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  1. Article ; Online: Graphene Oxide-Assisted Aptamer-Based Fluorescent Detection of Tetracycline Antibiotics

    Yang Zhou / Juewen Liu

    Chemistry, Vol 5, Iss 56, Pp 789-

    2023  Volume 799

    Abstract: Tetracyclines are a group of common antibiotics, but owing to their toxicity, most of them are only used in animal husbandry and veterinary medicine. A DNA aptamer for tetracyclines has recently been reported. Upon aptamer binding, the fluorescence of ... ...

    Abstract Tetracyclines are a group of common antibiotics, but owing to their toxicity, most of them are only used in animal husbandry and veterinary medicine. A DNA aptamer for tetracyclines has recently been reported. Upon aptamer binding, the fluorescence of tetracyclines was enhanced. This unique fluorescence enhancement was used to selectively detect the tetracyclines. The purpose of this study was to use graphene oxide (GO) to suppress the background fluorescence for enhanced detection. First, the adsorption of doxycycline on GO was studied. At pH 8.0, 82.7% of doxycycline was adsorbed by GO, and adding 2 µM aptamer desorbed 55.4% of doxycycline. With GO, the signal increase was comparable from pH 6 to 8, whereas without GO, the increase was significantly lower at pH 8. Under optimized condition, a detection limit of 1.6 nM doxycycline was achieved at pH 8.0 in the presence of GO, whereas without GO, the detection limit was 18.9 nM. This is an interesting example of the use of nanomaterials to enhance the performance of aptamer-based biosensors.
    Keywords aptamers ; tetracyclines ; doxycycline ; biosensors ; fluorescence ; Chemistry ; QD1-999
    Subject code 500
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Characterization of nanozyme kinetics for highly sensitive detection.

    Panferov, Vasily G / Wang, Xiaoqin / Liu, Juewen

    The Analyst

    2024  Volume 149, Issue 8, Page(s) 2223–2226

    Abstract: Nanozymes have been widely used as enzyme substitutes. Based on a comprehensive literature survey of 261 publications, we report the significant differences in the Michaelis-Menten constants ( ...

    Abstract Nanozymes have been widely used as enzyme substitutes. Based on a comprehensive literature survey of 261 publications, we report the significant differences in the Michaelis-Menten constants (
    MeSH term(s) Hydrogen Peroxide/chemistry ; Catalysis ; Peroxidases ; Peroxidase/chemistry ; Horseradish Peroxidase/chemistry ; Colorimetry/methods
    Chemical Substances Hydrogen Peroxide (BBX060AN9V) ; Peroxidases (EC 1.11.1.-) ; Peroxidase (EC 1.11.1.7) ; Horseradish Peroxidase (EC 1.11.1.-)
    Language English
    Publishing date 2024-04-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 210747-8
    ISSN 1364-5528 ; 0003-2654
    ISSN (online) 1364-5528
    ISSN 0003-2654
    DOI 10.1039/d4an00250d
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  3. Article ; Online: Metal-Mediated DNA Adsorption on Carboxylated, Hydroxylated, and Hydrogenated Nanodiamonds.

    Zandieh, Mohamad / Liu, Juewen

    Langmuir : the ACS journal of surfaces and colloids

    2023  Volume 39, Issue 33, Page(s) 11596–11602

    Abstract: Nanodiamonds (NDs) have attracted considerable attention owing to their quantum properties and versatility in biological applications. In this study, we systematically investigated the adsorption of DNA oligonucleotides onto NDs with three types of ... ...

    Abstract Nanodiamonds (NDs) have attracted considerable attention owing to their quantum properties and versatility in biological applications. In this study, we systematically investigated the adsorption of DNA oligonucleotides onto NDs with three types of surface groups: carboxylated (COOH-), hydroxylated (OH-), and hydrogenated (H-). Among them, only the H-NDs showed fluorescence quenching property that is useful for real-time DNA adsorption kinetic studies. The effect of common metal ions on DNA adsorption was studied. In the presence of Na
    MeSH term(s) Nanodiamonds ; Adsorption ; Kinetics ; DNA
    Chemical Substances Nanodiamonds ; hydroxide ion (9159UV381P) ; DNA (9007-49-2)
    Language English
    Publishing date 2023-08-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2005937-1
    ISSN 1520-5827 ; 0743-7463
    ISSN (online) 1520-5827
    ISSN 0743-7463
    DOI 10.1021/acs.langmuir.3c01066
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  4. Article ; Online: Pushing Adenosine and ATP SELEX for DNA Aptamers with Nanomolar Affinity.

