Guidelines for G-quadruplexes: I. In vitro characterization

Luo, Yu; Granzhan, Anton; Marquevielle, Julien; Cucchiarini, Anne; Lacroix, Laurent; Amrane, Samir; Verga, Daniela; Mergny, Jean‐Louis

doi:10.1016/j.biochi.2022.12.019

Cited by 15 publications

(17 citation statements)

References 121 publications

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“…To this end, we selected a panel of 36 sequences, containing four consecutive blocks of at least two guanines, distributed both on the chromosome and on the mini-chromosomes. To demonstrate the formation of the G4, we used a variety of methods ( 57 ). FRET-MC enables the testing of several sequences in a parallel fashion ( 44 ).…”

Section: Resultsmentioning

confidence: 99%

“…As several techniques are recommended to definitively demonstrate G4 formation ( 57 ), we used an alternative approach and investigated whether the fluorescence emission of G4 probes such as thioflavin T ( 45 ) and NMM ( 58 ) was increased in the presence of potential G4-forming H. volcanii sequences. When compared to the negative and positive controls, most sequences induced an increase in fluorescence emission of both G4 light probes (Figure 2B and 2C).…”

Section: Resultsmentioning

confidence: 99%

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G-quadruplexes inHaloferax volcanii

Aktary,

Cucchiarini,

Vesco

et al. 2024

Preprint

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The archaeal domain is a taxonomically rich component of microbial communities that inhabit a wide range of habitats on Earth, including the human body. Phylogenomic analyses have indicated that archaea represent the closest known relatives of eukaryotes, thus suggesting that eukaryotes may have evolved from an archaeal ancestor. G-quadruplex structures (G4), formed by guanine rich sequences, are among the most intensively studied local DNA/RNA structures and regulate key biological processes such as replication and gene expression. A bioinformatics analysis of the genome of the salt-loving archaea H. volcanii revealed a large number of potential G4 sequences (PQS). Biophysical analyses showed that a representative panel of these sequences form stable G4 structures under physiological conditions in vitro. In addition, immunofluorescence experiments using the G4-specific antibody, BG4, detected G4s in vivo at the single-cell level with super-resolution microscopy. Moreover, we directly visualized G4 in exponentially growing or stationary cells both at the DNA and RNA levels. G4s were also observed in the RNA and DNA of the hyperthermophile archaeon T. barophilus. Finally, we identified helicases potentially involved in G4 unfolding. Together, with H. volcanii as a new model, our work helps to fill the gap between bacteria and eukaryotic organisms for G4 studies and will aid in uncovering the evolutionary history of G4 structures in the tree of life.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

G-quadruplexes inHaloferax volcanii

Aktary,

Cucchiarini,

Vesco

et al. 2024

Preprint

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“…There is a growing number of bioinformatic tools for UNas prediction and biophysical characterization [45,[56][57][58][59] as well as for determining their roles in various diseases including cancer [60,61]. Contemporary, specific antibodies against cruciforms [62,63], lefthanded nucleic acids [64], G-quadruplexes [65], and i-motifs [66] have also been developed, allowing effective analyses of UNas both in vitro and in situ.…”

Section: Future Perspectivesmentioning

confidence: 99%

Special Issue “Bioinformatics of Unusual DNA and RNA Structures”

Bartas,

Brázda,

Pečinka

2024

IJMS

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“…Furthermore, the polymorphism of G4s depends on the number of chains, on the size of the oligonucleotide sequence, strand polarity and loops. [12][13][14] Diverse G4s systems have been investigated for loading multiple classes of anticancer drugs, such as acridine, 15 doxorubicin, 16 phthalocyanines [17][18][19] and porphyrin derivatives. 8,20 Additionally, it has been shown that certain G4s have the ability to recognize specific cancer markers per se, due to the high affinity to specific nucleic acids or proteins expressed in cancer cells.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, the polymorphism of G4s depends on the number of chains, on the size of the oligonucleotide sequence, strand polarity and loops. 12–14…”

Section: Introductionmentioning

confidence: 99%