Deoxyribonucleic acid glycosylase assays: Progress and prospects

Ng, Hua Zheng; Ng, Melanie; Eng, Cher Mui; Gao, Zhiqiang

doi:10.1016/j.trac.2016.08.005

Cited by 6 publications

(6 citation statements)

References 87 publications

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“…Human glycosylase is a large superfamily comprising six structural families, and the discrimination of one from other members has always been a challenge . To analyze the specificity of this nanodevice, an unspecific UDG and an irrelevant BSA were measured under identical conditions (Figure ).…”

Section: Results and Discussionmentioning

confidence: 99%

“…Human glycosylase is a large superfamily comprising six structural families, and the discrimination of one from other members has always been a challenge. 31 To analyze the specificity of this nanodevice, an unspecific UDG and an irrelevant BSA were measured under identical conditions (Figure 3). UDG is one type of monofunctional human glycosylases that can excise uracil (U) from mismatched U/A base pairs through the BER for generating an AP site.…”

mentioning

confidence: 99%

“…In addition, these methods mainly focus on the analysis of a single type of DNA glycosylase. As we know, DNA glycosylases are divided into six structural superfamilies and widely distributed across all domains of human life. − Therefore, the development of simple and sensitive strategies for sensing multiple glycosylases may facilitate the study of genome repair mechanisms and the improvement of diagnosis accuracy in clinical diagnosis.…”

mentioning

confidence: 99%

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Activatable Self-Dissociation of Watson–Crick Structures with Fluorescent Nucleotides for Sensing Multiple Human Glycosylases at Single-Cell Level

et al. 2022

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Nucleobase oxidation and alkylation can destroy Watson–Crick base-pairing to challenge the genomic integrity. Human 8-oxoguanine glycosylase 1 (hOGG1) and alkyladenine glycosylase (hAAG) are evolved to counter these two cytotoxic lesions through base-excision repair, and their deregulations are implicated with multifactorial diseases and cancers. Herein, we demonstrate activatable self-dissociation of Watson–Crick structures with fluorescent nucleotides for sensing multiple human glycosylases at single-cell level. The presence of hOGG1 and hAAG catalyzes 8-oxoG and deoxyinosine removal in functional probe 1 to release two trigger probes (1 and 2). Then, trigger probes hybridize with functional probe 2 to activate the autocatalytic degradation of functional probes 2 (Cycle I) and 3 (Cycle II), replicating abundant trigger probes (1–4) and releasing two fluorophores (2-aminopurine (2-AP) and pyrrolo-dC (P-dC)). New trigger probes (1, 2) and (3, 4), in turn, hybridize with free functional probes 2 and 3, repeating Cycles I and II turnovers. Through multicycle self-dissociation of Watson–Crick structures, 2-AP and P-dC are exponentially accumulated for the simultaneous quantification of hOGG1 and hAAG. This nanodevice exhibits high sensitivity with a detection limit of 2.9 × 10–3 U/mL for hOOG1 and 1.5 × 10–3 U/mL for hAAG, and it can measure enzymatic kinetics, identify potential inhibitors, discriminate glycosylases between cancer and normal cell lines, and even quantify glycosylase activities in a single HeLa cell. Moreover, this assay may be rapidly and isothermally performed in one tube with only one tool enzyme in a quencher-free manner, promising a simple and powerful platform for multiple human glycosylase detection.

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Section: Results and Discussionmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Activatable Self-Dissociation of Watson–Crick Structures with Fluorescent Nucleotides for Sensing Multiple Human Glycosylases at Single-Cell Level

et al. 2022

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“…Conventional glycosylase assays include radioactive methods, HPLC, and mass spectrometry. Recent advances of DNA nanosensors allow the detection of glycosylase (e.g., UDG and hOGG) with high sensitivity. − The success of detecting low-abundance lesions suggests that this method may be used for quantifying glycosylases with high sensitivity. The conversion rate of modified base to bulge is determined by the amount of glycosylase when the amounts of other enzymes are fixed.…”

Section: Resultsmentioning

confidence: 99%

Sensitive Detection of DNA Lesions by Bulge-Enhanced Highly Specific Coamplification at Lower Denaturation Temperature Polymerase Chain Reaction

Cai

Xiong

et al. 2017

Anal. Chem.

