151
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A secondary structure within a human piRNA modulates its functionality. Biochimie 2018; 157:72-80. [PMID: 30414834 DOI: 10.1016/j.biochi.2018.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/04/2018] [Indexed: 01/30/2023]
Abstract
The piwi-interacting RNAs (piRNAs) are small non-coding RNAs, mostly 24-32 nucleotides in length. The piRNAs are not known to have any conserved secondary structure or sequence motifs. Using bioinformatics analysis, we discovered the presence of putative G-quadruplex (GQ) forming sequences in human piRNAs. We studied human piR-48164/piR-GQ containing a potential GQ forming sequence and using biochemical and biophysical techniques confirmed its ability to form a GQ. Using EMSA, we discovered that the formation of GQ structure led to inhibition of the piRNA binding to the HIWI-PAZ domain as well as the complementary base pairing to a target RNA. The inability of the piR-GQ to interact with the PIWI protein might be detrimental to the function of the piRNA. To investigate if the formation of a GQ structure in piRNA prevents its target gene silencing in vivo, we used a reporter assay. The piR-GQ failed to inhibit the reporter gene expression while a mutated version that lacked the ability to form GQ inhibited reporter gene expression indicating that the presence of GQ in piRNA is detrimental to its function. These studies unraveled the dependence of a piRNA's functionality on an RNA secondary structure and added a new layer of regulation to their function.
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152
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Identification and characterization of G-quadruplex formation within the EP0 promoter of pseudorabies virus. Sci Rep 2018; 8:14029. [PMID: 30232344 PMCID: PMC6145870 DOI: 10.1038/s41598-018-32222-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/04/2018] [Indexed: 12/19/2022] Open
Abstract
EP0 is an important early gene that modulates the life cycle of pseudorabies virus (PRV). A guanine-rich sequence overlapping with three Sp1 binding sites is located upstream of the transcription start site (TSS) in the EP0 promoter. Using native polyacrylamide gel electrophoresis (PAGE) and circular dichroism (CD), we verified that the G-rich region in the EP0 promoter forms an intramolecular parallel G-quadruplex (G4) in the presence of K+ ions. Further dimethyl sulphate (DMS) footprinting and Taq polymerase stop assays indicates the potential polymorphic folding of G4. In addition, a small chemical ligand, pyridostatin (PDS), promotes and stabilizes the formation of G4. Interestingly, based on the results of electrophoretic mobility shift assays (EMSA), the Sp1 protein bound to G4-bearing DNA with more affinity than DNA lacking the G4 structure. According to the luciferase reporter assay, G4 negatively regulates the EP0 promoter activity. These results demonstrate that Sp1 and G4 cooperate to regulate EP0 promoter activity.
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153
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Villani G. Quantum Mechanical Investigation of the G-Quadruplex Systems of Human Telomere. ACS OMEGA 2018; 3:9934-9944. [PMID: 31459122 PMCID: PMC6644616 DOI: 10.1021/acsomega.8b01678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/09/2018] [Indexed: 05/17/2023]
Abstract
The three G-quadruplexes involved in the human telomere have been studied with an accurate quantum mechanical approach, and the possibility of reducing them to a simpler model has been tested. The similarities and the differences of these three systems are shown and discussed. Each system has been analyzed through different properties and compared to the others. In particular, we have considered: (1) the shape of the cavity and the atomic charges around it; (2) the electric field in and out of the cavity; (3) the stabilization energy due to the stacking of G-tetrads, to the H-bonds and to the ion interactions; and, finally, (4) to study the mechanism of the process of the ion inclusion in the cavity, the curves of potential energy due to the movement of the Na+ and K+ ions toward the cavity. The results suggest that a detailed study is essential in order to obtain the quantitative properties of these complex systems, but also that some qualitative behaviors can be schematized. Our study makes it clear that the entry of an ion in the cavity of these systems is a complex process, where it is possible to find stable structures with the ion out and in the cavity. Moreover, it is possible that more than one diabatic state is involved in this process.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM—CNR
(UOS Pisa), Area della Ricerca di Pisa, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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154
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Ding B, Liu C, Wu Q, Wang Y, Li L, Yang H. A Label-free and Highly Sensitive Fluorescence Strategy for Mercury Ion Detection Based on Exonuclease III-aided Recycling Amplification. ANAL SCI 2018. [PMID: 29526891 DOI: 10.2116/analsci.34.259] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this paper, we describe a simple and highly sensitive fluorescence strategy of mercury ions based on exonuclease III (Exo III)-aided target recycling amplification to ensure sensitivity. With an ultra high sensitivity (1 pM), our strategy has been simple and cost-effective, which does not need any artificial modification fluorescence groups, and can be carried out in a pot. It also shows excellent selectivity. Therefore, our new method provides an effective platform for mercury-ion detection.
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Affiliation(s)
- Baomiao Ding
- Jingchu Food Research and Development Center, College of Life Science, Yangtze University
| | - Chenguang Liu
- Edible and Medicinal Fungi Research Center, College of Life Science, Yangtze University
| | - Qinghua Wu
- Jingchu Food Research and Development Center, College of Life Science, Yangtze University
| | - Yun Wang
- Edible and Medicinal Fungi Research Center, College of Life Science, Yangtze University
| | - Li Li
- Edible and Medicinal Fungi Research Center, College of Life Science, Yangtze University
| | - Hualin Yang
- Edible and Medicinal Fungi Research Center, College of Life Science, Yangtze University
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155
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Lin C, Wu G, Wang K, Onel B, Sakai S, Shao Y, Yang D. Molecular Recognition of the Hybrid-2 Human Telomeric G-Quadruplex by Epiberberine: Insights into Conversion of Telomeric G-Quadruplex Structures. Angew Chem Int Ed Engl 2018; 57:10888-10893. [PMID: 29888501 PMCID: PMC6192034 DOI: 10.1002/anie.201804667] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/29/2018] [Indexed: 02/05/2023]
Abstract
Human telomeres can form DNA G-quadruplex (G4), an attractive target for anticancer drugs. Human telomeric G4s bear inherent structure polymorphism, challenging for understanding specific recognition by ligands or proteins. Protoberberines are medicinal natural-products known to stabilize telomeric G4s and inhibit telomerase. Here we report epiberberine (EPI) specifically recognizes the hybrid-2 telomeric G4 predominant in physiologically relevant K+ solution and converts other telomeric G4 forms to hybrid-2, the first such example reported. Our NMR structure in K+ solution shows EPI binding induces extensive rearrangement of the previously disordered 5'-flanking and loop segments to form an unprecedented four-layer binding pocket specific to the hybrid-2 telomeric G4; EPI recruits the (-1) adenine to form a "quasi-triad" intercalated between the external tetrad and a T:T:A triad, capped by a T:T base pair. Our study provides structural basis for small-molecule drug design targeting the human telomeric G4.