    Ding, Yuzhe / Liu, Juewen

    Journal of the American Chemical Society

    2023  Volume 145, Issue 13, Page(s) 7540–7547

    Abstract: The classical DNA aptamer for adenosine and ATP has been the most used small molecule binding aptamer for biosensing, imaging, and DNA nanotechnology. This sequence has recurred multiple times in previous aptamer selections, and all previous selections ... ...

    Abstract The classical DNA aptamer for adenosine and ATP has been the most used small molecule binding aptamer for biosensing, imaging, and DNA nanotechnology. This sequence has recurred multiple times in previous aptamer selections, and all previous selections used a high concentration of ATP as the target. Herein, two separate selections were performed using adenosine and ATP as targets. By pushing the target concentrations down to the low micromolar range, two new aptamers with
    MeSH term(s) Adenosine ; Aptamers, Nucleotide/chemistry ; SELEX Aptamer Technique/methods ; DNA/chemistry ; Adenosine Triphosphate
    Chemical Substances Adenosine (K72T3FS567) ; Aptamers, Nucleotide ; DNA (9007-49-2) ; Adenosine Triphosphate (8L70Q75FXE)
    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.3c00848
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Simultaneous Detection of L-Lactate and D-Glucose Using DNA Aptamers in Human Blood Serum.

    Huang, Po-Jung Jimmy / Liu, Juewen

    Angewandte Chemie (International ed. in English)

    2023  Volume 62, Issue 12, Page(s) e202212879

    Abstract: L-lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need additional oxidants. ... ...

    Abstract L-lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need additional oxidants. In this work, DNA aptamers for L-lactate were obtained using a library-immobilization selection method and the highest affinity aptamer reached a K
    MeSH term(s) Humans ; Glucose ; Aptamers, Nucleotide/chemistry ; Serum/metabolism ; Gene Library ; Lactic Acid ; Biosensing Techniques/methods
    Chemical Substances Glucose (IY9XDZ35W2) ; Aptamers, Nucleotide ; Lactic Acid (33X04XA5AT)
    Language English
    Publishing date 2023-02-09
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202212879
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  6. Article ; Online: Characterization of the Binding Properties of Ten Aptamers Using the Intrinsic Fluorescence of Oxytetracycline.

    Zhao, Yichen / Gao, Biwen / Liu, Juewen

    ChemistryOpen

    2024  , Page(s) e202300250

    Abstract: Tetracyclines are a class of commonly used four-ringed antibiotics. A series of DNA aptamers were recently obtained using the capture-SELEX (systematic evolution of ligands by exponential enrichment) method to bind to oxytetracycline, and one of the ... ...

    Abstract Tetracyclines are a class of commonly used four-ringed antibiotics. A series of DNA aptamers were recently obtained using the capture-SELEX (systematic evolution of ligands by exponential enrichment) method to bind to oxytetracycline, and one of the aptamers can bind to a few other tetracycline antibiotics as well. Upon binding to the aptamers, the intrinsic fluorescence of tetracycline antibiotics can be enhanced. At least 10 different DNA aptamers were isolated from the previous selection experiment. In this work, a systematic characterization of these ten aptamers was performed. Each of these aptamers shows a different degree of fluorescence enhancement ranging from around 1-fold to over 20-fold. Fluorescence enhancement was boosted in the presence of Mg
    Language English
    Publishing date 2024-02-05
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2655605-4
    ISSN 2191-1363 ; 2191-1363
    ISSN (online) 2191-1363
    ISSN 2191-1363
    DOI 10.1002/open.202300250
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  7. Article ; Online: Nanomaterials enabled and enhanced DNA-based biosensors.

    Stangherlin, Stefen / Liu, Juewen

    Journal of materials chemistry. B

    2023  Volume 11, Issue 30, Page(s) 6994–7003

    Abstract: DNA has excellent molecular recognition properties. At the same time, DNA has a programmable structure, high stability, and can be easily modified, making DNA attractive for biosensor design. To convert DNA hybridization or aptamer binding events to ... ...

    Abstract DNA has excellent molecular recognition properties. At the same time, DNA has a programmable structure, high stability, and can be easily modified, making DNA attractive for biosensor design. To convert DNA hybridization or aptamer binding events to physically detectable signals, various nanomaterials have been extensively exploited to take advantage of their optical and surface properties. A popular sensing scheme is through the adsorption of a fluorescently-labeled DNA probe, where detection is achieved by target-induced probe desorption and fluorescence recovery. Another method is to use DNA to protect the colloidal stability of nanomaterials, where subsequent target binding can decrease the protection ability and induce aggregation; this method has mainly been used for gold nanoparticles. This Perspective summarizes some of our work in examining the sensing mechanisms, and we articulate the importance of the understanding of DNA/surface and target/surface interactions for the development of practical DNA-based biosensors.
    MeSH term(s) Gold/chemistry ; Metal Nanoparticles/chemistry ; DNA/chemistry ; Biosensing Techniques/methods ; Nanostructures/chemistry
    Chemical Substances Gold (7440-57-5) ; DNA (9007-49-2)
    Language English
    Publishing date 2023-08-02
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2702241-9
    ISSN 2050-7518 ; 2050-750X
    ISSN (online) 2050-7518
    ISSN 2050-750X
    DOI 10.1039/d3tb01100c
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  8. Article ; Online: Intramolecular aptamer switches.

