1
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Wang Z, Cao Y, Yu Z, Tian Y, Ren J, Liu W, Fan L, Zhang Q, Cao C. High-resolution nucleic acid detection using online polyacrylamide gel electrophoresis platform. J Chromatogr A 2024; 1713:464571. [PMID: 38091846 DOI: 10.1016/j.chroma.2023.464571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/19/2023] [Accepted: 12/08/2023] [Indexed: 01/08/2024]
Abstract
Polyacrylamide gel electrophoresis (PAGE) is one of the most popular techniques for the separation and detection of nucleic acids. However, it requires a complicated detection procedure and offline detection format, which inevitably leads to band broadening and thus compromises the separation resolution. To overcome this problem, we developed an online PAGE (OPAGE) platform by integrating the gel electrophoresis apparatus with the gel imaging system, so as to obviate the need for the complicated detection procedure. Notably, OPAGE enabled the real-time monitoring of the separation process and the immediate imaging of the separation results once the electrophoresis ended. Using a series of synthetic DNAs with different lengths as samples, we demonstrated that the OPAGE platform enhanced 32-64 % of the number of theoretical plates, showed a robust dynamic range of 0.1-12.5 ng/μL, and realized a limit of detection as low as 0.08 ng/μL DNA. Based on our results, we anticipate that the OPAGE platform is a promising alternative to traditional nucleic acid gel electrophoresis for simple and high-resolution detection and quantification and nucleic acid.
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Affiliation(s)
- Zihao Wang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yiren Cao
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zixian Yu
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Youli Tian
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Life Science and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weiwen Liu
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liuyin Fan
- Student Innovation Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Qiang Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Chengxi Cao
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Life Science and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Interfacial behaviour of oligodeoxynucleotides prone to G-quadruplex formation on negatively charged electrode surface monitored by electrochemical probes. Electrochim Acta 2023. [DOI: 10.1016/j.electacta.2023.141878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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3
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Bansal A, Phogat P, Kukreti S. A novel G·G·T non-conventional intramolecular triplex formed by the double repeat sequence of Chlamydomonas telomeric DNA. RSC Adv 2022; 12:15918-15924. [PMID: 35733691 PMCID: PMC9134377 DOI: 10.1039/d2ra00861k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022] Open
Abstract
The competition among the DNA non-canonical structures has been widely studied in repetitive DNA sequences. The Chlamydomonas reinhardtii telomere (TTTTAGGG)n is found an exception to the general idea of forming folded G-quadruplex by few repeats of any telomeric sequence.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
- Department of Chemistry, Hansraj College, University of Delhi, (North Campus), Delhi, 110007, India
| | - Priyanka Phogat
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
| | - Shrikant Kukreti
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
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4
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Safitri FA, Tu ATT, Hoshi K, Shobo M, Zhao D, Witarto AB, Sumarsono SH, Giri-Rachman EA, Tsukakoshi K, Ikebukuro K, Yamazaki T. Enhancement of the Immunostimulatory Effect of Phosphodiester CpG Oligodeoxynucleotides by an Antiparallel Guanine-Quadruplex Structural Scaffold. Biomolecules 2021; 11:1617. [PMID: 34827615 PMCID: PMC8615816 DOI: 10.3390/biom11111617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 02/07/2023] Open
Abstract
Guanine-quadruplex-based CpG oligodeoxynucleotides (G4 CpG ODNs) have been developed as potent immunostimulatory agents with reduced sensitivity to nucleases. We designed new monomeric G4 ODNs with an antiparallel topology using antiparallel type duplex/G4 ODNs as robust scaffolds, and we characterized their topology and effects on cytokine secretion. Based on circular dichroism analysis and quantification of mRNA levels of immunostimulatory cytokines, it was found that monomeric antiparallel G4 CpG ODNs containing two CpG motifs in the first functional loop, named G2.0.0, could maintain antiparallel topology and generate a high level of immunostimulatory cytokines in RAW264 mouse macrophage-like cell lines. We also found that the flanking sequence in the CpG motif altered the immunostimulatory effects. Gc2c.0.0 and Ga2c.0.0 are monomeric antiparallel G4 CpG ODNs with one cytosine in the 3' terminal and one cytosine/adenine in the 5' terminal of CpG motifs that maintained the same resistance to degradation in serum as G2.0.0 and improved interleukin-6 production in RAW264 and bone marrow-derived macrophages. The immunostimulatory activity of antiparallel G4 CpG ODNs is superior to that of linear natural CpG ODNs. These results provide insights for the rational design of highly potent CpG ODNs using antiparallel G4 as a robust scaffold.