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Affiliation(s)
- Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47906, USA
| | - Guanhui Wu
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47906, USA
| | - Kaibo Wang
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47906, USA
| | - Buket Onel
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47906, USA
| | - Saburo Sakai
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47906, USA
- Institute of Biogeochemistry, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yong Shao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Danzhou Yang
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47906, USA
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156
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Lin C, Wu G, Wang K, Onel B, Sakai S, Shao Y, Yang D. Molecular Recognition of the Hybrid-2 Human Telomeric G-Quadruplex by Epiberberine: Insights into Conversion of Telomeric G-Quadruplex Structures. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Clement Lin
- Medicinal Chemistry and Molecular Pharmacology; College of Pharmacy; Purdue Center for Cancer Research; Purdue University; West Lafayette IN 47906 USA
| | - Guanhui Wu
- Medicinal Chemistry and Molecular Pharmacology; College of Pharmacy; Purdue Center for Cancer Research; Purdue University; West Lafayette IN 47906 USA
| | - Kaibo Wang
- Medicinal Chemistry and Molecular Pharmacology; College of Pharmacy; Purdue Center for Cancer Research; Purdue University; West Lafayette IN 47906 USA
| | - Buket Onel
- Medicinal Chemistry and Molecular Pharmacology; College of Pharmacy; Purdue Center for Cancer Research; Purdue University; West Lafayette IN 47906 USA
| | - Saburo Sakai
- Medicinal Chemistry and Molecular Pharmacology; College of Pharmacy; Purdue Center for Cancer Research; Purdue University; West Lafayette IN 47906 USA
- Institute of Biogeochemistry; Japan Agency for Marine-Earth Science and Technology; Yokosuka Kanagawa 237-0061 Japan
| | - Yong Shao
- College of Chemistry and Life Sciences; Zhejiang Normal University; Jinhua 321004 China
| | - Danzhou Yang
- Medicinal Chemistry and Molecular Pharmacology; College of Pharmacy; Purdue Center for Cancer Research; Purdue University; West Lafayette IN 47906 USA
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157
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Busto N, Calvo P, Santolaya J, Leal JM, Guédin A, Barone G, Torroba T, Mergny JL, García B. Fishing for G-Quadruplexes in Solution with a Perylene Diimide Derivative Labeled with Biotins. Chemistry 2018; 24:11292-11296. [DOI: 10.1002/chem.201802365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Natalia Busto
- Chemistry Department; University of Burgos; Pza. Misael Bañuelos s/n 09001 Burgos Spain
| | - Patricia Calvo
- Chemistry Department; University of Burgos; Pza. Misael Bañuelos s/n 09001 Burgos Spain
| | - Javier Santolaya
- Chemistry Department; University of Burgos; Pza. Misael Bañuelos s/n 09001 Burgos Spain
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche; Università di Palermo; 90128 Palermo PA Italy
| | - José M Leal
- Chemistry Department; University of Burgos; Pza. Misael Bañuelos s/n 09001 Burgos Spain
| | - Aurore Guédin
- ARNA Laboratory; INSERM U1212; CNRS UMR 5320; IECB; University of Bordeaux; 33600 Pessac France
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche; Chimiche e Farmaceutiche; Università di Palermo; 90128 Palermo PA Italy
| | - Tomás Torroba
- Chemistry Department; University of Burgos; Pza. Misael Bañuelos s/n 09001 Burgos Spain
| | - Jean-Louis Mergny
- ARNA Laboratory; INSERM U1212; CNRS UMR 5320; IECB; University of Bordeaux; 33600 Pessac France
- Institute of Biophysics, AS CR; v.v.i. Kralovopolska 135 612 65 Brno Czech Republic
| | - Begoña García
- Chemistry Department; University of Burgos; Pza. Misael Bañuelos s/n 09001 Burgos Spain
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158
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Syed A, Tainer JA. The MRE11-RAD50-NBS1 Complex Conducts the Orchestration of Damage Signaling and Outcomes to Stress in DNA Replication and Repair. Annu Rev Biochem 2018; 87:263-294. [PMID: 29709199 PMCID: PMC6076887 DOI: 10.1146/annurev-biochem-062917-012415] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genomic instability in disease and its fidelity in health depend on the DNA damage response (DDR), regulated in part from the complex of meiotic recombination 11 homolog 1 (MRE11), ATP-binding cassette-ATPase (RAD50), and phosphopeptide-binding Nijmegen breakage syndrome protein 1 (NBS1). The MRE11-RAD50-NBS1 (MRN) complex forms a multifunctional DDR machine. Within its network assemblies, MRN is the core conductor for the initial and sustained responses to DNA double-strand breaks, stalled replication forks, dysfunctional telomeres, and viral DNA infection. MRN can interfere with cancer therapy and is an attractive target for precision medicine. Its conformations change the paradigm whereby kinases initiate damage sensing. Delineated results reveal kinase activation, posttranslational targeting, functional scaffolding, conformations storing binding energy and enabling access, interactions with hub proteins such as replication protein A (RPA), and distinct networks at DNA breaks and forks. MRN biochemistry provides prototypic insights into how it initiates, implements, and regulates multifunctional responses to genomic stress.
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Affiliation(s)
- Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; ,
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; ,
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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159
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Kar A, Jones N, Arat NÖ, Fishel R, Griffith JD. Long repeating (TTAGGG) n single-stranded DNA self-condenses into compact beaded filaments stabilized by G-quadruplex formation. J Biol Chem 2018; 293:9473-9485. [PMID: 29674319 PMCID: PMC6005428 DOI: 10.1074/jbc.ra118.002158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/04/2018] [Indexed: 11/06/2022] Open
Abstract
Conformations adopted by long stretches of single-stranded DNA (ssDNA) are of central interest in understanding the architecture of replication forks, R loops, and other structures generated during DNA metabolism in vivo This is particularly so if the ssDNA consists of short nucleotide repeats. Such studies have been hampered by the lack of defined substrates greater than ∼150 nt and the absence of high-resolution biophysical approaches. Here we describe the generation of very long ssDNA consisting of the mammalian telomeric repeat (5'-TTAGGG-3') n , as well as the interrogation of its structure by EM and single-molecule magnetic tweezers (smMT). This repeat is of particular interest because it contains a run of three contiguous guanine residues capable of forming G quartets as ssDNA. Fluorescent-dye exclusion assays confirmed that this G-strand ssDNA forms ubiquitous G-quadruplex folds. EM revealed thick bead-like filaments that condensed the DNA ∼12-fold. The bead-like structures were 5 and 8 nm in diameter and linked by thin filaments. The G-strand ssDNA displayed initial stability to smMT force extension that ultimately released in steps that were multiples ∼28 nm at forces between 6 and 12 pN, well below the >20 pN required to unravel G-quadruplexes. Most smMT steps were consistent with the disruption of the beads seen by EM. Binding by RAD51 distinctively altered the force extension properties of the G-strand ssDNA, suggesting a stochastic G-quadruplex-dependent condensation model that is discussed.
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Affiliation(s)
- Anirban Kar
- From the Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599
| | - Nathan Jones
- the Department of Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio 43210
- the Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, Ohio 43210, and
| | - N Özlem Arat
- From the Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599
- the Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3T 1J4, Canada
| | - Richard Fishel
- the Department of Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio 43210,
- the Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, Ohio 43210, and
| | - Jack D Griffith
- From the Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599,
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160
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Merta TJ, Geacintov NE, Shafirovich V. Generation of 8-oxo-7,8-dihydroguanine in G-Quadruplexes Models of Human Telomere Sequences by One-electron Oxidation. Photochem Photobiol 2018; 95:244-251. [PMID: 29679477 PMCID: PMC6196120 DOI: 10.1111/php.12926] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/04/2018] [Indexed: 12/16/2022]
Abstract
The mechanistic aspects of one-electron oxidation of G-quadruplexes in the basket (Na+ ions) and hybrid (K+ ions) conformations were investigated by transient absorption laser kinetic spectroscopy and HPLC detection of the 8-oxo-7,8-dihydroguanine (8-oxoG) oxidation product. The photo-induced one-electron abstraction from G-quadruplexes was initiated by sulfate radical anions (SO4 ˙- ) derived from the photolysis of persulfate ions by 308 nm excimer laser pulses. In neutral aqueous solutions (pH 7.0), the transient absorbance of neutral guanine radicals, G(-H)˙, is observed following the complete decay of SO4 ˙- radicals (~10 μs after the actinic laser flash). In both basket and hybrid conformations, the G(-H)˙ decay is biphasic with one component decaying with a lifetime of ~0.1 ms, and the other with a lifetime of 20-30 ms. The fast decay component (~0.1 ms) in G-quadruplexes is correlated with the formation of 8-oxoG lesions. We propose that in G-quadruplexes, G(-H)˙ radicals retain radical cation character by sharing the N1-proton with the O6 -atom of G in the [G˙+ : G] Hoogsteen base pair; this [G(-H)˙: H+ G <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>⇄</mml:mo></mml:math> G˙+ : G] leads to the hydration of G˙+ radical cation within the millisecond time domain, and is followed by the formation of the 8-oxoG lesions.
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Affiliation(s)
- Tomasz J Merta
- Chemistry Program, NYU Shanghai, Pudong Xinqu, Shanghai Shi, China
| | - Nicholas E Geacintov
- Chemistry Program, NYU Shanghai, Pudong Xinqu, Shanghai Shi, China.,Chemistry Department, New York University, New York, NY
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161
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Prasad B, Jamroskovic J, Bhowmik S, Kumar R, Romell T, Sabouri N, Chorell E. Flexible Versus Rigid G-Quadruplex DNA Ligands: Synthesis of Two Series of Bis-indole Derivatives and Comparison of Their Interactions with G-Quadruplex DNA. Chemistry 2018; 24:7926-7938. [PMID: 29603472 DOI: 10.1002/chem.201800078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 12/30/2022]
Abstract
Small molecules that target G-quadruplex (G4) DNA structures are not only valuable to study G4 biology but also for their potential as therapeutics. This work centers around how different design features of small molecules can affect the interactions with G4 DNA structures, exemplified by the development of synthetic methods to bis-indole scaffolds. Our synthesized series of bis-indole scaffolds are structurally very similar but differ greatly in the flexibility of their core structures. The flexibility of the molecules proved to be an advantage compared to locking the compounds in the presumed bioactive G4 conformation. The flexible derivatives demonstrated similar or even improved G4 binding and stabilization in several orthogonal assays even though their entropic penalty of binding is higher. In addition, molecular dynamics simulations with the c-MYC G4 structure showed that the flexible compounds adapt better to the surrounding. This was reflected by an increased number of both stacking and polar interactions with both the residues in the G4 DNA structure and the DNA residues just upstream of the G4 structure.
