De-Ming Kong

Nankai University, T’ien-ching-shih, Tianjin Shi, China

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Publications (52)231.89 Total impact

  • Chan Song, Guan-Yao Wang, De-Ming Kong
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    ABSTRACT: This work investigated the interactions of α-Fe2O3 nanoparticles (NPs) with different structural nucleic acids and their fluorescence quenching ability towards fluorophore-labelled nucleic acid probes. Different from bulk α-Fe2O3 samples, nanoscale α-Fe2O3 particles exhibit the unique properties of strong adsorption and fluorescence quenching to fluorophore-labelled single-stranded DNA (ssDNA) probes. Based on these findings, a facile fluorescence method was developed for versatile quantification of nucleic acids. The size scale of NPs makes a significant impact on this sensing platform. Better selectivity was given by bigger NP (50–100 nm)-based nucleic acid-sensing platform compared with smaller NP (30 nm)-based one. In the 50–100 nm α-Fe2O3 NP-based sensing platform, single nucleotide mismatch or single base-pair mismatch can even be effectively discriminated. The targets of micro-RNA (miRNA), ssDNA and double-stranded DNA (dsDNA) are sensitively detected with detection limits of 0.8 nM, 1.1 nM and 0.64 nM (S/N=3), respectively. Significantly, α-Fe2O3 NPs possess different affinities towards ssDNA probes with different lengths, and can be used as a universal quencher for ssDNA probes labelled with different fluorescent dyes. On the basis of these properties, the pristine α-Fe2O3 NPs hold the potential to be widely utilized in the development of novel biosensors with signal amplification or simultaneous multiple target detection strategies.
    Biosensors & Bioelectronics 06/2015; 68. DOI:10.1016/j.bios.2015.01.006 · 6.45 Impact Factor
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    ABSTRACT: G-triplexes are non-canonical DNA structures formed by G-rich sequences with three G-tracts. Putative G-triplex-forming sequences are expected to be more prevalent than putative G-quadruplex-forming sequences. However, the research on G-triplexes is rare. In this work, the effects of molecular crowding and several physiologically important metal ions on the formation and stability of G-triplexes were examined using a combination of circular dichroism, thermodynamics, optical tweezers and calorimetry techniques. We determined that molecular crowding conditions and cations, such as Na(+), K(+), Mg(2+) and Ca(2+), promote the formation of G-triplexes and stabilize these structures. Of these four metal cations, Ca(2+) has the strongest stabilizing effect, followed by K(+), Mg(2+), and Na(+) in a decreasing order. The binding of K(+) to G-triplexes is accompanied by exothermic heats, and the binding of Ca(2+) with G-triplexes is characterized by endothermic heats. G-triplexes formed from two G-triad layers are not stable at physiological temperatures; however, G-triplexes formed from three G-triads exhibit melting temperatures higher than 37°C, especially under the molecular crowding conditions and in the presence of K(+) or Ca(2+). These observations imply that stable G-triplexes may be formed under physiological conditions.