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Affiliation(s)
- Fika Ayu Safitri
- Doctoral Program in Biology, School of Life Sciences and Technology, Institut Teknologi Bandung (ITB), Bandung 40132, West Java, Indonesia;
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
| | - Anh Thi Tram Tu
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
- Division of Life Science, Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan
| | - Kazuaki Hoshi
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
| | - Miwako Shobo
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
| | - Dandan Zhao
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
| | - Arief Budi Witarto
- Department of Molecular Biology and Biochemistry, Faculty of Medicine, Indonesia Defense University, Bogor 16810, West Java, Indonesia;
| | - Sony Heru Sumarsono
- Physiology, Developmental Biology and Biomedical Sciences Research Group, School of Life Sciences and Technology, ITB, Bandung 40132, West Java, Indonesia; (S.H.S.); (E.A.G.-R.)
| | - Ernawati Arifin Giri-Rachman
- Physiology, Developmental Biology and Biomedical Sciences Research Group, School of Life Sciences and Technology, ITB, Bandung 40132, West Java, Indonesia; (S.H.S.); (E.A.G.-R.)
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan; (K.T.); (K.I.)
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan; (K.T.); (K.I.)
| | - Tomohiko Yamazaki
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
- Division of Life Science, Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan
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5
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Kejnovská I, Renčiuk D, Palacký J, Vorlíčková M. CD Study of the G-Quadruplex Conformation. Methods Mol Biol 2019; 2035:25-44. [PMID: 31444742 DOI: 10.1007/978-1-4939-9666-7_2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Circular Dichroic (CD) spectroscopy is one of the most frequently used methods for guanine quadruplex studies and in general for studies of conformational properties of nucleic acids. The reason is its high sensitivity to even slight changes in mutual orientation of absorbing bases of DNA. CD can reveal formation of particular structural DNA arrangements and can be used to search for the conditions stabilizing the structures, to follow the transitions between various structural states, to explore kinetics of their appearance, to determine thermodynamic parameters, and also to detect formation of higher order structures. CD spectroscopy is an important complementary technique to NMR spectroscopy and X-ray diffraction in quadruplex studies due to its sensitivity, easy manipulation of studied samples, and relative inexpensiveness. In this part, we present the protocol for the use of CD spectroscopy in the study of guanine quadruplexes, together with practical advice and cautions about various, particularly interpretation, difficulties.
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Affiliation(s)
- Iva Kejnovská
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Daniel Renčiuk
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Jan Palacký
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Michaela Vorlíčková
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
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6
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Benabou S, Aviñó A, Lyonnais S, González C, Eritja R, De Juan A, Gargallo R. i-motif structures in long cytosine-rich sequences found upstream of the promoter region of the SMARCA4 gene. Biochimie 2017; 140:20-33. [DOI: 10.1016/j.biochi.2017.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/06/2017] [Indexed: 12/27/2022]
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7
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8
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Zhou J, Bourdoncle A, Rosu F, Gabelica V, Mergny JL. Tri-G-Quadruplex: Controlled Assembly of a G-Quadruplex Structure from Three G-Rich Strands. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205390] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Zhou J, Bourdoncle A, Rosu F, Gabelica V, Mergny JL. Tri-G-quadruplex: controlled assembly of a G-quadruplex structure from three G-rich strands. Angew Chem Int Ed Engl 2012; 51:11002-5. [PMID: 23038222 DOI: 10.1002/anie.201205390] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Indexed: 12/17/2022]
Abstract
In my (DNA) dreams: A tri-G-quadruplex was constructed from three strands (T1-T3) of DNA using duplex formation to guide the G-rich tracts into close proximity with the addition of Li(+) ions (see scheme). The defined G-quadruplex structure was formed upon addition of Na(+) ions and characterized by gel electrophoresis and spectroscopy.