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Affiliation(s)
- Bagineni Prasad
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Sudipta Bhowmik
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.,Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 700009, Kolkata, India
| | - Rajendra Kumar
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Tajanena Romell
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
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162
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Giassa IC, Rynes J, Fessl T, Foldynova-Trantirkova S, Trantirek L. Advances in the cellular structural biology of nucleic acids. FEBS Lett 2018; 592:1997-2011. [PMID: 29679394 DOI: 10.1002/1873-3468.13054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/31/2018] [Accepted: 04/09/2018] [Indexed: 01/01/2023]
Abstract
Conventional biophysical and chemical biology approaches for delineating relationships between the structure and biological function of nucleic acids (NAs) abstract NAs from their native biological context. However, cumulative experimental observations have revealed that the structure, dynamics and interactions of NAs might be strongly influenced by a broad spectrum of specific and nonspecific physical-chemical environmental factors. This consideration has recently sparked interest in the development of novel tools for structural characterization of NAs in the native cellular context. Here, we review the individual methods currently being employed for structural characterization of NA structure in a native cellular environment with a focus on recent advances and developments in the emerging fields of in-cell NMR and electron paramagnetic resonance spectroscopy and in-cell single-molecule FRET of NAs.
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Affiliation(s)
- Ilektra-Chara Giassa
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Rynes
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Silvie Foldynova-Trantirkova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Institute of Biophysics, Academy of Science of the Czech Republic, Brno, Czech Republic
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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163
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Novel Naphthalimide Derivatives as Selective G-Quadruplex DNA Binders. Appl Biochem Biotechnol 2018; 186:547-562. [PMID: 29671192 DOI: 10.1007/s12010-018-2749-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/25/2018] [Indexed: 01/08/2023]
Abstract
A new derivate of 4-bromo-1,8-naphthalic anhydride and its quaternized analogue have been prepared and characterized. The interactions of both derivatives with human telomere quadruplex-DNA and ds-DNA have been comparatively studied by UV-visible (UV-Vis), fluorescent intercalator displacement assays, competition dialysis, circular dichroism (CD), agarose gel electrophoresis, and polyacrylamide gel electrophoresis. The results show that both derivatives can stabilize G-quadruplexes DNA, and they show different binding affinities for G-quadruplexes-DNA and ds-DNA. All spectroscopic studies have shown that the derivatives have a modest selectivity for G-quadruplex versus ds-DNA.
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164
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Purohit G, Mukherjee AK, Sharma S, Chowdhury S. Extratelomeric Binding of the Telomere Binding Protein TRF2 at the PCGF3 Promoter Is G-Quadruplex Motif-Dependent. Biochemistry 2018; 57:2317-2324. [PMID: 29589913 DOI: 10.1021/acs.biochem.8b00019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Telomere repeat binding factor 2 (TRF2) is critical for the protection of chromosome ends. Mounting evidence suggests that TRF2 associates with extratelomeric sites and TRF2 functions may not be limited to telomeres. Here, we show that the PCGF3 promoter harbors a sequence capable of forming the DNA secondary structure G-quadruplex motif, which is required for binding of TRF2 at the PCGF3 promoter. We demonstrate that promoter binding by TRF2 mediates PCGF3 promoter activity, and both the N-terminal and C-terminal domains of TRF2 are necessary for promoter activity. Altogether, this shows for the first time that a telomere binding factor may regulate a component of the polycomb group of proteins.
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165
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Griffin BD, Bass HW. Review: Plant G-quadruplex (G4) motifs in DNA and RNA; abundant, intriguing sequences of unknown function. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:143-147. [PMID: 29606212 DOI: 10.1016/j.plantsci.2018.01.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/12/2018] [Accepted: 01/20/2018] [Indexed: 06/08/2023]
Abstract
DNA sequences capable of forming G-quadruplex (G4) structures can be predicted and mapped in plant genomes using computerized pattern search programs. Non-telomeric G4 motifs have recently been found to number in the thousands across many plant species and enriched around gene promoters, prompting speculation that they may represent a newly uncovered and ubiquitous family of cis-acting elements. Comparative analysis shows that monocots exhibit five to ten times higher G4 motif density than eudicots, but the significance of this difference has not been determined. The vast scale and complexity of G4 functions, actual or theoretical, are reviewed in relation to the multiple modes of action and myriad genetic functions for which G4s have been implicated in DNA and RNA. Future experimental strategies and opportunities include identifying plant G4-interactomes, resolving the structures of G4s with and without their binding partners, and defining molecular mechanisms through reporter gene, genetic, or genome editing approaches. Given the global importance of plants for food, clothing, medicine, and energy, together with the potential role of G4 motifs as a widely conserved set of DNA sequences that could coordinate gene regulation, future plant G4 research holds great potential for use in plant improvement strategies.
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Affiliation(s)
- Brianna D Griffin
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL, 32306-4295, USA.
| | - Hank W Bass
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL, 32306-4295, USA.
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166
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Lu C, Smith-Carpenter JE, Taylor JSA. Evidence for Reverse Hoogsteen Hairpin Intermediates in the Photocrosslinking of Human Telomeric DNA Sequences. Photochem Photobiol 2018; 94:685-697. [PMID: 29418001 DOI: 10.1111/php.12898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/04/2018] [Indexed: 12/28/2022]
Abstract
UVB irradiation of human telomeric d(GGGTTA)3 GGG sequences in potassium ion solution crosslinks the first and third TTA segments through anti cyclobutane pyrimidine dimer (CPD) formation. The photocrosslinking reaction was first proposed to occur through a form 3 two-tetrad G-quadruplex in which the lateral four-nucleotide GTTA loop can interact with an adjacent TTA loop. Curiously, the reaction does not occur with sodium ion, which was explained by the formation of a basket structure which only has three-nucleotide TTA loops that cannot interact. Sequences known or expected to favor the two-tetrad basket did not show enhanced photocrosslinking, suggesting that some other structure was the reactive intermediate. Herein, we report that anti CPDs form in human telomeric DNA sequences with lithium ion that is known to disfavor G-quadruplex formation, as well as with potassium ion when the bases are modified to interfere with G-quartet formation. We also show that anti CPDs form in sequences containing A's in place of G's that cannot form Hoogsteen hairpins, but can form reverse Hoogsteen hairpins. These results suggest that reverse Hoogsteen hairpins may play a hitherto unrecognized role in the biology and photoreactivity of DNA in telomeres, and possibly in other purine-rich sequences found in regulatory regions.
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Affiliation(s)
- Chen Lu
- Department of Chemistry, Washington University, St. Louis, MO
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167
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Rackwitz J, Bald I. Low-Energy Electron-Induced Strand Breaks in Telomere-Derived DNA Sequences-Influence of DNA Sequence and Topology. Chemistry 2018; 24:4680-4688. [PMID: 29359819 DOI: 10.1002/chem.201705889] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Indexed: 12/19/2022]
Abstract
During cancer radiation therapy high-energy radiation is used to reduce tumour tissue. The irradiation produces a shower of secondary low-energy (<20 eV) electrons, which are able to damage DNA very efficiently by dissociative electron attachment. Recently, it was suggested that low-energy electron-induced DNA strand breaks strongly depend on the specific DNA sequence with a high sensitivity of G-rich sequences. Here, we use DNA origami platforms to expose G-rich telomere sequences to low-energy (8.8 eV) electrons to determine absolute cross sections for strand breakage and to study the influence of sequence modifications and topology of telomeric DNA on the strand breakage. We find that the telomeric DNA 5'-(TTA GGG)2 is more sensitive to low-energy electrons than an intermixed sequence 5'-(TGT GTG A)2 confirming the unique electronic properties resulting from G-stacking. With increasing length of the oligonucleotide (i.e., going from 5'-(GGG ATT)2 to 5'-(GGG ATT)4 ), both the variety of topology and the electron-induced strand break cross sections increase. Addition of K+ ions decreases the strand break cross section for all sequences that are able to fold G-quadruplexes or G-intermediates, whereas the strand break cross section for the intermixed sequence remains unchanged. These results indicate that telomeric DNA is rather sensitive towards low-energy electron-induced strand breakage suggesting significant telomere shortening that can also occur during cancer radiation therapy.
