Label-free fluorescent and electrochemical biosensors based on defective G-quadruplexes

Zhang, Jing; Wang, Liangliang; Hou, Mei-Feng; Luo, Li-Pei; Liao, Yijuan; Xia, Yaokun; An, Yan; Weng, Yun-Ping; Zeng, Lupeng; Chen, Jinghua

doi:10.1016/j.bios.2018.07.033

Cited by 18 publications

(7 citation statements)

References 43 publications

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“…This was achieved either by introducing an abasic-site in the duplex, [32][33][34] or by omitting a whole guanine-nucleotide in a G-quadruplex. [35][36][37] These DNA complexes can reach a mM K d , and behave like traditional aptamers. However, they oen have a low specicity.…”

Section: Introductionmentioning

confidence: 99%

Engineering base-excised aptamers for highly specific recognition of adenosine

Liu

Huang

et al. 2020

Chem. Sci.

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The DNA aptamer for adenosine and ATP has been used as a model system for developing analytical biosensors. For practical reasons, it is important to distinguish adenosine from ATP, although this has yet to be achieved despite extensive efforts made on selection of new aptamers. We herein report a strategy of excising an adenine nucleotide from the backbone of a one-site adenosine aptamer, and the adenineexcised aptamer allowed highly specific binding of adenosine. Cognate analytes including AMP, ATP, guanosine, cytidine, uridine, and theophylline all failed to bind to the engineered aptamer according to the SYBR Green I (SGI) fluorescence spectroscopy and isothermal titration calorimetry (ITC) results. Our A-excised aptamer has two binding sites: the original aptamer binding site in the loop and the newly created one due to base excision from the DNA backbone. ITC demonstrated that the A-excised aptamer strand can bind to two adenosine molecules, with a K d of 14.8 AE 2.1 mM at 10 C and entropydriven binding. Since the wild-type aptamer cannot discriminate adenosine from AMP and ATP, we attributed this improved specificity to the excised site. Further study showed that these two sites worked cooperatively. Finally, the A-excised aptamer was tested in diluted fetal bovine serum and showed a limit of detection of 46.7 mM adenosine. This work provides a facile, cost-effective, and non-SELEX method to engineer existing aptamers for new features and better applications.

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Section: Introductionmentioning

confidence: 99%

Engineering base-excised aptamers for highly specific recognition of adenosine

Liu

Huang

et al. 2020

Chem. Sci.

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“…5 Besides this harmful effect, light is also used in sensors based on detection of G4 intrinsic fluorescence. 6 Therefore, in order to understand the mechanism of UV-induced lesion formation, on the one hand, and optimize G4-based devices, on the other, it is important to characterize the primary events triggered by UV absorption. So far, there has been no comprehensive study, combining theoretical calculations and time-resolved fluorescence spectroscopy to describe photoactivated processes that involve guanines of the G4 core.…”

mentioning

confidence: 99%

“…The biological functions of G4 may be perturbed as a result of chemical reactions, which, among others, are triggered by UV radiation . Besides this harmful effect, light is also used in sensors based on detection of G4 intrinsic fluorescence . Therefore, in order to understand the mechanism of UV-induced lesion formation, on the one hand, and optimize G4 -based devices, on the other, it is important to characterize the primary events triggered by UV absorption.…”

mentioning

confidence: 99%

Comprehensive Study of Guanine Excited State Relaxation and Photoreactivity in G-quadruplexes

Martínez‐Fernández

Changenet‐Barret

Bányász

et al. 2019

J. Phys. Chem. Lett.

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G-quadruplexes (G4) are four-stranded DNA/RNA structures playing a key role in many biological functions and promising for nanotechnology applications. Here, combining theoretical calculations and multiscale time-resolved fluorescence, we describe, for the first time, an ensemble of photoactivated processes involving the guanines of the G4 core. We use as showcase the G4 formed by the human telomeric sequence GGG(TTAGGG)3 in the presence of Na+ ions. According to quantum mechanical/molecular mechanics calculations, the hyperchromism at the red part of the absorption spectrum, typical of G4 structures, arises mainly from the inner Na+ ions. Various relaxation pathways, leading to excited states localized on individual bases, neutral excimers, and excited charge transfer states between two guanines or a guanine and a thymine in the loop, are mapped. Their fingerprints are detected in the fluorescence anisotropies and the fluorescence decays, spanning five decades of time. Finally, a reaction funnel leading to guanine dimerization is identified.

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“…After the addition of hemin, and in the presence of hydrogen peroxide, the G-quadruplex-hemin repeat units catalyzes the oxidation of TMB (Figure 6). An original strategy focused on the use of a bipedal DNA, was proposed for the ratiometric attomolar quantification of exosomal miRNA-21 [39]. The DNA walker released after magnetic separation of streptavidin-magnetic beads/capture DNA/DNA walker/miRNA-21 is dropped at the biorecognition platform of GCE-AuNPs modified by immobilization of a hairpin-MB producing a conformational change in the hairpin-1 that makes possible the hybridization with the hairpin-2 modified with Fc.…”

Section: 1d Amplification Schemes Based On Special Nucleic Acids Structuresmentioning

confidence: 99%

New trends in the development of electrochemical biosensors for the quantification of microRNAs

Mujica

Gallay

Perrachione

et al. 2020

Journal of Pharmaceutical and Biomedical Analysis

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

show abstract

Label-free fluorescent and electrochemical biosensors based on defective G-quadruplexes

Cited by 18 publications

References 43 publications

Engineering base-excised aptamers for highly specific recognition of adenosine

Engineering base-excised aptamers for highly specific recognition of adenosine

Comprehensive Study of Guanine Excited State Relaxation and Photoreactivity in G-quadruplexes

New trends in the development of electrochemical biosensors for the quantification of microRNAs

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