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Affiliation(s)
- Jun Zhou
- Univ. Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France
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10
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Payet L, Huppert JL. Stability and structure of long intramolecular G-quadruplexes. Biochemistry 2012; 51:3154-61. [PMID: 22417391 DOI: 10.1021/bi201750g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
G-quadruplexes are formed from guanine-rich sequences of DNA and RNA. They consist of stacks of square arrangements of guanines called G-quartets. Increasing evidence suggests that these structures are involved in cellular processes such as transcription or translation. Knowing their structure and their stability in vitro should help to predict their formation in vivo and to understand their biological functions. Many studies have been performed on isolated G-quadruplexes, but little attention has been given to their interactions. Here, we present non-denaturing gel electrophoresis, UV melting, and circular dichroism data obtained for long sequences of DNA which are capable of forming two simultaneous G-quadruplexes, namely, d(TG(3)T(3)G(3)T(3)G(3)T(3)G(3)T(n)G(3)T(3)G(3)T(3)G(3)T(3)G(3)T), with n varying from one to seven. These sequences can form up to two separate G-quadruplexes. We also study mutated versions of these sequences designed to form one G-quadruplex at specific positions on the strand. Comparing results from the original sequences and their mutated versions, we show that for the former different folded states coexist: either with six stacked G-quartets or only three, in various combinations. Which ones are favored depends on n. Moreover, for n greater than three, the thermodynamic stability stays constant, contrary to an expected decrease in stability if the six G-quartets were stacked together in a single structure. This result agrees with a beads-on-a-string folding model for long sequences of G-quadruplexes, where two adjacent G-quadruplexes fold independently.
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Affiliation(s)
- Linda Payet
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 OHE, UK.
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11
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De Rache A, Kejnovská I, Vorlíčková M, Buess-Herman C. Elongated thrombin binding aptamer: a G-quadruplex cation-sensitive conformational switch. Chemistry 2012; 18:4392-400. [PMID: 22362492 DOI: 10.1002/chem.201103381] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Indexed: 11/08/2022]
Abstract
Aptamer-based biosensors offer promising perspectives for high performance, specific detection of proteins. The thrombin binding aptamer (TBA) is a G-quadruplex-forming DNA sequence, which is frequently elongated at one end to increase its analytical performances in a biosensor configuration. Herein, we investigate how the elongation of TBA at its 5' end affects its structure and stability. Circular dichroism spectroscopy shows that TBA folds in an antiparallel G-quadruplex conformation with all studied cations (Ba(2+), Ca(2+), K(+), Mg(2+), Na(+), NH(4)(+), Sr(2+) and the [Ru(NH(3))(6)](2+/3+) redox marker) whereas other structures are adopted by the elongated aptamers in the presence of some of these cations. The stability of each structure is evaluated on the basis of UV spectroscopy melting curves. Thermal difference spectra confirm the quadruplex character of all conformations. The elongated sequences can adopt a parallel or an antiparallel structure, depending on the nature of the cation; this can potentially confer an ion-sensitive switch behavior. This switch property is demonstrated with the frequently employed redox complex [Ru(NH(3))(6)](3+), which induces the parallel conformation at very low concentrations (10 equiv per strand). The addition of large amounts of K(+) reverts the conformation to the antiparallel form, and opens interesting perspectives for electrochemical biosensing or redox-active responsive devices.
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Affiliation(s)
- Aurore De Rache
- Université Libre de Bruxelles, Faculté des Sciences, Service de Chimie Analytique et Chimie des Interfaces, CP 255, Boulevard du Triomphe 2, 1050 Bruxelles, Belgium
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12
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Dhamodharan V, Harikrishna S, Jagadeeswaran C, Halder K, Pradeepkumar PI. Selective G-quadruplex DNA Stabilizing Agents Based on Bisquinolinium and Bispyridinium Derivatives of 1,8-Naphthyridine. J Org Chem 2011; 77:229-42. [DOI: 10.1021/jo201816g] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- V. Dhamodharan
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - S. Harikrishna
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - C. Jagadeeswaran
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - K. Halder
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - P. I. Pradeepkumar
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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13
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Abstract
In most eukaryotes, telomeric DNA consists of repeats of a short motif that includes consecutive guanines and may hence fold into G-quadruplexes. Budding yeasts have telomeres composed of longer repeats and show variation in the degree of repeat homogeneity. Although telomeric sequences from several organisms have been shown to fold into G-quadruplexes in vitro, surprisingly, no study has been dedicated to the comparison of G-quadruplex folding and stability of known telomeric sequences. Furthermore, to our knowledge, folding of yeast telomeric sequences into intramolecular G-quadruplexes has never been investigated. Using biophysical and biochemical methods, we studied sequences mimicking about four repetitions of telomeric motifs from a variety of organisms, including yeasts, with the aim of comparing the G-quadruplex folding potential of telomeric sequences among eukaryotes. G-quadruplex folding did not appear to be a conserved feature among yeast telomeric sequences. By contrast, all known telomeric sequences from eukaryotes other than yeasts folded into G-quadruplexes. Nevertheless, while G(3)T(1-4)A repeats (found in a variety of organisms) and G(4)T(2,4) repeats (found in ciliates) folded into stable G-quadruplexes, G-quadruplexes formed by repetitions of G(2)T(2)A and G(2)CT(2)A motifs (found in many insects and in nematodes, respectively) appeared to be in equilibrium with non-G-quadruplex structures (likely hairpin-duplexes).