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Affiliation(s)
- Jenny Rackwitz
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
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168
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Tucker BA, Hudson JS, Ding L, Lewis E, Sheardy RD, Kharlampieva E, Graves D. Stability of the Na + Form of the Human Telomeric G-Quadruplex: Role of Adenines in Stabilizing G-Quadruplex Structure. ACS OMEGA 2018; 3:844-855. [PMID: 30023791 PMCID: PMC6045420 DOI: 10.1021/acsomega.7b01649] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/09/2018] [Indexed: 06/08/2023]
Abstract
G-quadruplexes are higher order DNA structures that play significant roles in gene transcription and telomeric maintenance. The formation and stability of the G-quadruplex structures are under thermodynamic control and may be of biological significance for regulatory function of cellular processes. Here, we report the structural influence and energetic contributions of the adenine bases in the loop sequences that flank G-repeats in human telomeric DNA sequence. Spectroscopic and calorimetric techniques are used to measure the thermal stability and thermodynamic contributions to the stability of human telomeric G-quadruplexes that have been designed with systematic changes of A to T throughout the telomeric sequence. These studies demonstrate that the thermal stability of the G-quadruplex structure is directly related to the number and position of the adenines that are present in the telomeric sequence. The melting temperature (Tm) was reduced from 59 °C for the wild-type sequence to 47 °C for the sequence where all four adenines were replaced with thymines (0123TTT). Furthermore, the enthalpy required for transitioning from the folded to unfolded G-quadruplex structure was reduced by 15 kcal/mol when the adenines were replaced with thymines (37 kcal/mol for the wild-type telomeric sequence reduced to 22 kcal/mol for the sequence where all four adenines were replaced with thymines (0123TTT)). The circular dichroism melting studies for G-quadruplex sequences having a single A to T change showed significantly sloping pretransition baselines and their differential scanning calorimetry (DSC) thermograms revealed biphasic melting profiles. In contrast, the deoxyoligonucleotides having sequences with two or more A to T changes did not exhibit sloping baselines or biphasic DSC thermograms. We attribute the biphasic unfolding profile and reduction in the enthalpy of unfolding to the energetic contributions of adenine hydrogen bonding within the loops as well as the adenine stacking to the G-tetrads of the G-quadruplex structure.
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Affiliation(s)
- Brenna A. Tucker
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Jason S. Hudson
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Lei Ding
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Edwin Lewis
- Department
of Chemistry, Mississippi State University, Mississippi, Mississippi
State 39762, United
States
| | - Richard D. Sheardy
- Department
of Chemistry & Biochemistry, Texas Women’s
University, Denton, Texas 782042, United States
| | - Eugenia Kharlampieva
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - David Graves
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
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169
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Serendipitous Discovery of a Guanine-rich DNA Molecule with a Highly Stable Structure in Urea. Sci Rep 2018; 8:1935. [PMID: 29386529 PMCID: PMC5792554 DOI: 10.1038/s41598-018-20248-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/15/2018] [Indexed: 11/16/2022] Open
Abstract
We have made an accidental discovery of an unusual, single-stranded, guanine-rich DNA molecule that is capable of adopting a folded structure in 7 M urea (7MU) known to denature nucleic acid structures. The folding of this molecule requires Na+ and Mg2+ and the folded structure remains stable when subjected to denaturing (7MU) polyacrylamide gel electrophoresis. Results from sequence mutagenesis, DNA methylation, and circular dichroism spectroscopy studies suggest that this molecule adopts an intramolecular guanine-quadruplex structure with 5 layers of guanine tetrads. Our finding indicates that DNA has the ability to create extremely stable structural folds despite its limited chemical repertoire, making it possible to develop DNA-based systems for unconventional applications.
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170
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Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chem Rev 2018; 118:1599-1663. [PMID: 29322778 DOI: 10.1021/acs.chemrev.7b00504] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.
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Affiliation(s)
- Alicia J Angelbello
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Zi-Fu Wang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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171
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Saxena S, Joshi S, Shankaraswamy J, Tyagi S, Kukreti S. Magnesium and molecular crowding of the cosolutes stabilize the i-motif structure at physiological pH. Biopolymers 2018; 107. [PMID: 28295161 DOI: 10.1002/bip.23018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 11/09/2022]
Abstract
Most of the important genomic regions, especially the G,C rich gene promoters, consist of sequences with potential to form G,C-tetraplexes on both the DNA strands. In this study, we used three C-rich oligonucleotides (11Py, 21Py, and HTPy), of which 11Py and 21Py are located at various transcriptional regulatory elements of the human genome while HTPy sequence is a C-rich strand of human telomere sequence. These C-rich oligonucleotides formed i-motif structures, verified by Circular Dichroism (CD), UV absorption melting experiments, and native gel electrophoresis. The CD spectra revealed that 11Py and 21Py form i-motif structures at acidic pH values of 4.5 and 5.7 in the presence of 100 mM NaCl but remain unstructured at pH 7.0. However, 21Py can form stable i-motif structure even at neutral pH in presence of 1 mM MgCl2 . UV-thermal melting studies showed stabilization of 21Py i-motif at pH 5.7 in the presence of Na+ or K+ with increasing concentration of MgCl2 or CaCl2 from 1 to 10 mM. Significant shift in the CD peak of HTPy sequence was observed as the positive peak from 286 nm shifted to 276 nm while the negative peak from 265 to 254 nm. Further, inevitable necessity of 1 mM Mg2+ to form i-motif structure at neutral pH was observed. Under similar ionic conditions and neutral pH, all the three C-rich sequences were able to form stable i-motif structures (11Py, 21Py) or altered i-motif/homoduplex structures (HTPy) in the presence of MgCl2 and cell mimicking molecular crowding conditions of 40 wt% PEG 200. It is concluded that presence of Mg2+ ions and molecular crowding agents induce and stabilize i-motif structures at physiological solution environment.
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Affiliation(s)
- Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Savita Joshi
- Department of Chemistry, Nucleic Acids Research laboratory, University of Delhi (North Campus), Delhi, 110007, India
| | - J Shankaraswamy
- Amity International Centre for Post Harvest Technology and Cold Chain Management, Amity University Uttar Pradesh, Noida, 201313, India
| | - Shikhar Tyagi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Shrikant Kukreti
- Department of Chemistry, Nucleic Acids Research laboratory, University of Delhi (North Campus), Delhi, 110007, India
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172
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Liu Y, Liao R, Wang H, Gong H, Chen C, Chen X, Cai C. Accurate and sensitive fluorescence detection of DNA based on G-quadruplex hairpin DNA. Talanta 2018; 176:422-427. [DOI: 10.1016/j.talanta.2017.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/28/2017] [Accepted: 08/01/2017] [Indexed: 11/26/2022]
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173
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Cheng R, Rose VE, Power B, Fridgen TD. Self-assembled uracil complexes containing tautomeric uracils: an IRMPD spectroscopic and computation study of the structures of gaseous uracilnCa2+ (n = 4, 5, or 6) complexes. Phys Chem Chem Phys 2018; 20:572-580. [DOI: 10.1039/c7cp07128k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structures of doubly-charged uracil (U) complexes with Ca2+, UnCa2+ (n = 4, 5, 6), were studied by infrared multiphoton dissociation (IRMPD) spectroscopy and computational methods.
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Affiliation(s)
- Ruodi Cheng
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | | | - Barry Power
- Department of Chemistry
- Memorial University
- St. John's
- Canada
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174
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Biswas B, Kandpal M, Vivekanandan P. A G-quadruplex motif in an envelope gene promoter regulates transcription and virion secretion in HBV genotype B. Nucleic Acids Res 2017; 45:11268-11280. [PMID: 28981800 PMCID: PMC5737607 DOI: 10.1093/nar/gkx823] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 09/07/2017] [Indexed: 12/20/2022] Open
Abstract
HBV genotypes differ in pathogenicity. In addition, genotype-specific differences in the regulation of transcription and virus replication exist in HBV, but the underlying mechanisms are unknown. Here, we show the presence of a G-quadruplex motif in the promoter of the preS2/S gene; this G-quadruplex is highly conserved only in HBV genotype B but not in other HBV genotypes. We demonstrate that this G-quadruplex motif forms a hybrid intramolecular G-quadruplex structure. Interestingly, mutations disrupting the G-quadruplex in HBV genotype B reduced the preS2/S promoter activity, leading to reduced hepatitis B surface antigen (HBsAg) levels. G-quadruplex ligands stabilized the G-quadruplex in genotype B and enhanced the preS2/S promoter activity. Furthermore, mutations disrupting the G-quadruplex in the full-length HBV genotype B constructs were associated with impaired virion secretion. In contrast to typical G-quadruplexes within promoters which are negative regulators of transcription the G-quadruplex in the preS2/S promoter of HBV represents an unconventional positive regulatory element. Our findings highlight (a) G-quadruplex mediated enhancement of transcription and virion secretion in HBV and (b) a yet unknown role for DNA secondary structures in complex genotype-specific regulatory mechanisms in virus genomes.
