Stabilization of novel immunoglobulin switch regions G-quadruplexes by naphthalene and quinoline-based ligands

Carvalho, Josué; Ferreira, João; Pereira, Patrícia; Coutinho, Eduarda; Guédin, Aurore; Nottelet, Pierre; Salgado, Gilmar F.; Mergny, Jean‐Louis; Queiroz, João A.; Sousa, Fani; Cabrita, Eurico J.; Cruz, Carla

doi:10.1016/j.tet.2016.01.022

Cited by 12 publications

(9 citation statements)

References 44 publications

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“…Data were converted into fraction folded (θ) as detailed in the literature . Data points where then fitted to a Boltzmann distribution (OriginPro 2015), and the melting temperatures ( T m ) were determined from the two-state transition model used, using the first derivative method …”

Section: Experimental Sectionmentioning

confidence: 99%

“…35 Data points where then fitted to a Boltzmann distribution (OriginPro 2015), and the melting temperatures (T m ) were determined from the two-state transition model used, using the first derivative method. 36 Zeta Potential. The zeta potential of RNA samples in presence and absence of [Ch][AA]-ILs were determined by dynamic light scattering (DLS) using a Zetasizer Nano ZS particle analyzer (Malvern Instruments, U.K.), equipped with a He−Ne laser, at 25 °C.…”

Section: ■ Introductionmentioning

confidence: 99%

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Integrated Extraction-Preservation Strategies for RNA Using Biobased Ionic Liquids

Quental

Pedro

Pereira

et al. 2019

ACS Sustainable Chem. Eng.

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The ubiquitous instability of RNA along with issues associated with its purity degree have been preventing its widespread use as low-cost biotherapeutics. On the basis of the well-known capacity of amino acids to specifically interact with RNA when used as chromatographic ligands, a set of amino-acid-based ionic liquids (AA-ILs) was herein investigated, both to act as preservation media and as phase-forming agents of aqueous biphasic systems (ABS). This set of strategies was combined with the goal of developing integrated extraction-preservation platforms. AA-ILs comprising the cholinium cation and anions derived from l-lysine ([Ch][Lys]), l-arginine ([Ch][Arg]), l-glutamic acid ([Ch][Glu]), and dl-aspartic acid ([Ch][Asp]) were studied. It is shown that the stability of RNA is preserved in aqueous solutions of the studied AA-ILs, even in the presence of ribonucleases (RNases). Furthermore, almost all the investigated AA-ILs display no cytotoxicity onto two distinct human cell lines. After identifying the most promising ILs, ABS formed by AA-ILs and polypropylene glycol with a molecular weight of 400 g mol–1 (PPG 400) were investigated as extraction and purification platforms for RNA. Both with pure RNA and bacterial lysate samples, RNA is successfully extracted to the IL-rich phase without compromising its integrity and stability. On the basis of these results, the integrated extraction-preservation process for RNA is finally demonstrated. RNA is initially extracted from the bacterial lysate sample using ABS, after which the IL-rich phase can be used as the preservation medium of RNA up to its use. RNA can be then recovered from the IL-rich phase by ethanol precipitation, and the ABS phase-forming components recovered and reused. Although improvements in the purity level of RNA are still required, the approach here reported represents a step forward in the development of sustainable processes to overcome the critical demand of high-quality/high-purity RNA to be used as biotherapeutics.

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Section: Experimental Sectionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Integrated Extraction-Preservation Strategies for RNA Using Biobased Ionic Liquids

Quental

Pedro

Pereira

et al. 2019

ACS Sustainable Chem. Eng.

View full text Add to dashboard Cite

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“…Interest in G4s emerges from the growing evidence that they play several important roles in biology. Bioinformatic analyses have shown that putative G4 sites (PQSs) are not randomly distributed along the genome, but cluster at defined regions such as telomeric repeats [ 3 ], immunoglobulin switch regions [ 4 ], replication origins [ 5 ], recombination sites [ 6 , 7 ], gene promoters [ 8 ], and copy number variation breakpoints [ 9 ]. PQSs are also often present in specific parts of transposable elements [ 10 ], particularly in human Alu repeats [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

Spontaneous DNA Synapsis by Forming Noncanonical Intermolecular Structures

et al. 2022

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We report the spontaneous formation of DNA-DNA junctions in solution in the absence of proteins visualised using atomic force microscopy. The synapsis position fits with potential G-quadruplex (G4) sites. In contrast to the Holliday structure, these conjugates have an affinity for G4 antibodies. Molecular modelling was used to elucidate the possible G4/IM-synaptic complex structures. Our results indicate a new role of the intermolecular noncanonical structures in chromatin architecture and genomic rearrangement.

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“…We have previously focused on the differences in G4 structure stability and demonstrated that the initial elongation efficiency of PCR decreases with increasing CpG methylation in G4-forming sequences [ 22 ]. G4 topology is dependent on the ion type and nucleotide sequence [ 23 , 24 , 25 ]. We have revealed that cytosine methylation in G4 structure also affects G4 topology using circular dichroism (CD) spectrum measurements [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands

Hasegawa

Sasaki

Tsukakoshi

et al. 2021

IJMS

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Genomic DNA methylation is involved in many diseases and is expected to be a specific biomarker for even the pre-symptomatic diagnosis of many diseases. Thus, a rapid and inexpensive detection method is required for disease diagnosis. We have previously reported that cytosine methylation in G-quadruplex (G4)-forming oligonucleotides develops different G4 topologies. In this study, we developed a method for detecting CpG methylation in G4-forming oligonucleotides based on the structural differences between methylated and unmethylated G4 DNAs. The differences in G4 topologies due to CpG methylation can be discriminated by G4 ligands. We performed a binding assay between methylated or unmethylated G4 DNAs and G4 ligands. The binding abilities of fluorescent G4 ligands to BCL-2, HRAS1, HRAS2, VEGF G4-forming sequences were examined by fluorescence-based microtiter plate assay. The differences in fluorescence intensities between methylated and unmethylated G4 DNAs were statistically significant. In addition to fluorescence detection, the binding of G4 ligand to DNA was detected by chemiluminescence. A significant difference was also detected in chemiluminescence intensity between methylated and unmethylated DNA. This is the first study on the detection of CpG methylation in G4 structures, focusing on structural changes using G4 ligands.

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Stabilization of novel immunoglobulin switch regions G-quadruplexes by naphthalene and quinoline-based ligands

Cited by 12 publications

References 44 publications

Integrated Extraction-Preservation Strategies for RNA Using Biobased Ionic Liquids

Integrated Extraction-Preservation Strategies for RNA Using Biobased Ionic Liquids

Spontaneous DNA Synapsis by Forming Noncanonical Intermolecular Structures

Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands

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