Induction of parallel human telomeric G-quadruplex structures by Sr2+

Pedroso, Ilene M.; Duarte, Luís F.; Yanez, Giscard; Baker, Asmaa M.; Fletcher, Terace M.

doi:10.1016/j.bbrc.2007.04.126

Cited by 43 publications

(34 citation statements)

References 31 publications

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“…However, the spectrum for T7-all with TRF2 B exhibited a slight increase in intensity at ∼270 nm. This spectrum has some similarity to those observed for T7-all and T8-all in Sr 2+ , which also had unusual UV spectra in the region of 290 nm; it did not quite coincide to that observed for known G-quadruplex structures (38). Therefore, it is not clear whether TRF2 B induces T7-all to form a G-quadruplex structure.…”

Section: Resultssupporting

confidence: 54%

The effect of the TRF2 N-terminal and TRFH regions on telomeric G-quadruplex structures

Pedroso

Hayward

Fletcher

2009

Nucleic Acids Research

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The sequence of human telomeric DNA consists of tandem repeats of 5′-d(TTAGGG)-3′. This guanine-rich DNA can form G-quadruplex secondary structures which may affect telomere maintenance. A current model for telomere protection by the telomere-binding protein, TRF2, involves the formation of a t-loop which is stabilized by a strand invasion-like reaction. This type of reaction may be affected by G-quadruplex structures. We analyzed the influence of the arginine-rich, TRF2 N-terminus (TRF2B), as well as this region plus the TRFH domain of TRF2 (TRF2BH), on the structure of G-quadruplexes. Circular dichroism results suggest that oligonucleotides with 4, 7 and 8 5′-d(TTAGGG)-3′ repeats form hybrid structures, a mix of parallel/antiparallel strand orientation, in K+. TRF2B stimulated the formation of parallel-stranded structures and, in some cases, intermolecular structures. TRF2BH also stimulated intermolecular but not parallel-stranded structures. Only full-length TRF2 and TRF2BH stimulated uptake of a telomeric single-stranded oligonucleotide into a plasmid containing telomeric DNA in the presence of K+. The results in this study suggest that G-quadruplex formation inhibits oligonucleotide uptake into the plasmid, but the inhibition can be overcome by TRF2. This study is the first analysis of the effects of TRF2 domains on G-quadruplex structures and has implications for the role of G-quadruplexes and TRF2 in the formation of t-loops.

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Section: Resultssupporting

confidence: 54%

The effect of the TRF2 N-terminal and TRFH regions on telomeric G-quadruplex structures

Pedroso

Hayward

Fletcher

2009

Nucleic Acids Research

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“…To investigate the possibility that GTP binding might play a role in the cellular function of G-quadruplex regulatory elements, we tested five well-studied examples for the ability to bind GTP: a transcriptional repressor in the human c-MYC promoter (Siddiqui-Jain et al, 2002; Seenisamy et al, 2004), an enhancer of 3’ end formation in the SV40 late transcript (Bagga et al, 1995), an internal ribosomal entry site (IRES) in the human VEGF gene (Morris et al, 2010), a translational repressor in the 5' UTR of the human NRAS gene (Kumari et al, 2008), and a G-quadruplex derived from the vertebrate telomere sequence (Blackburn, 2001). The GTP-binding activity of each of these regulatory elements was confirmed, although the telomere-derived sequence could only bind GTP in a buffer containing Sr 2+ , which is known to promote the formation of parallel strand telomeric G-quadruplexes (Pedroso et al, 2007) (Figures 5a and S4). Mutations known to reduce cellular activities of these elements also significantly reduced their abilities to bind GTP (Figure 5a).…”

Section: Resultsmentioning

confidence: 93%

Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA

Curtis

Liu

2013

Chemistry & Biology

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SUMMARY Biological RNAs that bind small-molecules have been implicated in a variety of regulatory and catalytic processes. Inspired by these examples, we used in vitro selection to search a pool of genomeencoded RNA fragments for naturally occurring GTP aptamers. Several classes of aptamers were identified, including one ("the G motif") with a G-quadruplex structure. Further analysis revealed that most RNA and DNA G-quadruplexes bind GTP. The G motif is abundant in eukaryotes, and the human genome contains ∼75,000 examples with dissociation constants comparable to the GTP concentration of a eukaryotic cell (∼300 µM). G-quadruplexes play roles in diverse cellular processes, and our findings raise the possibility that GTP may play a role in the function of these elements. Consistent with this possibility, the sequence requirements of several classes of regulatory G-quadruplexes parallel those of GTP binding.

