G-quadruplexes and helicases

Mendoza, Óscar; Bourdoncle, Anne; Boulé, Jean-Baptiste; Brosh, Robert M.; Mergny, Jean‐Louis

doi:10.1093/nar/gkw079

Cited by 389 publications

(370 citation statements)

References 168 publications

(243 reference statements)

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“…Several other helicase proteins possess ATP-dependent disruption activity toward DNA G4s, including RecQ, BLM, WRN, FANCJ, and Pif1 (13). Like DHX36, all of these proteins are thought to bind to ssDNA and translocate directionally during the course of ATP-dependent G4 disruption.…”

Section: Discussionmentioning

confidence: 99%

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The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism

Yangyuoru

Bradburn

et al. 2018

Journal of Biological Chemistry

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Single-stranded DNA (ssDNA) and RNA regions that include at least four closely spaced runs of three or more consecutive guanosines strongly tend to fold into stable G-quadruplexes (G4s). G4s play key roles as DNA regulatory sites and as kinetic traps that can inhibit biological processes, but how G4s are regulated in cells remains largely unknown. Here, we developed a kinetic framework for G4 disruption by DEAH-box helicase 36 (DHX36), the dominant G4 resolvase in human cells. Using tetramolecular DNA and RNA G4s with four to six G-quartets, we found that DHX36-mediated disruption is highly efficient, with rates that depend on G4 length under saturating conditions (k cat ) but not under subsaturating conditions (k cat /K M ). These results suggest that a step during G4 disruption limits the k cat value and that DHX36 binding limits k cat /K M . Similar results were obtained for unimolecular DNA G4s. DHX36 activity depended on a 3′ ssDNA extension and was blocked by a polyethylene glycol linker, indicating that DHX36 loads onto the extension and translocates 3′-5′ toward the G4. DHX36 unwound dsDNA poorly compared with G4s of comparable intrinsic lifetime. Interestingly, we observed that DHX36 has striking 3′-extension sequence preferences that differ for G4 disruption and dsDNA unwinding, most likely arising from differences in the rate-limiting step for the two activities. Our results indicate that DHX36 disrupts G4s with a conventional helicase mechanism that is tuned for great efficiency and specificity for G4s. The dependence of DHX36 on the 3′-extension sequence suggests that the extent of formation of genomic G4s may not track directly with G4 stability. ___________________________________Single-stranded DNA and RNA segments that include at least four closely-spaced runs of three or more consecutive guanosine nucleotides have a strong intrinsic propensity to fold into stable G-quadruplex structures (G4s) (1) (Fig. 1A, top left). The genomes of humans and many other eukaryotes are replete with putative G4-forming sequences, and pronounced, conserved patterns have been observed in their distribution, suggesting that Gquadruplex structures form at least transiently in cells and perform conserved functions (2-6). Supporting this hypothesis, G4s have been detected in cells for both .To function as regulatory elements, G4s must be folded and disrupted in a regulated way. In addition, processes that require single-stranded DNA or RNA, such as replication and translation, require that G4s be temporarily disrupted. The high stability and long intrinsic lifetime of G4s suggest Mechanism of G4 disruption by DHX362 that their efficient disruption requires the activity of ATP-dependent enzymes such as helicases.Supporting this view, incorporation of sequences predicted to form particularly stable G4s leads to genetic instability in yeast, suggesting that these G4 structures are not processed efficiently and pose blocks to replication (12). Indeed, several helicases have been shown to possess G4 disruption acti...

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Section: Discussionmentioning

confidence: 99%

“…Indeed, several helicases have been shown to possess G4 disruption activity (13). While some of these helicases associate specifically with molecular machines such as the replisome, the DEAH/RHA family helicase DHX36 (a.k.a.…”

Section: ___________________________________mentioning

confidence: 99%

The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism

Yangyuoru

Bradburn

et al. 2018

Journal of Biological Chemistry

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“…G4 structures are based on the stacking of several socalled G-quartets, which consist each of four guanine bases held together by Hoogsteen-type hydrogen bonding ( Figure 1.2(b)) [61]. G4 structures are further stabilized by the presence of cations (generally sodium and potassium) in the central channel of the helix.…”

Section: Alternative Dna Formsmentioning

confidence: 99%

“…A G4 motif can be formed by one or several DNA strands, oriented either in a parallel or antiparallel fashion. The structural diversity, folding properties and stabilities of G-quadruplex DNA have been extensively studied, both as a model for a non-canonical secondary DNA structure and as a pharmacological target for small molecules that have potential to impact gene expression [61].…”

Section: Alternative Dna Formsmentioning

confidence: 99%

Nanotechnology and the Unique Role of DNA

Schöneweiβ¹,

Jaekel²,

Saccá³

2017

DNA Nanotechnology for Bioanalysis

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“…Multiple lines of evidence suggest that repetitive DNA motifs in the genome fold into a variety of non-B DNA structures, which, in turn, affect many essential cellular processes including gene expression, DNA replication, and recombination (1)(2)(3). Defects in one or more of these processes can cause mutations and, consequently, lead to genome instability (1,2).…”

Section: Introductionmentioning

confidence: 99%

Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks

Kshirsagar

Khan

Hosur

et al. 2017

Biophysical Journal

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A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.

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G-quadruplexes and helicases

Cited by 389 publications

References 168 publications

The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism

The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism

Nanotechnology and the Unique Role of DNA

Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks

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