    Scientific Reports 03/2015; 5:9255. DOI:10.1038/srep09255 · 5.58 Impact Factor
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    ABSTRACT: pH measurement is widely used in many fields. Ratiometric pH-sensing is an important way to improve the detection accuracy. Herein, five water-soluble cationic porphyrin derivatives were synthesized and their optical property changes with pH value were investigated. Their pH-dependent assembly/disassembly behaviors caused significant changes in both absorption and fluorescence spectra, thus making them promising bimodal ratiometric probes for both colorimetric and fluorescent pH-sensing. Different substituent identity and position confer these probes with different sensitive pH-sensing ranges, and the substituent position gives a larger effect. By selecting different porphyrins, different signal intensity ratios and different fluorescence excitation wavelengths, sensitive pH-sensing can be achieved in the range of 2.1~8.0. Having demonstrated the excellent reversibility, good accuracy and low cytotoxicity of the probes, they were successfully applied in pH-sensing inside living cells. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Chemistry - An Asian Journal 03/2015; 10(6). DOI:10.1002/asia.201500106 · 3.94 Impact Factor
  • Hui Li, Hai-Wei Fu, Ting Zhao, De-Ming Kong
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    ABSTRACT: A simple, cost-effective and polymerase chain reaction (PCR)-free telomerase activity detection method was developed on the basis of telomerase-triggered formation of G-quadruplex-hemin DNAzyme. In this method, a short, unlabelled telomerase primer was used. Because this primer contains only three GGG repeats, it cannot fold into the stable G-quadruplex structure. In the presence of active telomerase and dGTP, a GGG repeat is added to the 3′-end of the primer. The extended primer can fold into the G-quadruplex, which is able to bind hemin to form catalytically active G-quadruplex-hemin DNAzyme, catalyzing the oxidation of 2,2′-azinobis (3-ethylbenzothiozoline)-6-sulfonic acid (ABTS) by H2O2 to green ABTS˙+. Because the primer extension product is very short, telomerase should show a high turnover rate, thus providing the method with improved sensitivity. Using this method, the telomerase activity originating from 200 HeLa cells can be detected.
    RSC Advances 01/2015; 5(9):6475-6480. DOI:10.1039/C4RA14460K · 3.71 Impact Factor
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    ABSTRACT: A simple mix-and-detect photoluminescence method was developed for the turn-on detection of acidic amino acids. To achieve this, graphene quantum dots (GQDs), which emit both down-conversion and up-conversion photoluminescence were prepared by solvothermal synthesis. The carboxylic acid-rich surface not only increases the water solubility of the prepared GQDs, but also makes Eu(3+)-triggered GQDs aggregation possible, thus causing the photoluminescence quenching of GQDs. The quenched photoluminescence can be recovered by the competition between acidic amino acids and GQDs for Eu(3+). Under optimized conditions, sensitive and specific acidic amino acids quantitation can be achieved by utilizing the changes in either down-conversion or up-conversion photoluminescence. Up-conversion mode gives a little lower detection limit than the down-conversion one. Nearly overlapped calibration curves were obtained for the two acidic amino acids, glutamic acid (Glu) and aspartic acid (Asp), thus suggesting that the proposed method can be used not only for the quantitation of individual acidic amino acids, but also for the detection of total amount of them. Copyright © 2014 Elsevier B.V. All rights reserved.
    Biosensors & Bioelectronics 10/2014; 65C:204-210. DOI:10.1016/j.bios.2014.10.043 · 6.45 Impact Factor
  • Na-Na Duan, Na Wang, Wei Yang, De-Ming Kong
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    ABSTRACT: The effects of linking loop structures between guanine (Gn) repeats on G-quadruplex formation were investigated. The results show that the unfavorable effects of long linking loops on G-quadruplex formation can be overcame by introducing double-stranded structures in linking loop regions. This finding provides a new way for sensor design. That is, the activity of G-quadruplex DNAzyme can be controlled by utilizing target-mediated formation of double-stranded structures in loops. As an example, T-T mismatches are introduced in long loops to destroy their double-stranded structures. The stabilization of Hg2+ to T-T mismatches promotes the reformation of double-stranded structure. Correspondingly, the oligonucleotide folds into G-quadruplex, which binds with Hemin to form peroxidase-like G-quadruplex DNAzyme. Hg2+ sensor is designed and by this method, Hg2+ quantitation is achieved in the concentration range of 10–700 nM, with a detection limit of 8.7 nM. Cysteine (Cys) would compete with T bases to bind with Hg2+, thus releasing Hg2+ from T-Hg2+-T base pairs. As a result, above Hg2+ sensor can also be used in the specific detection of Cys in the range of 20–700 nM with a detection limit of 14 nM.
    Chinese Journal of Analytical Chemistry 10/2014; DOI:10.1016/S1872-2040(14)60772-6 · 0.79 Impact Factor
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    ABSTRACT: A new coordination polymer which shows an unusual 2D inorganic connectivity was constructed. This compound exhibits distinct fluorescence quenching ability to the dye-labeled single-stranded DNA probes with different lengths, based on which an analytical method was developed for the activity assay of deoxyribonuclease I.
