Triple-Stranded DNA Containing 8-Oxo-7,8-dihydro-2′-deoxyguanosine: Implication in the Design of Selective Aptamer Sensors for 8-Oxo-7,8-dihydroguanine

Zhang, Qian; Wang, Yiqi; Meng, Xianyang; Dhar, Rik; Huang, Haidong

doi:10.1021/ac3033323

Cited by 37 publications

(27 citation statements)

References 39 publications

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“…[26] A subsequent study demonstrated specific binding of 8-oxo-guanine. [27] Ribonucleotide complexes studied by others attract ATP or GTP via Watson-Crick and Hoogsteen base-pairing, further confirming the usefulness of the binding mode. [28,29] In our earlier work, we showed that the dissociation constants of nucleotides can reach the sub-millimolar range and that the triplex-based motifs also bind an important class of second messengers (cAMP and cGMP), [25] but we did not evaluate other functional molecules.…”

Section: Introductionmentioning

confidence: 67%

Binding Cofactors with Triplex‐Based DNA Motifs

Kröner

Göckel

Liu

et al. 2013

Chemistry A European J

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Cofactors are pivotal compounds for the cell and many biotechnological processes. It is therefore interesting to ask how well cofactors can be bound by oligonucleotides designed not to convert but to store and release these biomolecules. Here we show that triplex-based DNA binding motifs can be used to bind nucleotides and cofactors, including NADH, FAD, SAM, acetyl CoA, and tetrahydrofolate (THF). Dissociation constants between 0.1 μM for SAM and 35 μM for THF were measured. A two-nucleotide gap still binds NADH. The selectivity for one ligand over the others can be changed by changing the sequence of the binding pocket. For example, a mismatch placed in one of the two triplets adjacent to the base-pairing site changes the selectivity, favoring the binding of FAD over that of ATP. Further, changing one of the two thymines of an A-binding motif to cytosine gives significant affinity for G, whereas changing the other does not. Immobilization of DNA motifs gives beads that store NADH. Exploratory experiments show that the beads release the cofactor upon warming to body temperature.

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Section: Introductionmentioning

confidence: 67%

Binding Cofactors with Triplex‐Based DNA Motifs

Kröner

Göckel

Liu

et al. 2013

Chemistry A European J

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“…We first asked how the designed binding pocket may be formed without involving the termini. Unlike known triplex-based motifs, [49,51,53,54] endless-type sequences contain a bridging Figure 1. Sequences of binding motifs and their affinities for purine-containing small molecules.…”

mentioning

confidence: 99%

Endless: A Purine‐Binding RNA Motif that Can Be Expressed in Cells

et al. 2014

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It is becoming increasingly clear that nature uses RNAs extensively for regulating vital functions of the cell, and short sequences are frequently used to suppress gene expression. However, controlling the concentration of small molecules intracellularly through designed RNA sequences that fold into ligand-binding structures is difficult. The development of "endless", a triplex-based folding motif that can be expressed in mammalian cells and binds the second messenger 3',5'-cyclic guanosine monophosphate (cGMP), is described. In vitro, DNA or RNA versions of endless show low micromolar to nanomolar dissociation constants for cGMP. To test its functionality in vivo, four endless RNA motifs arranged in tandem were co-expressed with a fluorescent cGMP sensor protein in murine vascular smooth muscle cells. Nitric oxide induced endogenous cGMP signals were suppressed in endless-expressing cells compared to cells expressing a control motif, which suggests that endless can act as a genetically encoded cGMP sink to modulate signal transduction in cells.

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“…Reactive oxygen species, such as superoxide radical, singlet oxygen, hydroxyl radicals, superoxide anion and peroxyl, are considered as harmful species due to their effect on oxidative DNA damage [1,2]. 8-hydroxy-2 0 -deoxyguanosine (8-OHdG, also known as 8-oxo-7, 8-dihydroguanine and 8-oxo-dGuo) (Scheme 1), one of the main products of oxidative DNA damage, can mispair with adenine, leading to G:C-T:A transverse mutation [3].…”

Section: Introductionmentioning

confidence: 99%

“…Fluorescent sensor is the another method for 8-OHdG detection which developed in recent years. Zhang et al [2] reported a DNA aptamer fluorescent sensor for 8-OHdG determination using two triple-stranded DNAs as the scaffolds, which shows inherently insufficient binding constants between aptamers and 8-OHdG due to the small molecule of 8-OHdG.…”

Section: Introductionmentioning

confidence: 99%

Electrochemiluminescence immunosensor for highly sensitive detection of 8-hydroxy-2′-deoxyguanosine based on carbon quantum dot coated Au/SiO2 core–shell nanoparticles

Zhang

Zhao

Fan

et al. 2015

Talanta

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An electrochemiluminescence (ECL) immunosensor using Pt electrode modified with carbon quantum dot (CQDs) coated Au/SiO2 core-shell nanoparticles was proposed for sensitive detection of 8-hydroxy-2'-deoxyguanosine (8-OHdG) in this work. Rabbit anti-8-OHdG antibody was covalently bound to CQDs on the surface of Au/SiO2 core-shell nanoparticles. Through signal amplification of Au/SiO2 core-shell nanoparticles, 8-fold enhancement of the ECL signals was achieved. Under optimal conditions, a good linear range from 0.2 to 200 ng mL(-1) with a low detection limit of 0.085 ng mL(-1) (S/N=3) for 8-OHdG detection was obtained. Interfering substances tests showed that the corresponding ECL intensity (ΔECL) of 8-OHdG is 8-18 times higher than that of guanine, uric acid (UA) and ascorbic acid, demonstrating its good selectivity for 8-OHdG detection. The ECL immunosensor exhibits long-term stability with a relative standard deviation (RSD) of 8.5% even after 16 cycles of continuous potential scans. The result of analytical detection of 8-OHdG in real samples was satisfactory. The proposed ECL immunosensor shows good performance with high sensitivity, specificity, repeatability, stability and provided a powerful tool for 8-OHdG monitoring in clinical samples.

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Triple-Stranded DNA Containing 8-Oxo-7,8-dihydro-2′-deoxyguanosine: Implication in the Design of Selective Aptamer Sensors for 8-Oxo-7,8-dihydroguanine

Cited by 37 publications

References 39 publications

Binding Cofactors with Triplex‐Based DNA Motifs

Binding Cofactors with Triplex‐Based DNA Motifs

Endless: A Purine‐Binding RNA Motif that Can Be Expressed in Cells

Electrochemiluminescence immunosensor for highly sensitive detection of 8-hydroxy-2′-deoxyguanosine based on carbon quantum dot coated Au/SiO2 core–shell nanoparticles

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