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Affiliation(s)
- Banhi Biswas
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Manish Kandpal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
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175
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Interaction of Quindoline derivative with telomeric repeat–containing RNA induces telomeric DNA-damage response in cancer cells through inhibition of telomeric repeat factor 2. Biochim Biophys Acta Gen Subj 2017; 1861:3246-3256. [DOI: 10.1016/j.bbagen.2017.09.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/24/2017] [Accepted: 09/19/2017] [Indexed: 11/22/2022]
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176
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Telomerase activity is required for the telomere G-overhang structure in Trypanosoma brucei. Sci Rep 2017; 7:15983. [PMID: 29167542 PMCID: PMC5700094 DOI: 10.1038/s41598-017-16182-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/08/2017] [Indexed: 01/24/2023] Open
Abstract
Trypanosoma brucei causes fatal human African trypanosomiasis and evades the host immune response by regularly switching its major surface antigen, VSG, which is expressed exclusively from subtelomeric loci. Telomere length and telomere proteins play important roles in regulating VSG silencing and switching. T. brucei telomerase plays a key role in maintaining telomere length, and T. brucei telomeres terminate in a single-stranded 3′ G-rich overhang. Understanding the detailed structure of the telomere G-overhang and its maintenance will contribute greatly to better understanding telomere maintenance mechanisms. Using an optimized adaptor ligation assay, we found that most T. brucei telomere G-overhangs end in 5′ TTAGGG 3′, while a small portion of G-overhangs end in 5′ TAGGGT 3′. Additionally, the protein and the RNA components of the telomerase (TbTERT and TbTR) and TbKu are required for telomere G-overhangs that end in 5′ TTAGGG 3′ but do not significantly affect the 5′ TAGGGT 3′-ending overhangs, indicating that telomerase-mediated telomere synthesis is important for the telomere G-overhang structure. Furthermore, using telomere oligo ligation-mediated PCR, we showed for the first time that the T. brucei telomere 5′ end sequence – an important feature of the telomere terminal structure – is not random but preferentially 5′ CCTAAC 3′.
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177
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Abou Assi H, El-Khoury R, González C, Damha MJ. 2'-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA. Nucleic Acids Res 2017; 45:11535-11546. [PMID: 29036537 PMCID: PMC5714228 DOI: 10.1093/nar/gkx838] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
Human telomeres and promoter regions of genes fulfill a significant role in cellular aging and cancer. These regions comprise of guanine and cytosine-rich repeats, which under certain conditions can fold into G-quadruplex (G4) and i-motif structures, respectively. Herein, we use UV, circular dichroism and NMR spectroscopy to study several human telomeric sequences and demonstrate that G4/i-motif-duplex interconversion kinetics are slowed down dramatically by 2'-β-fluorination and the presence of G4/i-motif-duplex junctions. NMR-monitored kinetic experiments on 1:1 mixtures of native and modified C- and G-rich human telomeric sequences reveal that strand hybridization kinetics are controlled by G4 or i-motif unfolding. Furthermore, we provide NMR evidence for the formation of a hybrid complex containing G4 and i-motif structures proximal to a duplex DNA segment at neutral pH. While the presence of i-motif and G4 folds may be mutually exclusive in promoter genome sequences, our results suggest that they may co-exist transiently as intermediates in telomeric sequences.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Carlos González
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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178
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Belotserkovskii BP, Soo Shin JH, Hanawalt PC. Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter. Nucleic Acids Res 2017; 45:6589-6599. [PMID: 28498974 PMCID: PMC5499740 DOI: 10.1093/nar/gkx403] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 02/07/2023] Open
Abstract
Guanine-rich (G-rich) homopurine–homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA–DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA–DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription ‘bursting’) and may also have practical implications for the design of expression vectors.
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Affiliation(s)
| | - Jane Hae Soo Shin
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Philip C Hanawalt
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
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179
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Warner KD, Sjekloća L, Song W, Filonov GS, Jaffrey SR, Ferré-D’Amaré AR. A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nat Chem Biol 2017; 13:1195-1201. [PMID: 28945234 PMCID: PMC5663454 DOI: 10.1038/nchembio.2475] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 08/03/2017] [Indexed: 11/09/2022]
Abstract
Corn, a 28-nucleotide RNA, increases yellow fluorescence of its cognate ligand 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO) by >400-fold. Corn was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer. Unusually, the dimer interface, in which six unpaired adenosines break overall two-fold symmetry, lacks any intermolecular base pairs. The homodimer encapsulates one DFHO at its interprotomer interface, sandwiching it with a G-quadruplex from each protomer. Corn and the green-fluorescent Spinach RNA are structurally unrelated. Their convergent use of G-quadruplexes underscores the usefulness of this motif for RNA-induced small-molecule fluorescence. The asymmetric dimer interface of Corn could provide a basis for the development of mutants that only fluoresce as heterodimers. Such variants would be analogous to Split GFP, and may be useful for analyzing RNA co-expression or association, or for designing self-assembling RNA nanostructures.
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Affiliation(s)
- Katherine Deigan Warner
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
| | - Ljiljana Sjekloća
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Grigory S. Filonov
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
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180
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Liu Y, Shen T, Li J, Gong H, Chen C, Chen X, Cai C. Ratiometric Fluorescence Sensor for the MicroRNA Determination by Catalyzed Hairpin Assembly. ACS Sens 2017; 2:1430-1434. [PMID: 28936869 DOI: 10.1021/acssensors.7b00313] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel catalyzed hairpin assembly-based turn-on ratiometric fluorescence biosensor was constructed for the determination of microRNA-122 (miRNA-122) by using 2-aminopurine (2-AP) and thioflavin T (ThT) as detection signal sources. Hairpin DNA sequence (H1) includes the complementary strands of miRNA-122 and G-quadruplex-forming sequence. When miRNA-122 was presented, hybridization occurred between miRNA-122 and part of H1, causing a double-stranded DNA and a G-quadruplex formed. The formed double-stranded DNA significantly decreased the fluorescence intensity of 2-AP. Furthermore, after binding with ThT, the formed G-quadruplex led to the fluorescent enhancement. The hairpin DNA sequence (H2) hybridized with the unfolded H1 and displaced miRNA-122. Finally, the displaced miRNA-122 again hybridized with the H1 and initiated cycle amplification. This sensor showed a linear ranges of 0.5-50 nM and the limit of detection for miRNA-122 assay was 72 pM (with the lowest measured concentration of 500 pM) for determination of miRNA-122 when no other miRNA was present. Measurements on cell lysates from 100, 1000, and 10 000 cells of three different cell lines provided increasing signal ratios, which showed the application potential of the sensor for miRNA determination in real samples.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Tian Shen
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Jing Li
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Hang Gong
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Chunyan Chen
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Xiaoming Chen
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Changqun Cai
- Key Laboratory of Environmentally
Friendly Chemistry and Applications of Ministry of Education, College
of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
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181
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Singh A, Kukreti S. A triple stranded G-quadruplex formation in the promoter region of human myosin β(Myh7) gene. J Biomol Struct Dyn 2017; 36:2773-2786. [PMID: 28927343 DOI: 10.1080/07391102.2017.1374211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Regulatory regions in human genome, enriched in guanine-rich DNA sequences have the propensity to fold into G-quadruplex structures. On exploring the genome for search of G-tracts, it was interesting to find that promoter of Human Myosin Gene (MYH7) contains a conserved 23-mer G-rich sequence (HM-23). Mutations in this gene are associated with familial cardiomyopathy. Enrichment of MYH7 gene in G-rich sequences could possibly play a critical role in its regulation. We used polyacrylamide gel electrophoresis (PAGE), UV-Thermal denaturation (UV-Tm) and Circular Dichroism (CD), to demonstrate the formation of a G-quadruplex by 23-mer G-rich sequence HM23 in promoter location of MYH7 gene. We observed that the wild G-rich sequence HM23 containing consecutive G5 stretch in two stacks adopt G-quadruplexes of diverse molecularity by involvement of four-strand, three-strand and two-strands with same parallel topology. Interestingly, the mutated sequence in the absence of continuous G5 stretch obstructs the formation of three-stranded G-quadruplex. We demonstrated that continuous G5 stretch is mandatory for the formation of a unique three-stranded G-quadruplex. Presence of various transcription factors (TF) in vicinity of the sequence HM23 leave fair possibility of recognition by TF binding sites, and so modulate gene expression. These findings may add on our understanding about the effect of base change in the formation of varied structural species in similar solution condition. This study may give insight about structural polymorphism arising due to recognition of non-Watson-Crick G-quadruplex structures by cellular proteins and designing structure specific molecules.