    Chemical Communications 08/2014; 50(76). DOI:10.1039/c4cc04272g · 6.72 Impact Factor
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    ABSTRACT: Ligands that can interact specifically with telomeric multimeric G-quadruplexes could be developed as promising anticancer drugs with few side effects related to other G-quadruplex-forming regions. In this paper, a new cationic porphyrin derivative, m-TMPipEOPP, was synthesized and characterized. Its multimeric G-quadruplex recognition specificity under molecular crowding conditions was compared to its isomer p-TMPipEOPP. The slight structural difference accounts for different multimeric G-quadruplex recognition specificity for the two isomers. p-TMPipEOPP can barely discriminate between multimeric and monomeric G-quadruplexes. By contrast, m-TMPipEOPP can bind with multimeric but not with monomeric G-quadruplexes. p-TMPipEOPP might bind to multimeric G-quadruplexes by two modes: sandwich-like end-stacking mode and pocket-dependent intercalative mode. Increasing the pocket size between adjacent two G-quadruplex uints is beneficial for the latter mode. m-TMPipEOPP might bind to multimeric G-quadruplexes by a side binding mode, which confers m-TMPipEOPP with higher multimeric G-quadruplex recognition specificity compared to p-TMPipEOPP. m-TMPipEOPP increases the stability of multimeric G-quadruplex under both dilute and molecular crowding conditions but its G-quadruplex-stabilizing ability is a little weaker than p-TMPipEOPP. These results provide important information for the design of highly specific multimeric G-quadruplex ligands. Another interesting finding is that pocket size is an important factor in determining the stability of multimeric G-quadruplexes.
    Nucleic Acids Research 06/2014; 42(13). DOI:10.1093/nar/gku526 · 9.11 Impact Factor
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    ABSTRACT: As a two-dimensional (2D) ordered porous organic framework (POF), PAF-6 is demonstrated to have an extraordinarily high fluorescence quenching ability to dye-labeled single-stranded DNA (ssDNA). Based on its different affinities to ssDNA and double-stranded DNA (dsDNA), and to ssDNAs with different lengths, PAF-6 is firstly utilized as a simple, cost-efficient, sensitive and selective sensing platform for sequence-specific detection of DNA and activity analysis of exonuclease I (Exo I). In these two systems, the sensing approach is accomplished by simply mixing the dye-labeled ssDNA probe with the targets and PAF-6. The targets of DNA and Exo I are specifically and sensitively detected with detection limits of 0.6 nM and 0.03 U mL−1 (S/N = 3), respectively, by using PAF-6 as a fluorescence quencher of the dye-labeled ssDNA probe. The results of this study suggest that PAF-6 can be developed as an excellent platform for the detection of nucleic acid and nuclease activity. In addition, PAF-6 exhibits a remarkable ability to protect ssDNA probe from enzymatic digestion, which may greatly extend the applications of the proposed ssDNA probe/PAF-6 sensing system to bioanalysis and biomedicine.
    02/2014; 2(11). DOI:10.1039/C3TB21461C
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    ABSTRACT: With a flexible aromatic ligand, bis-(3,5-dicarboxy-phenyl)terephthalamide (H4L), two metal–organic frameworks, Cd(L)·(HDMA)2(DMF)(H2O)3 (1) and Zn(L)·(HDMA)2(DMF)(H2O)6 (2), were synthesized using a solvothermal method. Both 1 and 2 possess a 3D open framework. These two compounds exhibit strong photoluminescence in suspensions, and their luminescence could be efficiently and selectively quenched by a series of nitroaromatics. Thus, 1 and 2 could be used as excellent luminescent probes for nitroaromatic explosives. Additionally, 1 and 2 could also be utilized as the sensing platforms for DNA strands, which is attributed to their different affinities for single- and double-stranded DNAs. With this method, 0.05 nM of target DNA could be detected, and the selectivity could be down to a single nucleotide mismatch. This work shows the potential of MOFs for the sensing of versatile chemicals.