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Affiliation(s)
- Phong Lan Thao Tran
- INSERM, U565, Acides Nucléiques: Dynamique, Ciblage et Fonctions Biologiques, Muséum National d'Histoire Naturelle, CNRS, UMR7196, Département de Régulations, Développement et Diversité Moléculaire, 43 rue Cuvier, CP26, Paris Cedex 5 -75231, France
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Guédin A, Gros J, Alberti P, Mergny JL. How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Res 2010; 38:7858-68. [PMID: 20660477 PMCID: PMC2995061 DOI: 10.1093/nar/gkq639] [Citation(s) in RCA: 316] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compared here 80 different sequences containing four tracts of three guanines with loops of variable length (between 1 and 15 bases for unmodified sequences, up to 30 for fluorescently labeled oligonucleotides). All sequences were capable of forming stable quadruplexes, with Tm above physiological temperature in most cases. Unsurprisingly, the melting temperature was systematically lower in sodium than in potassium but the difference between both ionic conditions varied between 1 and >39°C (average difference: 18.3°C). Depending on the sequence context, and especially for G4 sequences involving two very short loops, the third one may be very long without compromising the stability of the quadruplex. A strong inverse correlation between total loop length and Tm was found in K+: each added base leads to a 2°C drop in Tm or ∼0.3 kcal/mol loss in ΔG°. The trend was less clear in Na+, with a longer than expected optimal loop length (up to 5 nt). This study will therefore extend the sequence repertoire of quadruplex-prone sequences, arguing for a modification of the widely used consensus (maximal loop size of 7 bases).
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Affiliation(s)
- Aurore Guédin
- INSERM, U869, European Institute of Chemistry and Biology, Bordeaux 2 University, 2 rue Robert Escarpit, Pessac F-33607, France
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15
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Gomez D, Guédin A, Mergny JL, Salles B, Riou JF, Teulade-Fichou MP, Calsou P. A G-quadruplex structure within the 5'-UTR of TRF2 mRNA represses translation in human cells. Nucleic Acids Res 2010; 38:7187-98. [PMID: 20571083 PMCID: PMC2978344 DOI: 10.1093/nar/gkq563] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Telomeres protect chromosome ends from being recognized as double-stranded breaks. Telomeric function is ensured by the shelterin complex in which TRF2 protein is an essential player. The G-rich strand of telomere DNA can fold into G-quadruplex (G4) structure. Small molecules stabilizing G4 structures, named G4 ligands, have been shown to alter telomeric functions in human cells. In this study, we show that a guanine-rich RNA sequence located in the 5′-UTR region of the TRF2 mRNA (hereafter 91TRF2G) is capable of forming a stable quadruplex that causes a 2.8-fold decrease in the translation of a reporter gene in human cells, as compared to a mutant 5′-UTR unable to fold into G4. We also demonstrate that several highly selective G4 ligands, the pyridine dicarboxamide derivative 360A and bisquinolinium compounds Phen-DC(3) and Phen-DC(6), are able to bind the 91TRF2G:RNA sequence and to modulate TRF2 protein translation in vitro. Since the naturally occurring 5′-UTR TRF2:RNA G4 element was used here, which is conserved in several vertebrate orthologs, the present data substantiate a potential translational mechanism mediated by a G4 RNA motif for the downregulation of TRF2 expression.