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Affiliation(s)
- Anju Singh
- a Nucleic Acids Research Laboratory, Department of Chemistry , University of Delhi , North Campus, Delhi 110007 , India
| | - Shrikant Kukreti
- a Nucleic Acids Research Laboratory, Department of Chemistry , University of Delhi , North Campus, Delhi 110007 , India
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182
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Wang X, Goodrich KJ, Gooding AR, Naeem H, Archer S, Paucek RD, Youmans DT, Cech TR, Davidovich C. Targeting of Polycomb Repressive Complex 2 to RNA by Short Repeats of Consecutive Guanines. Mol Cell 2017; 65:1056-1067.e5. [PMID: 28306504 DOI: 10.1016/j.molcel.2017.02.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 12/20/2016] [Accepted: 02/01/2017] [Indexed: 11/18/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that trimethylates H3K27, a mark of repressed chromatin. Mammalian PRC2 binds RNA promiscuously, with thousands of target transcripts in vivo. But what does PRC2 recognize in these RNAs? Here we show that purified human PRC2 recognizes G > C,U ≫ A in single-stranded RNA and has a high affinity for folded guanine quadruplex (G4) structures but little binding to duplex RNAs. Importantly, G-tract motifs are significantly enriched among PRC2-binding transcripts in vivo. DNA sequences coding for PRC2-binding RNA motifs are enriched at PRC2-binding sites on chromatin and H3K27me3-modified nucleosomes. Collectively, the abundance of PRC2-binding RNA motifs rationalizes the promiscuous RNA binding of PRC2, and their enrichment at Polycomb target genes provides a means for RNA-mediated regulation.
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Affiliation(s)
- Xueyin Wang
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Karen J Goodrich
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Anne R Gooding
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Haroon Naeem
- Monash Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Stuart Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Richard D Paucek
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Daniel T Youmans
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA; University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas R Cech
- Department of Chemistry & Biochemistry, BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, CO 80309, USA.
| | - Chen Davidovich
- Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, VIC 3800, Australia.
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183
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Gao M, Harish B, Berghaus M, Seymen R, Arns L, McCallum SA, Royer CA, Winter R. Temperature and pressure limits of guanosine monophosphate self-assemblies. Sci Rep 2017; 7:9864. [PMID: 28852183 PMCID: PMC5574928 DOI: 10.1038/s41598-017-10689-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/14/2017] [Indexed: 12/31/2022] Open
Abstract
Guanosine monophosphate, among the nucleotides, has the unique property to self-associate and form nanoscale cylinders consisting of hydrogen-bonded G-quartet disks, which are stacked on top of one another. Such self-assemblies describe not only the basic structural motif of G-quadruplexes formed by, e.g., telomeric DNA sequences, but are also interesting targets for supramolecular chemistry and nanotechnology. The G-quartet stacks serve as an excellent model to understand the fundamentals of their molecular self-association and to unveil their application spectrum. However, the thermodynamic stability of such self-assemblies over an extended temperature and pressure range is largely unexplored. Here, we report a combined FTIR and NMR study on the temperature and pressure stability of G-quartet stacks formed by disodium guanosine 5′-monophosphate (Na25′-GMP). We found that under abyssal conditions, where temperatures as low as 5 °C and pressures up to 1 kbar are reached, the self-association of Na25′-GMP is most favoured. Beyond those conditions, the G-quartet stacks dissociate laterally into monomer stacks without significantly changing the longitudinal dimension. Among the tested alkali cations, K+ is the most efficient one to elevate the temperature as well as the pressure limits of GMP self-assembly.
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Affiliation(s)
- Mimi Gao
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Balasubramanian Harish
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, United States
| | - Melanie Berghaus
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Rana Seymen
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Loana Arns
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Scott A McCallum
- NMR Facility Center for Biotechnology and Interdisciplinary Science, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Catherine A Royer
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, United States
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany.
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184
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Scalabrin M, Palumbo M, Richter SN. Highly Improved Electrospray Ionization-Mass Spectrometry Detection of G-Quadruplex-Folded Oligonucleotides and Their Complexes with Small Molecules. Anal Chem 2017; 89:8632-8637. [PMID: 28787153 PMCID: PMC5588092 DOI: 10.1021/acs.analchem.7b01282] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
G-quadruplexes
are nucleic acids structures stabilized by physiological
concentration of potassium ions. Because low stability G-quadruplexes
are hardly detectable by mass spectrometry, we optimized solvent conditions:
isopropanol in a triethylamine/hexafluoroisopropanol mixture highly
increased G-quadruplex sensitivity with no modification of the physiological
G-quadruplex conformation. G-quadruplexes/G-quadruplex-ligand complexes
were also correctly detected at concentration as low as 40 nM. Detection
of the physiological conformation of G4s and their complexes opens
up the possibility to perform high-throughput screening of G-quadruplex
ligands for the development of drug molecules effective against critical
human diseases.
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Affiliation(s)
- Matteo Scalabrin
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua , via Marzolo 5, 35131 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
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185
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Qian C, Fu H, Kovalchik KA, Li H, Chen DDY. Specific Binding Constant and Stoichiometry Determination in Free Solution by Mass Spectrometry and Capillary Electrophoresis Frontal Analysis. Anal Chem 2017; 89:9483-9490. [DOI: 10.1021/acs.analchem.7b02443] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Cheng Qian
- National
and Local Joint Engineering Research Center of Biomedical Functional
Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional
Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
- Department
of Chemistry, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Hengqing Fu
- National
and Local Joint Engineering Research Center of Biomedical Functional
Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional
Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Kevin A. Kovalchik
- Department
of Chemistry, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Huihui Li
- National
and Local Joint Engineering Research Center of Biomedical Functional
Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional
Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - David Da Yong Chen
- National
and Local Joint Engineering Research Center of Biomedical Functional
Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional
Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
- Department
of Chemistry, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
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186
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Selvam S, Mandal S, Mao H. Quantification of Chemical and Mechanical Effects on the Formation of the G-Quadruplex and i-Motif in Duplex DNA. Biochemistry 2017; 56:4616-4625. [PMID: 28738141 DOI: 10.1021/acs.biochem.7b00279] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The formation of biologically significant tetraplex DNA species, such as G-quadruplexes and i-motifs, is affected by chemical (ions and pH) and mechanical [superhelicity (σ) and molecular crowding] factors. Because of the extremely challenging experimental conditions, the relative importance of these factors on tetraplex folding is unknown. In this work, we quantitatively evaluated the chemical and mechanical effects on the population dynamics of DNA tetraplexes in the insulin-linked polymorphic region using magneto-optical tweezers. By mechanically unfolding individual tetraplexes, we found that ions and pH have the largest effects on the formation of the G-quadruplex and i-motif, respectively. Interestingly, superhelicity has the second largest effect followed by molecular crowding conditions. While chemical effects are specific to tetraplex species, mechanical factors have generic influences. The predominant effect of chemical factors can be attributed to the fact that they directly change the stability of a specific tetraplex, whereas the mechanical factors, superhelicity in particular, reduce the stability of the competing species by changing the kinetics of the melting and annealing of the duplex DNA template in a nonspecific manner. The substantial dependence of tetraplexes on superhelicity provides strong support that DNA tetraplexes can serve as topological sensors to modulate fundamental cellular processes such as transcription.
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Affiliation(s)
- Sangeetha Selvam
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
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187
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Siebenmorgen T, Zacharias M. Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations. Biophys J 2017; 112:2280-2290. [PMID: 28591601 DOI: 10.1016/j.bpj.2017.04.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/12/2017] [Accepted: 04/24/2017] [Indexed: 11/29/2022] Open
Abstract
Telomeric DNA consists of tandem repeats of the sequence d(TTAGGG) that form G-quadruplex structures made of stacked guanines with monovalent cations bound at a central cavity. Although different ions can stabilize a G-quadruplex structure, the preferred bound ions are typically K+ or Na+. Several different strand-folding topologies have been reported for Q-quadruplexes formed from telomeric repeats depending on DNA length and ion solution condition. This suggests a possible dependence of the ion selectivity of the central pore on the folding topology of the quadruplex. Molecular dynamics free energy perturbation has been employed to systematically study the relative affinity of the central quadruplex pore for different cation types and the associated energetic and solvation contributions to ion selectivity. The calculations have been performed on two different common quadruplex folding topologies. For both topologies, the same ion selectivity was found with a preference for K+ followed by Rb+ and Na+, which agrees with the experimentally determined preference for most investigated quadruplexes. The selectivity is determined by a balance between attractive Coulomb interactions and loss of hydration but also modulated by van der Waals contributions. Specificity is mediated by the central guanines and no significant contribution of the nucleic acid backbone. The simulations indicate that different topologies might be stabilized by ions bound at the surface or alternative sites of the quadruplex because the ion specificity of the central pore does not depend on the strand folding topology.
