Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine

Xiao, Chao-Da; Ishizuka, Takumi; Xu, Yan

doi:10.1038/s41598-017-07050-w

Cited by 29 publications

(21 citation statements)

References 50 publications

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“…This property represents a limitation to the use of BioTASQ for G4 detection, especially for G4-DNAs, which have higher conformational diversity than G4-RNAs. We have not yet tested the affinity of BioTASQ on the recently reported antiparallel G4-RNA 29 . While the cellular prevalence of G4-RNA with antiparallel topology remains to be established, they may provide key insights into the topological preference of TASQ ligands.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

et al. 2018

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Guanine-rich RNA sequences can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), whose biological roles are poorly understood, and in vivo existence is debated. To profile biologically relevant G4-RNA in the human transcriptome, we report here on G4RP-seq, which combines G4-RNA-specific precipitation (G4RP) with sequencing. This protocol comprises a chemical crosslinking step, followed by affinity capture with the G4-specific small-molecule ligand/probe BioTASQ, and target identification by sequencing, allowing for capturing global snapshots of transiently folded G4-RNAs. We detect widespread G4-RNA targets within the transcriptome, indicative of transient G4 formation in living human cells. Using G4RP-seq, we also demonstrate that G4-stabilizing ligands (BRACO-19 and RHPS4) can change the G4 transcriptomic landscape, most notably in long non-coding RNAs. G4RP-seq thus provides a method for studying the G4-RNA landscape, as well as ways of considering the mechanisms underlying G4-RNA formation, and the activity of G4-stabilizing ligands.

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Section: Resultsmentioning

confidence: 99%

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

et al. 2018

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“…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 and are otherwise primarily known from Z‐RNA . 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: 98%

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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“…This propensity for changing the direction of the hydrogen‐bond network and thus the tetrad polarity was subsequently generalized by using other sequences and modifications . On the other hand, substitutions within the central tetrad of tetramolecular quadruplexes have resulted in rather inconsistent behavior ranging from structural conservation to the formation of antiparallel topologies or a polarity reversal of the preceding tetrad for RNA sequences …”

Section: Figurementioning

confidence: 99%

Fluorine‐Mediated Editing of a G‐Quadruplex Folding Pathway

Dickerhoff

Weisz

2018

ChemBioChem

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A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G-tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and inter-residual F⋅⋅⋅H8-C8 pseudo-hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes.

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Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine

Cited by 29 publications

References 50 publications

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

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

Fluorine‐Mediated Editing of a G‐Quadruplex Folding Pathway

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