The circular dichroism and differential scanning calorimetry study of the properties of DNA aptamer dimers

Poniková, Slavomíra; Tlučková, Katarína; Antalı́k, Marián; Víglaský, Viktor; Hianik, Tibor

doi:10.1016/j.bpc.2011.02.004

Cited by 33 publications

(19 citation statements)

References 27 publications

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“…The aptamers DNA2 and DNA3 containing complementary oligonucleotides were prepared as follows: 0.5 mL of each aptamer solution in a concentration of 5 mM were mixed and then immersed in a 958C water bath (volume approximately 50 mL) and subsequently allowed to cool to room temperature (approximately 25 8C). This ensures full DNA hybridization as we approved earlier by circular dichroism [35].…”

Section: Preparation Of the Biosensor And The Samplesmentioning

confidence: 82%

“…The phase transition temperature for most stable aptamers in the presence of 20 mM Ca 2 + has been 48.3 AE 0.5 8C, which is close to the melting temperature of DNA aptamers sensitive to the fibrinogen binding site of thrombin that also contains one guanine quadruplex. For this aptamers the quadruplex structure has been well established using various methods including circular dichroism (CD) [35]. Most recently the existence of a quadruplex in OTA aptamers has been approved by CD method [31].…”

Section: Resultsmentioning

confidence: 99%

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Impedimetric DNA Aptasensor for Sensitive Detection of Ochratoxin A in Food

et al. 2011

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We report a high sensitive biosensor based on DNA aptamers for detection of ochratoxin A (OTA). The thiolated DNA aptamers specific to OTA of different configurations have been immobilized by chemisorption to the surface of a gold electrode. Electrochemical impedance spectroscopy (EIS) in the presence of a redox probe [Fe(CN) has been used for the determination of the charge transfer resistance, R ct , followed by addition of OTA. The R ct increased with increasing OTA concentration in the range of 0.1-100 nM. The limit of detection (0.12-0.40 nM) depended on the configuration of the aptamers. The sensor was regenerable and validated in food samples with satisfactory recovery.

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Section: Preparation Of the Biosensor And The Samplesmentioning

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Impedimetric DNA Aptasensor for Sensitive Detection of Ochratoxin A in Food

et al. 2011

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“…CD spectroscopy is a primary tool for the characterization of G4 structures/topologies [51], also particularly useful in the study of dimeric sequences [52]. Typical antiparallel G4 structures show positive Cotton effects with bands centered at ca.…”

Section: Spectra and Svd Analysismentioning

confidence: 99%

Tuning the Polymorphism of the Anti-VEGF G-rich V7t1 Aptamer by Covalent Dimeric Constructs

Riccardi

Musumeci

Platella

et al. 2020

IJMS

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In the optimization process of nucleic acid aptamers, increased affinity and/or activity are generally searched by exploring structural analogues of the lead compound. In many cases, promising results have been obtained by dimerization of the starting aptamer. Here we studied a focused set of covalent dimers of the G-quadruplex (G4) forming anti-Vascular Endothelial Growth Factor (VEGF) V7t1 aptamer with the aim of identifying derivatives with improved properties. In the design of these covalent dimers, connecting linkers of different chemical nature, maintaining the same polarity along the strand or inverting it, have been introduced. These dimeric aptamers have been investigated using several biophysical techniques to disclose the conformational behavior, molecularity and thermal stability of the structures formed in different buffers. This in-depth biophysical characterization revealed the formation of stable G4 structures, however in some cases accompanied by alternative tridimensional arrangements. When tested for their VEGF165 binding and antiproliferative activity in comparison with V7t1, these covalent dimers showed slightly lower binding ability to the target protein but similar if not slightly higher antiproliferative activity on human breast adenocarcinoma MCF-7 cells. These results provide useful information for the design of improved dimeric aptamers based on further optimization of the linker joining the two consecutive V7t1 sequences.

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“…When a molecule increases or decreases its volume without any change of surface charge, then its mobility decreases or increases, respectively. For example, G-quadruplex DNA dimers move more slowly than monomers after denaturation induced by a temperature increase [ 3 ], and vice versa. In contrast, the mobility of monomolecular G-quadruplex DNA is higher at lower temperature and decreases during the unfolding process [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Polyacrylamide Temperature Gradient Gel Electrophoresis

Víglaský

2013

Methods in Molecular Biology

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Temperature Gradient Gel Electrophoresis (TGGE) is a form of electrophoresis in which temperature gradient is used to denature molecules as they move through either acrylamide or agarose gel. TGGE can be applied to analyze DNA, RNA, protein-DNA complexes, and, less commonly, proteins. Separation of double-stranded DNA molecules during TGGE relies on temperature-dependent melting of the DNA duplex into two single-stranded DNA molecules. Therefore, the mobility of DNA reflects not only the size of the molecule but also its nucleotide composition, thereby allowing separation of DNA molecules of similar size with different sequences. Depending on the relative orientation of electric field and temperature gradient, TGGE can be performed in either a parallel or a perpendicular mode. The former is used to analyze multiple samples in the same gel, whereas the later allows detailed analysis of a single sample. This chapter is focused on analysis of DNA by polyacrylamide TGGE using the perpendicular mode.

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The circular dichroism and differential scanning calorimetry study of the properties of DNA aptamer dimers

Cited by 33 publications

References 27 publications

Impedimetric DNA Aptasensor for Sensitive Detection of Ochratoxin A in Food

Impedimetric DNA Aptasensor for Sensitive Detection of Ochratoxin A in Food

Tuning the Polymorphism of the Anti-VEGF G-rich V7t1 Aptamer by Covalent Dimeric Constructs

Polyacrylamide Temperature Gradient Gel Electrophoresis

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