Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Sci Rep
2013 Jan 01;3:1811. doi: 10.1038/srep01811.
Show Gene links
Show Anatomy links
Existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy.
Yuan L
,
Tian T
,
Chen Y
,
Yan S
,
Xing X
,
Zhang Z
,
Zhai Q
,
Xu L
,
Wang S
,
Weng X
,
Yuan B
,
Feng Y
.
???displayArticle.abstract???
Existence of G-quadruplex DNA in vivo always attract widespread interest in the field of biology and biological chemistry. We reported our findings for the existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy. Probes for selective G-quadruplex cross-linking was designed and synthesized that show high selectivity for G-quadruplex cross-linking. Further biological studies demonstrated its good inhibition activity against murine melanoma cells. To further investigate if G-quadruplex DNA was formed in vivo and as the target, a derivative was synthesized and pull-down process toward chromosome DNAs combined with circular dichroism and high throughput deep sequencing were performed. Several simulated intracellular conditions, including X. laevis oocytes, Ficoll 70 and PEG, was used to investigate the compound's pure cross-linking ability upon preformed G-quadruplex. Thus, as a potent G-quadruplex cross-linking agent, our strategy provided both valuable evidence of G-quadruplex structures in vivo and intense potential in anti-cancer therapy.
Figure 1. a) Structures of compound 1 and o-quinone intermediate induced by tyrosinase. b) CD spectra of Pu27 DNA (20â μM) in 10â mM Tris/HCl buffer at pH 7.0 in the absence or presence of compound 1 ([compound 1]/[DNA strand] = 5) without or with incubation with tyrosinase (400 Units) at 37°C for 1â h. c) CD melting of Pu27 DNA curves in the presence of compound 1 ([compound 1]/[DNA strand] = 5) without or with incubation with tyrosinase (400 Units) at 37°C for 1â h, as monitored by the CD intensity at 265â nm. Tm values of the two G-quadruplexes are 30.3°C and 59.9°C, respectively.
Figure 2. a) Concentration dependence of compound 1 for tyrosinase oxidation DNA alkylating were incubated with 5â²-end TAMRA labeled Pu27 DNA in 10â mM Tris/HCl buffer at pH 7.0 for 1â h at 37°C. The amounts of labeled DNA and tyrosinase were fixed as 10â pmol and 40 Units, respectively. Lane 1â3 are control lanes, lane 4â11 are increasing concentrations of compound 1 (10â μM, 20â μM, 50â μM, 0.1â mM, 0.2â mM, 0.5â mM, 1â mM, 2â mM) incubation with labeled Pu27 DNA and tyrosinase (40 Units). The alkylated oligo was separated from the nonreacted DNA by 20% denaturing polyacrylamide gel. b) Compound 1 (1â mM) was incubated with labeled Pu27 DNA (10â pmol) and tyrosinase (40â Units) in the presence of increasing molar ratios (0.5, 1, 2, 5, 10) of unlabeled Pu27 DNA(G4) or unlabeled ds-Pu27 DNA(double-stranded, ds) for 1 h at 37°C. The alkylated oligo was separated from the nonreacted DNA by 20% denaturing polyacrylamide gel. âCâ refers to labeled Pu27 DNA (10â pmol) treated at 37°C for 1â h, and âRâ refers to the Pu27-compound 1 reaction product in the absence of any competitor DNA.
Figure 3. a) Analysis of cross-linking G-quadruplex in the presence of complementary strand of Pu27 DNA (Pu27-c) in 10â mM Tris/HCl buffer at pH 7.0 and 10â mM KCl by 20% polyacrylamide gel. Lane 1: labeled Pu27 DNA (10â pmol) treated at 37°C for 1â h in 10â mM KCl; lane 2: control lane without tyrosinase and compound 1; lane 3: control lane only with tyrosinase and without the compound 1; lane 4: control lane only with compound 1 and without the tyrosinase; lane 5: compound 1 (2â mM) incubation with labeled Pu27 DNA (10â pmol) and tyrosinase (40â Uints) in the presence of excess of Pu27-c (20â pmol). b) CD spectrum for examining the structural features of the cross-linked complex which was extracted from gel. c) CD melting curves of the cross-linked complex as monitored by the CD intensity at 265â nm. d) MALDI-TOF MS spectrum of the cross-linked complex, calcd. [M + Na-2H]â 9649.77, found: 9648.32. e) MALDI-TOF MS spectrum of the cross-linked complex degradation products by DNase I, calcd. [M + H]+ 1037.52, found: 1037.57.
