Stabilization of a DNA aptamer by ligand binding

Santos, Tiago; Lopes-Nunes, Jéssica; Alexandre, Daniela; Miranda, André; Figueiredo, Joana; Silva, Micael; Mergny, Jean‐Louis; Cruz, Carla

doi:10.1016/j.biochi.2022.05.002

Cited by 13 publications

(16 citation statements)

References 40 publications

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“…The previous results indicate that a decrease in either the bulge or linker size of AT11 leads to an increase in thermal stability (AT11-B1, AT11-B0 and AT11-L0) [ 8 ]. The AT11 derivatives have also been studied as delivery systems for cervical and oral cancer cells [ 11 , 12 , 13 ]. However, the AT11-L2 derivative remains unexplored.…”

Section: Resultsmentioning

confidence: 99%

“…Titrations performed with two molar equivalents of PhenDC3 ( Figure S2 ) resulted in a broadening of the imino protons, suggesting a poorly defined binding mode of the ligand to the G4 structure and/or the formation of higher molecularity complexes [ 13 ].…”

Section: Resultsmentioning

confidence: 99%

“…In this experiment, DMSO- d 6 was added until it reached 8% of the final volume, in order to avoid PhenDC3 aggregation, as previously described [ 13 ]. Additionally, the NMR spectrum was acquired to check if the G4 structure was maintained under 37 °C in the presence of PhenDC3.…”

Section: Resultsmentioning

confidence: 99%

“…Since AT11-L2 is an AT11 derivative (itself a modified version of AS1411) reported as NCL aptamers [ 8 , 11 , 13 ], it was of interest to investigate the binding affinity and ligands complex formation of AT11-L2 G4 with NCL. The K D values of 5′-Cy5-AT11-L2 G4/ligand complex towards NCL were determined by fluorometric titrations and fitted to Hill saturation binding mode or Michaelis–Menten ( Figure S4 ).…”

Section: Resultsmentioning

confidence: 99%

“…In 2017, Phan et al, identified more derivatives of AT11 aptamer, termed AT11-B1, AT11-B0, AT11-L0 and AT11-L2 [ 8 ]. Recently, our group showed that AT11, AT11-B0, AT11-L0 and AT11-B1 recognized NCL, and these aptamers can be used as potential drug delivery systems for cervical and tongue cancer cell lines [ 10 , 11 , 12 , 13 ]. Moreover, we also found that improving G4 aptamer stability through changing linker/bulge/loop nucleotides at the appropriate positions and associated ligands could also be a strategy to select a preferential conformation and obtain a more selective drug delivery system [ 10 , 11 , 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

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G-Quadruplex Aptamer-Ligand Characterization

et al. 2022

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In this work we explore the structure of a G-rich DNA aptamer termed AT11-L2 (TGGTGGTGGTTGTTGTTGGTGGTGGTGGT; derivative of AT11) by evaluating the formation and stability of G-quadruplex (G4) conformation under different experimental conditions such as KCl concentration, temperature, and upon binding with a variety of G4 ligands (360A, BRACO-19, PDS, PhenDC3, TMPyP4). We also determined whether nucleolin (NCL) can be a target of AT11-L2 G4. Firstly, we assessed by circular dichroism, UV and NMR spectroscopies the formation of G4 by AT11-L2. We observed that, for KCl concentrations of 65 mM or less, AT11-L2 adopts hybrid or multiple topologies. In contrast, a parallel topology predominates for buffer containing 100 mM of KCl. The Tm of AT11-L2 in 100 mM of KCl is 38.9 °C, proving the weak stability of this sequence. We also found that upon titration with two molar equivalents of 360A, BRACO-19 and PhenDC3, the G4 is strongly stabilized and its topology is maintained, while the addition of 3.5 molar equivalents of TMPyP4 promotes the disruption of G4. The KD values between AT11-L2 G4, ligands and NCL were obtained by fluorescence titrations and are in the range of µM for ligand complexes and nM when adding NCL. In silico studies suggest that four ligands bind to the AT11-L2 G4 structure by stacking interactions, while the RBD1,2 domains of NCL interact preferentially with the thymines of AT11-L2 G4. Finally, AT11-L2 G4 co-localized with NCL in NCL-positive tongue squamous cell carcinoma cell line.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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G-Quadruplex Aptamer-Ligand Characterization

et al. 2022

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Aptamer‐Modified Nanohydrogel Microarrays for Bioselective Cancer Cell Immobilization

Lamberger

Bargel

Humeník

2022

Adv Funct Materials

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Photolithography combined with surface nucleated protein self-assembly of azido-modified spider silk proteins is used to create an arbitrarily shaped, inherently cell repellent micropattern based on nanofibrillar networks. Using "click" chemistry with dibenzocyclooctin modified oligonucleotides, the microstructures are functionalized with DNA-aptamers, which selectively bind cancer cell markers protein tyrosine kinase 7 or nucleolin. The epitopespecific cell interaction on the aptamer-modified surfaces is tested using human non-adherend leukemia T cells (Jurkat), as well as adherent cervix carcinoma (HeLa) and neuroblastoma (Kelly) cells. The cells can be immobilized with high precision and cell densities on the pattern, also revealing spatially defined proliferation and spreading into distinct morphologies upon cultivation. The formation of integrin-based focal adhesions occurs in the case of the aptamer immobilized cancer cells, similarly to those anchored on RGD-modified pattern. The firm aptamer-marker anchorage allows for the formation of integrin-dependent cell adhesions. Due to the amenability of the recombinant spider silk protein towards chemical and genetical modifications, the presented micropatterned fibrous networks have great potential for further development of adjustable and biocompatible cell-specific arrays, enabling applications in circulating cancer cell isolation and cultivation, studies on the cell's pathogenesis, progression and metastasis capabilities as well as enabling development of platforms for personalized medicine.

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Optimization of G‐Quadruplex Ligands through a SAR Study Combining Parallel Synthesis and Screening of Cationic Bis(acylhydrazones)

Reznichenko

Leclercq

Pinto

et al. 2022

Chemistry A European J

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General remarks: All commercially available chemicals were reagent grade and used without further purification. NMR spectra were measured with a Bruker Avance 300 spectrometer ( 1 H: 300 MHz, 13 C: 75 MHz) at 25 °C; chemical shifts are given in ppm (δ) values. Multiplicities of 13 C NMR signals were determined from DEPT-135 experiments. The melting points were determined in open-end capillaries with a digital melting point instrument (SMP30, Stuart).

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Stabilization of a DNA aptamer by ligand binding

Cited by 13 publications

References 40 publications

G-Quadruplex Aptamer-Ligand Characterization

G-Quadruplex Aptamer-Ligand Characterization

Aptamer‐Modified Nanohydrogel Microarrays for Bioselective Cancer Cell Immobilization

Optimization of G‐Quadruplex Ligands through a SAR Study Combining Parallel Synthesis and Screening of Cationic Bis(acylhydrazones)

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