An intramolecular antiparallel G-quadruplex formed by human telomere RNA

Xiao, Chao-Da; Shibata, Tomokazu; Yamamoto, Yasuhiko; Xu, Yan

doi:10.1039/c8cc01427b

Cited by 52 publications

(42 citation statements)

References 21 publications

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“…CD has been used extensively for inferring whether RNAs or DNAs form G-quadruplexes. RNA can form both parallel and antiparallel G-quadruplex topologies [14,15]. The CD spectra of GQes3 and GQes12, with positive peaks at 260 nm and troughs at around 240 nm ( Fig 2B), are consistent with RNA G-quadruplexes [16].…”

Section: Methodsmentioning

confidence: 56%

Profusion of G-quadruplexes on both subunits of metazoan ribosomes

et al. 2019

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Mammalian and bird ribosomes are nearly twice the mass of prokaryotic ribosomes in part because of their extraordinarily long rRNA tentacles. Human rRNA tentacles are not fully observable in current three-dimensional structures and their conformations remain to be fully resolved. In previous work we identified sequences that favor G-quadruplexes in silico and in vitro in rRNA tentacles of the human large ribosomal subunit. We demonstrated by experiment that these sequences form G-quadruplexes in vitro. Here, using a more recent motif definition, we report additional G-quadruplex sequences on surfaces of both subunits of the human ribosome. The revised sequence definition reveals expansive arrays of potential G-quadruplex sequences on LSU tentacles. In addition, we demonstrate by a variety of experimental methods that fragments of the small subunit rRNA form G-quadruplexes in vitro. Prior to this report rRNA sequences that form G-quadruplexes were confined to the large ribosomal subunit. Our combined results indicate that the surface of the assembled human ribosome contains numerous sequences capable of forming G-quadruplexes on both ribosomal subunits. The data suggest conversion between duplexes and G-quadruplexes in response to association with proteins, ions, or other RNAs. In some systems it seems likely that the integrated population of RNA G-quadruplexes may be dominated by rRNA, which is the most abundant cellular RNA.

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Section: Methodsmentioning

confidence: 56%

Profusion of G-quadruplexes on both subunits of metazoan ribosomes

et al. 2019

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“…[40] Likewise, a syn rG in r(14,15) seems highly unfavorable considering RNA's preference for an anti glycosidic torsion angle. In fact, rGs in the syn conformation have rarely been reported with a few notable exceptions in non-parallel G4 structures [44][45][46] and are otherwise primarily known from Z-RNA. [47] This suggests, that it is the propensity for a north-type sugar pucker rather than glycosidic torsion angle preferences of the modified nucleosides that critically determines the folding of ODN (14,15).…”

Section: Discussionmentioning

confidence: 99%

Sugar Puckering Drives G‐Quadruplex Refolding: Implications for V‐Shaped Loops

Haase

Dickerhoff

Weisz

2019

Chemistry A European J

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A DNA G‐quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti‐favoring 2′‐deoxy‐2′‐fluoro‐riboguanosine (FrG) analogues. The two substitutions promoted a structural rearrangement to a topology with the 5′‐terminal G residue located in the central tetrad and the two modified residues linked by a V‐shaped zero‐nucleotide loop. Strikingly, whereas a sugar pucker in the preferred north domain is found for both modified nucleotides, the FrG analogue preceding the V‐loop is forced to adopt the unfavored syn conformation in the new quadruplex fold. Apparently, a preferred C3′‐endo sugar pucker within the V‐loop architecture outweighs the propensity of the FrG analogue to adopt an anti glycosidic conformation. Refolding into a V‐loop topology is likewise observed for a sequence modified at corresponding positions with two riboguanosine substitutions. In contrast, 2′‐F‐arabinoguanosine analogues with their favored south‐east sugar conformation do not support formation of the V‐loop topology. Examination of known G‐quadruplexes with a V‐shaped loop highlights the critical role of the sugar conformation for this distinct structural motif.

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“…The potential G4 structures are highly occurrent in telomeres and promoter regions of oncogenes [23,24]. Besides telomeres and promoter regions, ribosomal DNA [25], 5′untranslated region of mRNA [26], or TERRA [27] are also potent to form the G4 structures.…”

Section: The Distribution Of G-quadruplex Structures In Genomementioning

confidence: 99%

The DNA secondary structures at telomeres and genome instability

Tan

Lan

2020

Cell Biosci

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Telomeric DNA are TTA GGG tandem repeats, which are susceptible for oxidative DNA damage and hotspot regions for formation of DNA secondary structures such as t-loop, D-loop, G-quadruplexes (G4), and R-loop. In the past two decades, unique DNA or RNA secondary structures at telomeres or some specific regions of genome have become promising therapeutic targets. G-quadruplex and R-loops at telomeres or transcribed regions of genome have been considered as the potential targets for cancer therapy. Here we discuss the potentials to target the secondary structures (G4s and R-loops) in genome as therapy approaches.

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An intramolecular antiparallel G-quadruplex formed by human telomere RNA

Cited by 52 publications

References 21 publications

Profusion of G-quadruplexes on both subunits of metazoan ribosomes

Profusion of G-quadruplexes on both subunits of metazoan ribosomes

Sugar Puckering Drives G‐Quadruplex Refolding: Implications for V‐Shaped Loops

The DNA secondary structures at telomeres and genome instability

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