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Mutagenic modifications of nucleotides or DNA lesions that result from environmental stress have proven to be associated with a variety of diseases, particularly cancer. The method for accurately detecting the lesions is therefore of great importance for biomedical research and toxicity study. We develop a sensitive and low-cost bulge-enhanced coamplification at lower denaturation temperature polymerase chain reaction (COLD-PCR) method for detecting DNA lesions (uracil and 8-oxoguanine) by combining an in vitro base excision repair (BER) pathway and COLD-PCR. The modified bases are converted to bulge via the BER pathway involving converting modified bases to an apurinic/apyrimidinic (AP) site, cleavage at the AP site, and break ligation. The presence of the bulge induces a large change of the hybridization thermodynamics of double-stranded DNA, eventually enhancing the specificity of COLD-PCR. Besides, we used the free energy of hybridization as a reference to optimize the critical denaturation temperature (T) of COLD-PCR obtaining more specific amplification than empirical T. Taking advantage of the proposed bulge-enhanced COLD-PCR, we are able to identify the presence of DNA lesion-containing strands at low abundance down to 0.01%. This method also exhibits high sensitivity for glycosylase with a detection limit of 10 U/mL [3 S/N (signal-to-noise ratio)] that is superior than some recently reported methods. With the design of the repair guide probe, the level of oxidative damage in genomic DNA caused by chemicals and photodynamic therapy (PDT) can be evaluated, heralding more applications in clinical diagnosis and epigenetic study.

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“…Single enantiomer drugs have better pharmacological effects on organisms, lower toxicity, and fewer side effects. [1][2][3][4] As a chiral drug, ketoprofen can effectively treat arthritis, joint pain, gout, and pain caused by nerve injury, but ketoprofen can produce gastrointestinal reactions such as nausea and abdominal discomfort. Ketoprofen can also cause allergic reactions and damage to kidney function.…”

Section: Introductionmentioning

confidence: 99%

Chiral resolution of ketoprofen by modified polymethyl methacrylate microspheres

Zhang,

Yuan,

et al. 2024

J of Applied Polymer Sci

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Due to unique structural characteristics and chiral environment, β‐cyclodextrin (β‐CD) has a strong chiral separation ability. 4‐Chlorophenyl isocyanate (4CPI) also plays an important role in separating chiral drugs. In this paper, a chiral stationary phase: 4‐CPI‐β‐CD stationary phase (4CPI‐β‐CD@PMMA) was designed and prepared. Polymethyl methacrylate (PMMA) microspheres with uniform particle size and good monodispersity were prepared by modified seed polymerization and seed expansion methods. Using diazo resin as a coupling agent, PMMA microspheres were connected with 4CPI‐β‐CD to prepare a stationary phase with chiral recognition ability. PMMA microspheres and 4CPI‐β‐CD were also characterized. Compared with the traditional silica gel column, PMMA microspheres have higher preparation efficiency, better monodispersity, and better mechanical properties as chromatographic fillers. Finally, the chiral separation of ketoprofen was carried out by reversed‐phase high‐performance liquid chromatography, and the separation conditions were optimized. This paper is a good idea for the preparation of the chiral stationary phase.

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Deoxyribonucleic acid glycosylase assays: Progress and prospects

Cited by 6 publications

References 87 publications

Activatable Self-Dissociation of Watson–Crick Structures with Fluorescent Nucleotides for Sensing Multiple Human Glycosylases at Single-Cell Level

Activatable Self-Dissociation of Watson–Crick Structures with Fluorescent Nucleotides for Sensing Multiple Human Glycosylases at Single-Cell Level

Sensitive Detection of DNA Lesions by Bulge-Enhanced Highly Specific Coamplification at Lower Denaturation Temperature Polymerase Chain Reaction

Chiral resolution of ketoprofen by modified polymethyl methacrylate microspheres

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