Figure 4. Western Blot was used to determine the expression of c-myc gene in the B16-F1 cells treated with compound 1.The cells were treated with medium (Line 1) and increasing concentrations of compound 1(20, 40 and 50â μM) for 3â days, and the total protein was extracted and subjected to Western Blot for c-Myc, and β-actin (control).
Figure 5. a) Experimental design for detecting formation of G-quadruplexes and sequencing in oncogene promoters in B16-F1 cells. b)1.5% agarose gel. Lane 1: DNA ladder and lane 2: approximately 100â bp sonicated in genomic DNA. c) CD spectrum of genomic DNA short fragments which was extracted from B16-F1 cells in the absence or presence of compound 1a (40â μM) for 3d.
Figure 6. G-quadruplex formation in long dsDNA carrying G-quadruplex-forming sequence from the c-myc gene examined by native gel electrophoresis.a) DNA samples were loaded on 8% polyacrylamide gel containing 150â mM KCl, 40% (w/v) PEG 200 and electrophoresed at in 1à TBE buffer containing 150â mM KCl. Lane 1:c-myc and c-myc-c without PEG; Lane 2: c-myc and c-myc-c with PEG; Lane 3 and 4 are control lanes, c-myc and c-myc-c incubation with compound 1a (2â mM) or tyrosinase (40â Units); lane 5-10 are increasing concentrations of compound 1a (100â μM, 200â μM, 500â μM, 1â mM, 2â mM) incubation with c-myc and c-myc-c in the presence of tyrosinase (40â Units); Lane 10: c-myc-c only. All samples contain 150â mM KCl. b) DNA samples were loaded on 8% polyacrylamide gel containing 40% (w/v) PEG 200 and electrophoresed at in 1à TBE buffer. Lane 1: c-myc-c only; Lane 2: c-myc and c-myc-c without PEG; Lane 3: c-myc and c-myc-c with PEG; Lane 4 and 5 are control lanes, c-myc and c-myc-c incubation with compound 1a (2â mM) or tyrosinase (40 Units); lane 6-8 are increasing concentrations of compound 1a (500â μM, 1â mM, 2â mM) incubation with c-myc and c-myc-c in the presence of tyrosinase (40â Units), All samples were free off KCl.
Anderson,
Shotgun DNA sequencing using cloned DNase I-generated fragments.
1981, Pubmed
Anderson,
Shotgun DNA sequencing using cloned DNase I-generated fragments.
1981,
Pubmed
Bai,
Highly selective suppression of melanoma cells by inducible DNA cross-linking agents: bis(catechol) derivatives.
2010,
Pubmed
Balasubramanian,
Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?
2011,
Pubmed
Biffi,
Quantitative visualization of DNA G-quadruplex structures in human cells.
2013,
Pubmed
Bugaut,
Exploring the differential recognition of DNA G-quadruplex targets by small molecules using dynamic combinatorial chemistry.
2008,
Pubmed
Cederberg,
DNA damage detected by the alkaline comet assay in the liver of mice after oral administration of tetrachloroethylene.
2010,
Pubmed
Celli,
Role of GRP58 in mitomycin C-induced DNA cross-linking.
2003,
Pubmed
Cooney,
Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro.
1988,
Pubmed
Davis,
Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene.
1989,
Pubmed
Di Antonio,
Quinone methides tethered to naphthalene diimides as selective G-quadruplex alkylating agents.
