (GQ) is a four stranded DNA secondary structure that arises from a guanine rich sequence. Stable formation of GQ in genomic DNA can be counteracted by the resolving activity of specialized helicases including RNA helicase AU (associated with AU rich elements) (RHAU) (G4 resolvase 1), Bloom helicase (BLM), and Werner helicase (WRN). However, their substrate specificity and the mechanism involved in GQ unfolding remain uncertain. Here, we report that RHAU, BLM, and WRN exhibit distinct GQ conformation specificity, but use a common mechanism of repetitive unfolding that leads to disrupting GQ structure multiple times in succession. Such unfolding activity of RHAU leads to efficient annealing exclusively within the same DNA molecule. The same resolving activity is sufficient to dislodge a stably bound GQ ligand, including BRACO-19, NMM, and Phen-DC3. Our study demonstrates a plausible biological scheme where different helicases are delegated to resolve specific GQ structures by using a common repetitive unfolding mechanism that provides a robust resolving power.
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66
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Kim M, Kreig A, Lee CY, Rube HT, Calvert J, Song JS, Myong S. Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA. Nucleic Acids Res 2016; 44:4807-17. [PMID: 27095201 PMCID: PMC4889947 DOI: 10.1093/nar/gkw272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
G-quadruplex (GQ) is a four-stranded DNA structure that can be formed in guanine-rich sequences. GQ structures have been proposed to regulate diverse biological processes including transcription, replication, translation and telomere maintenance. Recent studies have demonstrated the existence of GQ DNA in live mammalian cells and a significant number of potential GQ forming sequences in the human genome. We present a systematic and quantitative analysis of GQ folding propensity on a large set of 438 GQ forming sequences in double-stranded DNA by integrating fluorescence measurement, single-molecule imaging and computational modeling. We find that short minimum loop length and the thymine base are two main factors that lead to high GQ folding propensity. Linear and Gaussian process regression models further validate that the GQ folding potential can be predicted with high accuracy based on the loop length distribution and the nucleotide content of the loop sequences. Our study provides important new parameters that can inform the evaluation and classification of putative GQ sequences in the human genome.
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Affiliation(s)
- Minji Kim
- Department of Electrical and Computer Engineering, University of Illinois; 306 N. Wright St. Urbana, IL 61801, USA Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA
| | - Alex Kreig
- Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA
| | - Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University; 3400 N. Charles St. Baltimore, MD 21218 USA
| | - H Tomas Rube
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jacob Calvert
- Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA School of Mathematics, University of Bristol; University Walk, Bristol BS8 1TW, UK
| | - Jun S Song
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA Department of Physics, University of Illinois; 1110 West Green Street, Urbana, IL 61801-3080, USA Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St. Urbana, IL 61801, USA
| | - Sua Myong
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA Department of Biophysics, Johns Hopkins University; 3400 N. Charles St. Baltimore, MD 21218 USA Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St. Urbana, IL 61801, USA
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Lu L, Wang W, Yang C, Kang TS, Leung CH, Ma DL. Iridium(iii) complexes with 1,10-phenanthroline-based N^N ligands as highly selective luminescent G-quadruplex probes and application for switch-on ribonuclease H detection. J Mater Chem B 2016; 4:6791-6796. [DOI: 10.1039/c6tb02316a] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A study was performed to investigate the relationship between molecular structure and G4 sensing ability for a series of iridium(iii) complexes. The complex7was used to construct a G4-based assay for RNase H.
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Affiliation(s)
- Lihua Lu
- College of Chemistry and Pharmaceutical Sciences
- Qingdao Agricultural University
- Qingdao 266109
- China
- Department of Chemistry
| | - Wanhe Wang
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Hong Kong
- China
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