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Affiliation(s)
- Till Siebenmorgen
- Physics Department, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany.
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188
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Yadav K, Meka PNR, Sadhu S, Guggilapu SD, Kovvuri J, Kamal A, Srinivas R, Devayani P, Babu BN, Nagesh N. Telomerase Inhibition and Human Telomeric G-Quadruplex DNA Stabilization by a β-Carboline-Benzimidazole Derivative at Low Concentrations. Biochemistry 2017; 56:4392-4404. [PMID: 28737386 DOI: 10.1021/acs.biochem.7b00008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Guanine rich regions in DNA, which can form highly stable secondary structures, namely, G-quadruplex or G4 DNA structures, affect DNA replication and transcription. Molecules that stabilize G4 DNA have become important in recent years. In this study, G4 DNA stabilization, inhibition of telomerase, and anticancer activity of synthetic β-carboline-benzimidazole derivatives (5a, 5d, 5h, and 5r) were studied. Among them, derivatives containing a 4-methoxyphenyl ring at C1 and a 6-methoxy-substituted benzimidazole at C3 (5a) were found to stabilize telomeric G-quadruplex DNA efficiently. The stoichiometry and interaction of a synthetic, β-carboline-benzimidazole derivative, namely, 3-(6-methoxy-1H-benzo[d]imidazol-2-yl)-1-(4-methoxyphenyl)-9H-pyrido[3,4-b]indole (5a), with human intermolecular G-quadruplex DNA at low concentrations were examined using electrospray ionization mass spectrometry. Spectroscopy techniques indicate that 5a may intercalate between the two stacks of G-quadruplex DNA. This model is supported by docking studies. When cancer cells are treated with 5a, the cell cycle arrest occurs at the sub-G1 phase. In addition, an apoptosis assay and fluorescence microscopy studies using cancer cells indicate that 5a can induce apoptosis. Results of biochemical assays such as the polymerase chain reaction stop assay and telomerase activity assay indicate that 5a has the potential to stabilize G-quadruplex DNA, and thereby, it may interfere with in vitro DNA synthesis and decrease telomerase activity. The results of this study reveal that the β-carboline-benzimidazole derivative (5a) is efficient in G-quadruplex DNA stabilization over double-stranded DNA, inhibits telomerase activity, and induces apoptosis in cancer cells.
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Affiliation(s)
- Kranthikumar Yadav
- Analytical Chemistry and Mass Spectrometry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Penchala Narasimha Rao Meka
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Sudeshna Sadhu
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
| | - Sravanthi Devi Guggilapu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Jeshma Kovvuri
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Ahmed Kamal
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India.,Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Ragampeta Srinivas
- Analytical Chemistry and Mass Spectrometry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Panuganti Devayani
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
| | - Bathini Nagendra Babu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Narayana Nagesh
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
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189
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Kshirsagar R, Khan K, Joshi MV, Hosur RV, Muniyappa K. Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks. Biophys J 2017; 112:2056-2074. [PMID: 28538144 DOI: 10.1016/j.bpj.2017.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022] Open
Abstract
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.
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Affiliation(s)
- Rucha Kshirsagar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Krishnendu Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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190
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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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191
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McAninch DS, Heinaman AM, Lang CN, Moss KR, Bassell GJ, Rita Mihailescu M, Evans TL. Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR. MOLECULAR BIOSYSTEMS 2017; 13:1448-1457. [PMID: 28612854 PMCID: PMC5544254 DOI: 10.1039/c7mb00070g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
G quadruplex structures have been predicted by bioinformatics to form in the 5'- and 3'-untranslated regions (UTRs) of several thousand mature mRNAs and are believed to play a role in translation regulation. Elucidation of these roles has primarily been focused on the 3'-UTR, with limited focus on characterizing the G quadruplex structures and functions in the 5'-UTR. Investigation of the affinity and specificity of RNA binding proteins for 5'-UTR G quadruplexes and the resulting regulatory effects have also been limited. Among the mRNAs predicted to form a G quadruplex structure within the 5'-UTR is the survival motor neuron domain containing 1 (SMNDC1) mRNA, encoding a protein that is critical to the spliceosome. Additionally, this mRNA has been identified as a potential target of the fragile X mental retardation protein (FMRP), whose loss of expression leads to fragile X syndrome. FMRP is an RNA binding protein involved in translation regulation that has been shown to bind mRNA targets that form G quadruplex structures. In this study we have used biophysical methods to investigate G quadruplex formation in the 5'-UTR of SMNDC1 mRNA and analyzed its interactions with FMRP. Our results show that SMNDC1 mRNA 5'-UTR forms an intramolecular, parallel G quadruplex structure comprised of three G quartet planes, which is bound specifically by FMRP both in vitro and in mouse brain lysates. These findings suggest a model by which FMRP might regulate the translation of a subset of its mRNA targets by recognizing the G quadruplex structure present in their 5'-UTR, and affecting their accessibility by the protein synthesis machinery.
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Affiliation(s)
- Damian S McAninch
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA.
| | - Ashley M Heinaman
- Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
| | - Cara N Lang
- Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
| | - Kathryn R Moss
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA.
| | - Timothy L Evans
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA. and Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
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192
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Kendrick S, Muranyi A, Gokhale V, Hurley LH, Rimsza LM. Simultaneous Drug Targeting of the Promoter MYC G-Quadruplex and BCL2 i-Motif in Diffuse Large B-Cell Lymphoma Delays Tumor Growth. J Med Chem 2017; 60:6587-6597. [PMID: 28605593 DOI: 10.1021/acs.jmedchem.7b00298] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Secondary DNA structures are uniquely poised as therapeutic targets due to their molecular switch function in turning gene expression on or off and scaffold-like properties for protein and small molecule interaction. Strategies to alter gene transcription through these structures thus far involve targeting single DNA conformations. Here we investigate the feasibility of simultaneously targeting different secondary DNA structures to modulate two key oncogenes, cellular-myelocytomatosis (MYC) and B-cell lymphoma gene-2 (BCL2), in diffuse large B-cell lymphoma (DLBCL). Cotreatment with previously identified ellipticine and pregnanol derivatives that recognize the MYC G-quadruplex and BCL2 i-motif promoter DNA structures lowered mRNA levels and subsequently enhanced sensitivity to a standard chemotherapy drug, cyclophosphamide, in DLBCL cell lines. In vivo repression of MYC and BCL2 in combination with cyclophosphamide also significantly slowed tumor growth in DLBCL xenograft mice. Our findings demonstrate concurrent targeting of different DNA secondary structures offers an effective, precise, medicine-based approach to directly impede transcription and overcome aberrant pathways in aggressive malignancies.