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Affiliation(s)
- Dennis Gomez
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, 31077 Toulouse, Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
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16
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Guédin A, Alberti P, Mergny JL. Stability of intramolecular quadruplexes: sequence effects in the central loop. Nucleic Acids Res 2009; 37:5559-67. [PMID: 19581426 PMCID: PMC2760802 DOI: 10.1093/nar/gkp563] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/16/2009] [Accepted: 06/17/2009] [Indexed: 01/06/2023] Open
Abstract
Hundreds of thousands of putative quadruplex sequences have been found in the human genome. It is important to understand the rules that govern the stability of these intramolecular structures. In this report, we analysed sequence effects in a 3-base-long central loop, keeping the rest of the quadruplex unchanged. A first series of 36 different sequences were compared; they correspond to the general formula GGGTTTGGGHNHGGGTTTGGG. One clear rule emerged from the comparison of all sequence motifs: the presence of an adenine at the first position of the loop was significantly detrimental to stability. In contrast, adenines have no detrimental effect when present at the second or third position of the loop. Cytosines may either have a stabilizing or destabilizing effect depending on their position. In general, the correlation between the T(m) or DeltaG degrees in sodium and potassium was weak. To determine if these sequence effects could be generalized to different quadruplexes, specific loops were tested in different sequence contexts. Analysis of 26 extra sequences confirmed the general destabilizing effect of adenine as the first base of the loop(s). Finally, analysis of some of the sequences by microcalorimetry (DSC) confirmed the differences found between the sequence motifs.
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Affiliation(s)
- Aurore Guédin
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 43 rue Cuvier, CP26, Paris Cedex 05, F-75231 and Muséum National d’Histoire Naturelle (MNHN) USM503, CNRS, UMR7196, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, 43 rue Cuvier, CP26, Paris Cedex 5, F-75231, France
| | - Patrizia Alberti
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 43 rue Cuvier, CP26, Paris Cedex 05, F-75231 and Muséum National d’Histoire Naturelle (MNHN) USM503, CNRS, UMR7196, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, 43 rue Cuvier, CP26, Paris Cedex 5, F-75231, France
| | - Jean-Louis Mergny
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 43 rue Cuvier, CP26, Paris Cedex 05, F-75231 and Muséum National d’Histoire Naturelle (MNHN) USM503, CNRS, UMR7196, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, 43 rue Cuvier, CP26, Paris Cedex 5, F-75231, France
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17
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Kumar N, Maiti S. A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes. Nucleic Acids Res 2008; 36:5610-22. [PMID: 18757890 PMCID: PMC2553590 DOI: 10.1093/nar/gkn543] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Loop length and its composition are important for the structural and functional versatility of quadruplexes. To date studies on the loops have mainly concerned model sequences compared with naturally occurring quadruplex sequences which have diverse loop lengths and compositions. Herein, we have characterized 36 quadruplex-forming sequences from the promoter regions of various proto-oncogenes using CD, UV and native gel electrophoresis. We examined folding topologies and determined the thermodynamic profile for quadruplexes varying in total loop length (5–18 bases) and composition. We found that naturally occurring quadruplexes have variable thermodynamic stabilities (ΔG37) ranging from −1.7 to −15.6 kcal/mol. Overall, our results suggest that both loop length and its composition affect quadruplex structure and thermodynamics, thus making it difficult to draw generalized correlations between loop length and thermodynamic stability. Additionally, we compared the thermodynamic stability of quadruplexes and their respective duplexes to understand quadruplex–duplex competition. Our findings invoke a discussion on whether biological function is associated with quadruplexes with lower thermodynamic stability which undergo facile formation and disruption, or by quadruplexes with high thermodynamic stability.