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“…It was reported 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 slower band migrates similarly to that of the dimeric marker; the faster band is close to that of the monomeric marker, which means the formed unstable G-quadruplex contains more than one structure. 40 For the cases of 2 mM and 5 mM K + , the slower and faster bands become clearer, which is indicative of the formation of more stable monomeric and dimeric G-quadruplex. 5,[40][41] The results demonstrates that PW17 folds into a relatively loose G-quadruplex containing dimer and monomer.…”

Section: Resultsmentioning

confidence: 93%

“…40 For the cases of 2 mM and 5 mM K + , the slower and faster bands become clearer, which is indicative of the formation of more stable monomeric and dimeric G-quadruplex. 5,[40][41] The results demonstrates that PW17 folds into a relatively loose G-quadruplex containing dimer and monomer. Upon increasing K + from 5 mM to 40 mM, the slower and faster bands become much clearer, and the faster bands are gradually disappeared, which means the compact and stable monomeric G-quadruplex gradually forms more compact and stable dimeric G-quadruplex.…”

Section: Resultsmentioning

confidence: 93%

Aptamer-Based K⁺ Sensor: Process of Aptamer Transforming into G-Quadruplex

Zhang

Han

et al. 2016

J. Phys. Chem. B

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G-rich aptamers have been widely applied to develop various sensors for detecting proteins, small molecules, and cations, which is based on the target-induced conformational transfer from single strand to G-quadruplex. However, the transforming process is unclear. Here, with PW17 as an aptamer example, the forming process of G-quadruplex induced by K(+) is investigated by circular dichroism spectroscopy, electrospray ionization mass spectroscopy, and native gel electrophoresis. The results demonstrate that PW17 undergoes a conformational transforming process from loose and unstable to compact and stable G-quadruplex, which is strictly K(+) concentration-dependent. The process contains three stages: (1) K(+) (<0.5 mM) could induce PW17 forming a loose and unstable G-quadruplex; (2) the compact and stable K(+)-stabilized G-quadruplex is almost formed when K(+) is equal to or larger than 7 mM; and (3) when K(+) ranges from 0.5 mM to 7 mM, the transformation of K(+)-stabilized PW17 from loose and unstable to compact and stable occurs. Interestingly, dimeric G-quadruplex through 5'-5' stacking is involved in the forming process until completely formed at 40 mM K(+). Moreover, the total process is thermodynamically controlled. With PW17 as a sensing probe and PPIX as a fluorescent probe for detection of K(+), three linear fluorescent ranges are observed, which corresponds to the three forming stages of G-quadruplex. Clarifying the forming process provides a representative example to deeply understand and further design aptamer-based biosensers and logic devices.

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Induction of parallel human telomeric G-quadruplex structures by Sr2+

Cited by 43 publications

References 31 publications

The effect of the TRF2 N-terminal and TRFH regions on telomeric G-quadruplex structures

The effect of the TRF2 N-terminal and TRFH regions on telomeric G-quadruplex structures

Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA

Aptamer-Based K⁺ Sensor: Process of Aptamer Transforming into G-Quadruplex

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Induction of parallel human telomeric G-quadruplex structures by Sr2+

Cited by 43 publications

References 31 publications

The effect of the TRF2 N-terminal and TRFH regions on telomeric G-quadruplex structures

The effect of the TRF2 N-terminal and TRFH regions on telomeric G-quadruplex structures

Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA

Aptamer-Based K+ Sensor: Process of Aptamer Transforming into G-Quadruplex

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Aptamer-Based K⁺ Sensor: Process of Aptamer Transforming into G-Quadruplex