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Affiliation(s)
- Samantha Kendrick
- Department of Pathology, University of Arizona , 1501 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Andrea Muranyi
- Ventana Medical Systems, Inc. , 1910 Innovation Park Drive, Tucson, Arizona 85755, United States
| | - Vijay Gokhale
- BIO5 Institute, University of Arizona , 1657 East Helen Street, Tucson, Arizona 85721, United States
| | - Laurence H Hurley
- College of Pharmacy, University of Arizona , 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Lisa M Rimsza
- Department of Pathology, University of Arizona , 1501 North Campbell Avenue, Tucson, Arizona 85724, United States.,Mayo Clinic, 13400 East Shea Boulevard, Scottsdale, Arizona 85259, United States
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193
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Trachman RJ, Truong L, Ferré-D'Amaré AR. Structural Principles of Fluorescent RNA Aptamers. Trends Pharmacol Sci 2017; 38:928-939. [PMID: 28728963 DOI: 10.1016/j.tips.2017.06.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/21/2017] [Accepted: 06/21/2017] [Indexed: 11/26/2022]
Abstract
Several aptamer RNAs have been selected in vitro that bind to otherwise weakly fluorescent small molecules and enhance their fluorescence several thousand-fold. By genetically tagging cellular RNAs of interest with these aptamers and soaking cells in their cell-permeable cognate small-molecule fluorophores, it is possible to use them to study RNA localization and trafficking. These aptamers have also been fused to metabolite-binding RNAs to generate fluorescent biosensors. The 3D structures of three unrelated fluorogenic RNAs have been determined, and reveal a shared reliance on base quadruples (tetrads) to constrain the photo-excited chromophore. The structural diversity of fluorogenic RNAs and the chemical diversity of potential fluorophores to be activated are likely to yield a variety of future fluorogenic RNA tags that are optimized for different applications in RNA imaging and in the design of fluorescent RNA biosensors.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Lynda Truong
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
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194
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Bay DH, Busch A, Lisdat F, Iida K, Ikebukuro K, Nagasawa K, Karube I, Yoshida W. Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands. BMC Mol Biol 2017; 18:17. [PMID: 28655335 PMCID: PMC5488298 DOI: 10.1186/s12867-017-0094-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/23/2017] [Indexed: 12/29/2022] Open
Abstract
Background G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay. Results When G-quadruplex-forming sequences from the Dele and Cdc6 genes have been cloned in reporter vectors carrying a minimal promoter and the luciferase gene, luciferase expression is activated. This has also been detected in experiments applying a promoterless reporter vector. Mutational analysis reveals that guanine bases, which form the G-tetrads, are important in the activation. In addition, the activation has been found to decrease by the telomestatin derivative L1H1-7OTD which can bind to the G-quadruplex DNA. When Dele and Cdc6 CpG islands, containing the G-quadruplex-forming sequence, have been cloned in the promoterless reporter vector, the luciferase expression is activated. Mutational analysis reveals that the expression level is decreased by mutation on Dele G-quadruplex; however, increased by mutation on Cdc6 G-quadruplex. Conclusion Dele and Cdc6 G-quadruplex formation is significant in the transcriptional regulation. Dele and Cdc6 G-quadruplex DNA alone possess enhancer and promotor function. When studied in more complex CpG islands Dele G-quadruplex also demonstrates promotor activity, whereas Cdc6 G-quadruplex may possess a dual function of transcriptional regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12867-017-0094-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniyah H Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Annika Busch
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Fred Lisdat
- Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Keisuke Iida
- Graduate School of Science and Engineering, Saitama University, c/o Saitama Cancer Center, Saitama, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
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195
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Kshirsagar R, Ghodke I, Muniyappa K. Saccharomyces cerevisiae Red1 protein exhibits nonhomologous DNA end-joining activity and potentiates Hop1-promoted pairing of double-stranded DNA. J Biol Chem 2017. [PMID: 28642366 DOI: 10.1074/jbc.m117.796425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elucidation of the function of synaptonemal complex (SC) in Saccharomyces cerevisiae has mainly focused on in vivo analysis of recombination-defective meiotic mutants. Consequently, significant gaps remain in the mechanistic understanding of the activities of various SC proteins and the functional relationships among them. S. cerevisiae Hop1 and Red1 are essential structural components of the SC axial/lateral elements. Previous studies have demonstrated that Hop1 is a structure-selective DNA-binding protein exhibiting high affinity for the Holliday junction and promoting DNA bridging, condensation, and pairing between double-stranded DNA molecules. However, the exact mode of action of Red1 remains unclear, although it is known to interact with Hop1 and to suppress the spore viability defects of hop1 mutant alleles. Here, we report the purification and functional characterization of the full-length Red1 protein. Our results revealed that Red1 forms a stable complex with Hop1 in vitro and provided quantitative insights into their physical interactions. Mechanistically, Red1 preferentially associated with the Holliday junction and 3-way junction rather than with single- or double-stranded DNA with overhangs. Although Hop1 and Red1 exhibited similar binding affinities toward several DNA substrates, the two proteins displayed some significant differences. Notably, Red1, by itself, lacked DNA-pairing ability; however, it potentiated Hop1-promoted intermolecular pairing between double-stranded DNA molecules. Moreover, Red1 exhibited nonhomologous DNA end-joining activity, thus revealing an unexpected role for Red1 in recombination-based DNA repair. Collectively, this study presents the first direct insights into Red1's mode of action and into the mechanism underlying its role in chromosome synapsis and recombination.
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Affiliation(s)
- Rucha Kshirsagar
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Indrajeet Ghodke
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - K Muniyappa
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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196
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Dey S, Rühl CL, Jäschke A. Catalysis of Michael Additions by Covalently Modified G-Quadruplex DNA. Chemistry 2017; 23:12162-12170. [DOI: 10.1002/chem.201700632] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Surjendu Dey
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; 69120 Heidelberg Germany
| | - Carmen L. Rühl
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology; Heidelberg University; 69120 Heidelberg Germany
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197
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The Effects of Replication Stress on S Phase Histone Management and Epigenetic Memory. J Mol Biol 2017; 429:2011-2029. [DOI: 10.1016/j.jmb.2016.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 12/14/2022]
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198
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Trachman RJ, Demeshkina NA, Lau MWL, Panchapakesan SSS, Jeng SCY, Unrau PJ, Ferré-D'Amaré AR. Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nat Chem Biol 2017; 13:807-813. [PMID: 28553947 PMCID: PMC5550021 DOI: 10.1038/nchembio.2392] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/22/2017] [Indexed: 02/08/2023]
Abstract
Genetically encoded fluorescent protein tags revolutionized proteome studies, while the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1-Biotin (Kd ~3 nM), and in complex with related ligands, is one of the most red-shifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1.7 Å resolution co-crystal structure. Unexpectedly, the entire ligand, including TO, biotin, and the linker connecting them, abuts one of the near-planar faces of the three-tiered G-quadruplex. The two heterocycles of TO are held in place by two loop adenines and make a 45° angle with respect to each other. Minimizing this angle would increase quantum yield and further improve this tool for in vivo RNA visualization.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Natalia A Demeshkina
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Matthew W L Lau
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | | | - Sunny C Y Jeng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
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199
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Islam B, Stadlbauer P, Gil-Ley A, Pérez-Hernández G, Haider S, Neidle S, Bussi G, Banas P, Otyepka M, Sponer J. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. J Chem Theory Comput 2017; 13:2458-2480. [PMID: 28475322 PMCID: PMC5514396 DOI: 10.1021/acs.jctc.7b00226] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
We
have carried out a series of extended unbiased molecular dynamics
(MD) simulations (up to 10 μs long, ∼162 μs in
total) complemented by replica-exchange with the collective variable
tempering (RECT) approach for several human telomeric DNA G-quadruplex
(GQ) topologies with TTA propeller loops. We used different AMBER
DNA force-field variants and also processed simulations by Markov
State Model (MSM) analysis. The slow conformational transitions in
the propeller loops took place on a scale of a few μs, emphasizing
the need for long simulations in studies of GQ dynamics. The propeller
loops sampled similar ensembles for all GQ topologies and for all
force-field dihedral-potential variants. The outcomes of standard
and RECT simulations were consistent and captured similar spectrum
of loop conformations. However, the most common crystallographic loop
conformation was very unstable with all force-field versions. Although
the loss of canonical γ-trans state of the
first propeller loop nucleotide could be related to the indispensable
bsc0 α/γ dihedral potential, even supporting this particular
dihedral by a bias was insufficient to populate the experimentally
dominant loop conformation. In conclusion, while our simulations were
capable of providing a reasonable albeit not converged sampling of
the TTA propeller loop conformational space, the force-field description
still remained far from satisfactory.
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Affiliation(s)
- Barira Islam
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Guillermo Pérez-Hernández
- Department for Mathematics and Computer Science, Freie Universität Berlin , Arnimallee 6, Berlin 14195, Germany
| | - Shozeb Haider
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Pavel Banas
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
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200
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Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions. Nat Commun 2017; 8:15355. [PMID: 28513602 PMCID: PMC5442326 DOI: 10.1038/ncomms15355] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/23/2017] [Indexed: 12/13/2022] Open
Abstract
Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical families, G-quadruplexes and i-motifs, that have been a focus of intense research due to their potential biological impact in G- and C-rich DNA regions, respectively. High-resolution structures determined by solution-state nuclear magnetic resonance (NMR) spectroscopy demonstrate that AGCGA-quadruplexes comprise four 5′-AGCGA-3′ tracts and are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets, respectively. Residues in the core of the structure are connected with edge-type loops. Sequences of alternating 5′-AGCGA-3′ and 5′-GGG-3′ repeats could be expected to form G-quadruplexes, but are shown herein to form AGCGA-quadruplexes instead. Unique structural features of AGCGA-quadruplexes together with lower sensitivity to cation and pH variation imply their potential biological relevance in regulatory regions of genes responsible for basic cellular processes that are related to neurological disorders, cancer and abnormalities in bone and cartilage development. DNA tetrahelical structures such as G-quadruplexes are known to play important roles in DNA replication and repair. Here the authors present the structure of 5′-AGCGA-3′-quadruplexes enriched in genetic regulatory regions.
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