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Affiliation(s)
- Niti Kumar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Guédin A, De Cian A, Gros J, Lacroix L, Mergny JL. Sequence effects in single-base loops for quadruplexes. Biochimie 2008; 90:686-96. [DOI: 10.1016/j.biochi.2008.01.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 01/18/2008] [Indexed: 10/22/2022]
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Gros J, Rosu F, Amrane S, De Cian A, Gabelica V, Lacroix L, Mergny JL. Guanines are a quartet's best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes. Nucleic Acids Res 2007; 35:3064-75. [PMID: 17452368 PMCID: PMC1888817 DOI: 10.1093/nar/gkm111] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Parallel tetramolecular quadruplexes may be formed with short oligodeoxynucleotides bearing a block of three or more guanines. We analyze the properties of sequence variants of parallel quadruplexes in which each guanine of the central block was systematically substituted with a different base. Twelve types of substitutions were assessed in more than 100 different sequences. We conducted a comparative kinetic analysis of all tetramers. Electrospray mass spectrometry was used to count the number of inner cations, which is an indicator of the number of effective tetrads. In general, the presence of a single substitution has a strong deleterious impact on quadruplex stability, resulting in reduced quadruplex lifetime/thermal stability and in decreased association rate constants. We demonstrate extremely large differences in the association rate constants of these quadruplexes depending on modification position and type. These results demonstrate that most guanine substitutions are deleterious to tetramolecular quadruplex structure. Despite the presence of well-defined non-guanine base quartets in a number of NMR and X-ray structures, our data suggest that most non-guanine quartets do not participate favorably in structural stability, and that these quartets are formed only by virtue of the docking platform provided by neighboring G-quartets. Two notable exceptions were found with 8-bromo-guanine (X) and 6-methyl-isoxanthopterin (P) substitutions, which accelerate quadruplex formation by a factor of 10 when present at the 5′ end. The thermodynamic and kinetic data compiled here are highly valuable for the design of DNA quadruplex assemblies with tunable association/dissociation properties.
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Affiliation(s)
- Julien Gros
- Laboratoire de Biophysique, Muséum National d’Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France and Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie, Bat. B6c, B-4000 Liège, Belgium
| | - Frédéric Rosu
- Laboratoire de Biophysique, Muséum National d’Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France and Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie, Bat. B6c, B-4000 Liège, Belgium
| | - Samir Amrane
- Laboratoire de Biophysique, Muséum National d’Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France and Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie, Bat. B6c, B-4000 Liège, Belgium
| | - Anne De Cian
- Laboratoire de Biophysique, Muséum National d’Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France and Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie, Bat. B6c, B-4000 Liège, Belgium
| | - Valérie Gabelica
- Laboratoire de Biophysique, Muséum National d’Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France and Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie, Bat. B6c, B-4000 Liège, Belgium
| | - Laurent Lacroix
- Laboratoire de Biophysique, Muséum National d’Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France and Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie, Bat. B6c, B-4000 Liège, Belgium
| | - Jean-Louis Mergny
- Laboratoire de Biophysique, Muséum National d’Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France and Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie, Bat. B6c, B-4000 Liège, Belgium
- *To whom correspondence should be addressed. +33-1 40 79 36 89+33-1 40 79 37 05
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Cian AD, Mergny JL. Quadruplex ligands may act as molecular chaperones for tetramolecular quadruplex formation. Nucleic Acids Res 2007; 35:2483-93. [PMID: 17395639 PMCID: PMC1885647 DOI: 10.1093/nar/gkm098] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 02/03/2007] [Accepted: 02/03/2007] [Indexed: 11/24/2022] Open
Abstract
G-quadruplexes are a family of four-stranded DNA structures, stabilized by G-quartets, that form in the presence of monovalent cations. Efforts are currently being made to identify ligands that selectively bind to G-quadruplex motifs as these compounds may interfere with the telomere structure, telomere elongation/replication and proliferation of cancer cells. The kinetics of quadruplex-ligands interactions are poorly understood: it is not clear whether quadruplex ligands lock into the preformed structure (i.e. increase the lifetime of the structure by lowering the dissociation constant, k(off)) or whether ligands actively promote the formation of the complex and act as quadruplex chaperones by increasing the association constant, k(on). We studied the effect of a selective quadruplex ligand, a bisquinolinium pyridine dicarboxamide compound called 360A, to distinguish these two possibilities. We demonstrated that, in addition to binding to and locking into preformed quadruplexes, this molecule acted as a chaperone for tetramolecular complexes by acting on k(on). This observation has implications for in vitro and in vivo applications of quadruplexes and should be taken into account when evaluating the cellular responses to these agents.
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Affiliation(s)
| | - Jean-Louis Mergny
- Laboratoire de Biophysique, Muséum National d′Histoire Naturelle USM 503, INSERM UR 565, CNRS UMR 5153, 43 rue Cuvier, 75231 Paris cedex 05, France
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