Fluorescent oligonucleotide probe based on G-quadruplex scaffold for signal-on ultrasensitive protein assay

Wu, Zai‐Sheng; Hu, Peng; Zhou, Hui; Shen, Guo‐Li; Yu, Ru‐Qin

doi:10.1016/j.biomaterials.2009.11.054

Cited by 14 publications

(11 citation statements)

References 44 publications

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“…[1][2][3][4][5][6] These highly ordered structures have been exploited for the identification of ligands specifically interacting with proteins. [7][8][9][10][11][12][13] One wellknown example is the thrombin binding aptamer (TBA). TBA is a 15-mer DNA oligonucleotide with the sequence 5′-GGT TGG TGT GGT TGG-3′, which was discovered in 1992 by Bock.…”

Section: Introductionmentioning

confidence: 99%

Stability and bioactivity of thrombin binding aptamers modified withd-/l-isothymidine in the loop regions

et al. 2014

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Thrombin binding aptamer (TBA) is a 15-mer single-strand DNA that was identified by SELEX screening technology. It adopts a chair-type antiparallel G-quadruplex and can specifically interact with thrombin, thus inhibiting blood coagulation. Isonucleoside (isoNA) is a type of nucleoside isomer in which the base is shifted to 2′-positions of the glycosyl group, endowed with the ability to modulate local conformation of nucleotides, and L-isoNA could alter the conformation more due to the inversion of glycosyl configuration. Incorporation of L-isothymidine (L-isoT) at T3, T9, T12 positions and D-isoT at the T7 position in TBA's loop regions promoted the formation of G-quadruplex, resulting in enhanced affinity with thrombin and an increased anticoagulant effect. Computer simulation indicated that TBA-12L showed the strongest binding with thrombin, which was consistent with experimental results. The bioactivity of double isoNA incorporated TBA with D-IsoT at T7 and L-IsoT at T12 was comparable to that of TBA-12L, suggesting that the T12 of TBA was very important in interaction with thrombin. Our study also suggested that TBA might interact with two thrombin molecules through the TT loops (T3T4, T12T13) and TGT loop, but the second bonding did not show additional biological effects.

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Section: Introductionmentioning

confidence: 99%

Stability and bioactivity of thrombin binding aptamers modified withd-/l-isothymidine in the loop regions

et al. 2014

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“…The highly complex sensing method ensured IgE determination in a wide dynamic concentration range [131]. Another enzymatic method was developed based on a multicomponent G-quadruplex and monopyrene-based system, where 95.4 fM LOD was achieved using the digestion by S1 nuclease that differentiates between double stranded and single stranded DNA strands [132].…”

Section: Detection Principlementioning

confidence: 99%

“…The method can be multiplexed using different fluorophores with non-overlapping emission peaks, providing a robust, simple and high-throughput option [136]. Molecular Light Switch Complex 100-800 100 [128] Fluorescence enhancement using a DNA aptamer 92-37,000 57 [130] Amplification through allostery-triggered enzymatic recycling amplification NA 5 [131] Fluorescent oligonucleotide probe based on G-quadruplex scaffold for signal-on ultrasensitive protein assay 4.72-7560 0.095 [132] Fluorescence anisotropy 1000-60,000 350 [133] Fluorescence anisotropy assay NA 20 [134] Fluorescence protection assay 100-50,000 100 [136] Aptamer-barcode-based assay based on instantaneous derivatization chemiluminescence coupled to magnetic beads 4.88-20,000 4.6 [137] Competitive fluorescence quenching assay 350-35,000 170 [138] Rapid fluorescence detection of immunoglobulin E using an aptamer switch based on a binding-induced pyrene excimer NA 1600 [139] 6.1.…”

Section: Detection Principlementioning

confidence: 99%

Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications

Bognár

Gyurcsányi

2020

IJMS

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Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets—IgA, IgM, IgG and IgE—have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast.

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“…Immunoglobulin E is considered to be an attractive target for aptamer selection and design of aptamer-based detection assays [ 126 ]. A multi-component system constructed for the IgE detection was reported in [ 143 ] ( Figure 18 c). After incubation of the anti-IgE aptamer with the target, a monopyrene-modified G-rich probe complementary to the aptamer sequence and able to form an intermolecular parallel tetrameric G-quadruplex was added.…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

et al. 2017

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In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

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Fluorescent oligonucleotide probe based on G-quadruplex scaffold for signal-on ultrasensitive protein assay

Cited by 14 publications

References 44 publications

Stability and bioactivity of thrombin binding aptamers modified withd-/l-isothymidine in the loop regions

Stability and bioactivity of thrombin binding aptamers modified withd-/l-isothymidine in the loop regions

Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

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