    Shi, Lu / Jin, Yan / Liu, Juewen

    The Analyst

    2024  Volume 149, Issue 3, Page(s) 745–750

    Abstract: Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile, affordable, and simpler than classical "open-close" and strand displacement-based aptamer ... ...

    Abstract Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile, affordable, and simpler than classical "open-close" and strand displacement-based aptamer switches. Recently, many new aptamers with an overall hairpin structure have been reported. In this study, intramolecular aptamer switches were developed by adding new base pairs to the end of aptamers. The additional nucleotides can pair with the internal domains of the aptamer, causing a change in its conformation from the original secondary structure without a target. When a target binds to an aptamer, a marked change in the structure of the aptamer is expected. As models for testing this intramolecular aptamer switch idea, aptamers of oxytetracycline (OTC), 17β-estradiol (E2), and adenosine were employed. When the additional base pairs are too long, binding the target to the aptamer becomes more challenging. This research offers valuable insights into the development of intramolecular aptamer switches and their potential applications in biosensor design.
    MeSH term(s) Aptamers, Nucleotide/chemistry ; Oxytetracycline ; Nucleic Acid Conformation ; Adenosine ; Biosensing Techniques
    Chemical Substances Aptamers, Nucleotide ; Oxytetracycline (X20I9EN955) ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2024-01-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 210747-8
    ISSN 1364-5528 ; 0003-2654
    ISSN (online) 1364-5528
    ISSN 0003-2654
    DOI 10.1039/d3an02022c
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  9. Article ; Online: Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers.

    Ding, Yuzhe / Liu, Juewen

    Analytical chemistry

    2023  Volume 95, Issue 39, Page(s) 14651–14658

    Abstract: Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture- ... ...

    Abstract Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.
    MeSH term(s) Gold ; SELEX Aptamer Technique/methods ; Metal Nanoparticles ; Aptamers, Nucleotide/genetics ; DNA
    Chemical Substances Gold (7440-57-5) ; Aptamers, Nucleotide ; DNA (9007-49-2)
    Language English
    Publishing date 2023-09-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.3c02477
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  10. Article ; Online: Nanozymes: Definition, Activity, and Mechanisms.

    Zandieh, Mohamad / Liu, Juewen

    Advanced materials (Deerfield Beach, Fla.)

    2023  Volume 36, Issue 10, Page(s) e2211041

    Abstract: Nanozyme" is used to describe various catalysts from immobilized inorganic metal complexes, immobilized enzymes to inorganic nanoparticles. Here, the history of nanozymes is dvescribed in detail, and they can be largely separated into two types. Type 1 ... ...

    Abstract "Nanozyme" is used to describe various catalysts from immobilized inorganic metal complexes, immobilized enzymes to inorganic nanoparticles. Here, the history of nanozymes is dvescribed in detail, and they can be largely separated into two types. Type 1 nanozymes refer to immobilized catalysts or enzymes on nanomaterials, which were dominant in the first decade since 2004. Type 2 nanozymes, which rely on the surface catalytic properties of inorganic nanomaterials, are the dominating type in the past decade. The definition of nanozymes is evolving, and a definition based on the same substrates and products as enzymes are able to cover most currently claimed nanozymes, although they may have different mechanisms compared to their enzyme counterparts. A broader definition can inspire application-based research to replace enzymes with nanomaterials for analytical, environmental, and biomedical applications. Comparison with enzymes also requires a clear definition of a nanozyme unit. Four ways of defining a nanozyme unit are described, with iron oxide and horseradish peroxidase activity comparison as examples in each definition. Growing work is devoted to understanding the catalytic mechanism of nanozymes, which provides a basis for further rational engineering of active sites. Finally, future perspective of the nanozyme field is discussed.
    MeSH term(s) Nanostructures/chemistry ; Nanoparticles ; Enzymes, Immobilized ; Catalysis ; Surface Properties
    Chemical Substances Enzymes, Immobilized
    Language English
    Publishing date 2023-02-17
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1474949-X
    ISSN 1521-4095 ; 0935-9648
    ISSN (online) 1521-4095
    ISSN 0935-9648
    DOI 10.1002/adma.202211041
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