2009,
Pubmed
Doria,
Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures.
2012,
Pubmed
Drygin,
Anticancer activity of CX-3543: a direct inhibitor of rRNA biogenesis.
2009,
Pubmed
Ghani,
New potent inhibitors of tyrosinase: novel clues to binding of 1,3,4-thiadiazole-2(3H)-thiones, 1,3,4-oxadiazole-2(3H)-thiones, 4-amino-1,2,4-triazole-5(4H)-thiones, and substituted hydrazides to the dicopper active site.
2010,
Pubmed
Grand,
The cationic porphyrin TMPyP4 down-regulates c-MYC and human telomerase reverse transcriptase expression and inhibits tumor growth in vivo.
2002,
Pubmed
Hänsel,
The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions.
2011,
Pubmed
,
Xenbase
Huppert,
Prevalence of quadruplexes in the human genome.
2005,
Pubmed
Ito,
Inhibition of translation by small RNA-stabilized mRNA structures in human cells.
2011,
Pubmed
Karsisiotis,
Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism.
2011,
Pubmed
Kudugunti,
Biochemical mechanism of caffeic acid phenylethyl ester (CAPE) selective toxicity towards melanoma cell lines.
2010,
Pubmed
Müller,
Small-molecule-mediated G-quadruplex isolation from human cells.
2010,
Pubmed
Nadai,
Naphthalene diimide scaffolds with dual reversible and covalent interaction properties towards G-quadruplex.
2011,
Pubmed
Ou,
Inhibition of cell proliferation by quindoline derivative (SYUIQ-05) through its preferential interaction with c-myc promoter G-quadruplex.
2011,
Pubmed
Ou,
G-quadruplexes: targets in anticancer drug design.
2008,
Pubmed
Phan,
Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter.
2004,
Pubmed
Reyes-Gutiérrez,
Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature.
2016,
Pubmed
Rodriguez,
Ligand-driven G-quadruplex conformational switching by using an unusual mode of interaction.
2007,
Pubmed
Rodriguez,
Small-molecule-induced DNA damage identifies alternative DNA structures in human genes.
2012,
Pubmed
Salavati-Niasari,
Synthesis, characterization and catalytic oxidation of para-xylene by a manganese(III) Schiff base complex on functionalized multi-wall carbon nanotubes (MWNTs).
2010,
Pubmed
Schaffitzel,
In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei.
2001,
Pubmed
Seenisamy,
Design and synthesis of an expanded porphyrin that has selectivity for the c-MYC G-quadruplex structure.
2005,
Pubmed
Siddiqui-Jain,
Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription.
2002,
Pubmed
Siebenlist,
Chromatin structure and protein binding in the putative regulatory region of the c-myc gene in Burkitt lymphoma.
1984,
Pubmed
Slamon,
Expression of cellular oncogenes in human malignancies.
1984,
Pubmed
Song,
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
2011,
Pubmed
Wang,
Conformational switching of G-quadruplex DNA by photoregulation.
2010,
Pubmed
Wang,
A potent, water-soluble and photoinducible DNA cross-linking agent.
2003,
Pubmed
Weng,
Synthesis and biological studies of inducible DNA cross-linking agents.
2007,
Pubmed
Xu,
Click chemistry for the identification of G-quadruplex structures: discovery of a DNA-RNA G-quadruplex.
2009,
Pubmed
Yang,
Engineering bisquinolinium/thiazole orange conjugates for fluorescent sensing of G-quadruplex DNA.
2009,
Pubmed
Ye,
Screening of Chinese herbal medicines for antityrosinase activity in a cell free system and B16 cells.
2010,
Pubmed
Yuan,
Corrigendum: Existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy.
2018,
Pubmed
Yue,
Transcriptional regulation by small RNAs at sequences downstream from 3' gene termini.
2010,
Pubmed
Zahler,
Inhibition of telomerase by G-quartet DNA structures.
1991,
Pubmed
Zheng,
Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA.
2010,
Pubmed