Role of loops in the guanine quadruplex formation by DNA/RNA hybrid analogs of G4T4G4

Vondrušková, Jitka; Kypr, Jaroslav; Kejnovská, Iva; Fialová, Markéta; Vorlı́čková, Michaela

doi:10.1016/j.ijbiomac.2008.08.013

Cited by 10 publications

(7 citation statements)

References 48 publications

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“…This experimental confirmation is important for these motifs, as their G4-Hunter scores are relatively low, and some candidate sequences may prefer formation of other structures and/or fail to form stable G4 (100% confidence in predicted motifs can only be achieved for relatively high scores, typically above 1.6). To confirm the ability of the most conserved PQS to form G4 in vitro, we used a combination of two biophysical methods, circular dichroism (CD) spectroscopy and the Thioflavin T (ThT) fluorescent assay [30,31], results are shown in SM_06. We tested nine synthetic oligonucleotides derived from the LOGO sequence listed in Fig.…”

Section: Resultsmentioning

confidence: 99%

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G-quadruplexes in H1N1 influenza genomes

et al. 2021

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Background Influenza viruses are dangerous pathogens. Seventy-Seven genomes of recently emerged genotype 4 reassortant Eurasian avian-like H1N1 virus (G4-EA-H1N1) are currently available. We investigated the presence and variation of potential G-quadruplex forming sequences (PQS), which can serve as targets for antiviral treatment. Results PQS were identified in all 77 genomes. The total number of PQS in G4-EA-H1N1 genomes was 571. Interestingly, the number of PQS per genome in individual close relative viruses varied from 4 to 12. PQS were not randomly distributed in the 8 segments of the G4-EA-H1N1 genome, the highest frequency of PQS being found in the NP segment (1.39 per 1000 nt), which is considered a potential target for antiviral therapy. In contrast, no PQS was found in the NS segment. Analyses of variability pointed the importance of some PQS; even if genome variation of influenza virus is extreme, the PQS with the highest G4Hunter score is the most conserved in all tested genomes. G-quadruplex formation in vitro was experimentally confirmed using spectroscopic methods. Conclusions The results presented here hint several G-quadruplex-forming sequences in G4-EA-H1N1 genomes, that could provide good therapeutic targets.

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Section: Resultsmentioning

confidence: 99%

“…A set of four scans with a data pitch of 0.5 nm and 200 nm/min scan speed was averaged for each sample. CD signal is expressed as the difference in molar absorption, Δε, of the left-and righthanded circularly polarized light [31].…”

Section: Spectroscopymentioning

confidence: 99%

G-quadruplexes in H1N1 influenza genomes

et al. 2021

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“…The G 4 u 4 G 4 quadruplex is, interestingly, more thermostable in K + solutions than the g 4 u 4 g 4 . In contrast, the T 4 loop destabilizes the parallel quadruplex of g 4 u 4 g 4 , and the positive 260 nm CD band of the g 4 T 4 g 4 is of lower intensity than that of g 4 u 4 g 4 [54]. The dodecamers g 4 u 4 g 4 and G 4 u 4 G 4 form a mixture of bimolecular and tetramolecular quadruplexes, whereas g 4 T 4 g 4 forms only a bimolecular one, as does G 4 T 4 G 4 , in the presence of K + .…”

Section: Rna Quadruplexesmentioning

confidence: 94%

“…5. CD spectra corresponding to parallel quadruplexes are also displayed by the hybrid molecules G 4 u 4 G 4 and g 4 T 4 g 4 under all conditions examined [54]. The u 4 loop of G 4 u 4 G 4 forces DNA tetrads into the same conformation as that adopted by g 4 u 4 g 4 .…”

Section: Rna Quadruplexesmentioning

confidence: 95%

Circular dichroism and guanine quadruplexes

Vorlı́čková

Kejnovská

Sági³

et al. 2012

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“…A single g for a G changed the topology. With the exception of GGGGTTTTGGGg, which adopted an antiparallel structure, all hybrids formed parallel, bimolecular GQs [ 138 , 139 ]. For an NMR study, various GQ-forming sequences like the Myc and htel were systematically modified by single riboguanosine substitutions at anti dG positions.…”

Section: Stabilization or Destabilization Of A Gq By The Same Syntmentioning

confidence: 99%

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Sági¹

2017

Journal of Nucleic Acids

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Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.

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Role of loops in the guanine quadruplex formation by DNA/RNA hybrid analogs of G4T4G4

Cited by 10 publications

References 48 publications

G-quadruplexes in H1N1 influenza genomes

G-quadruplexes in H1N1 influenza genomes

Circular dichroism and guanine quadruplexes

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

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