    01/2014; 2(7). DOI:10.1039/C3TA14199C
  • Hong-Xin Jiang, De-Ming Kong, Han-Xi Shen
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    ABSTRACT: As two commonly used tool enzymes, DNA ligase and polynucleotide kinase/phosphatase (PNKP) play important roles in DNA metabolism. More and more studies show that regulation of their activity represents promising means for cancer therapy. To detect the activity of DNA ligase with high sensitivity and specificity, a G-quadruplex DNAzyme-based DNA ligase sensor was developed. In this sensor, the use of G-quadruplex DNAzyme eliminated the needs for any labeled oligonucleotide probes, thus making label-free detection possible. The introduction of rolling circle amplification (RCA) reaction could lead to the formation of multimeric G-quadruplexes containing thousands of G-quadruplex units, which can provide highly active hemin-binding sites, thus significantly improving the sensitivity of the sensor. The proposed sensor allowed specific detection of T4 DNA ligase with a detection limit of 0.0019U/mL. By adding a PNKP-triggered 5'-phosphroylation step of the template DNA, the above sensing strategy could be easily extended to the design of PNKP sensor. The established sensor allowed specific detection of T4 PNKP with a detection limit of 0.0018U/mL. In addition, these two sensors could also be used for the studies on inhibitors of these two enzymes.
    Biosensors & Bioelectronics 12/2013; 55C:133-138. DOI:10.1016/j.bios.2013.12.001 · 6.45 Impact Factor
  • PLoS ONE 10/2013; 8(10). DOI:10.1371/annotation/57871216-6f4e-4b63-98aa-a5f56c59bc2e · 3.53 Impact Factor
  • Qi Zhang, De-Ming Kong
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    ABSTRACT: Using graphene oxide (GO) as a nanoquencher, a universal sensor design strategy was developed on the basis of significantly different binding affinities of GO to single-stranded DNAs (ss-DNAs) with different lengths. The proposed sensors could be used for the activity detection of both exonucleases and restriction endonucleases. To achieve this, a single-labeled fluorescent oligonucleotide probe, which had a single-stranded structure or a hairpin structure with a long single-stranded loop, was used. Such a probe could be efficiently absorbed on the surface of GO, resulting in the quenching of the fluorescent signal. Excision of the single-stranded probe by exonucleases or site-specific cleavage at the double-stranded stem of the hairpin probe by restriction endonuclease released fluorophore-labeled nucleotide, which could not be efficiently absorbed by GO, thus leading to increase in fluorescence of the corresponding sensing system. As examples, three sensors, which were used for activity detection of the exonuclease Exo 1 and the restriction endonucleases EcoR I and Hind III, were developed. These three sensors could specifically and sensitively detect the activities of Exo 1, EcoR I and Hind III with detection limits of 0.03 U mL(-1), 0.06 U mL(-1) and 0.04 U mL(-1), respectively. Visual detection was also possible.
    The Analyst 09/2013; 138(21). DOI:10.1039/c3an01447a · 3.91 Impact Factor
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    ABSTRACT: Label-free metal ion detection methods were developed. To achieve these, a reconstructed Cu(2+)-specific DNA-cleaving DNAzyme (Cu(2+)-specific DNAzyme) with an intramolecular stem-loop structure was used. G-quadruplex-forming G-rich sequence(s), linked at the ends of double-helix stem of an intramolecular stem-loop structure, was partly caged in an intramolecular duplex or formed a split G-quadruplex. Cu(2+)-triggered DNA cleavage at a specific site decreased the stability of the double-helix stem, resulting in the formation or destruction of G-quadruplex DNAzyme that can effectively catalyze the 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS)-H2O2 reaction. Based on these, two label-free, cost-effective and simple Cu(2+) sensors were designed. These two sensors followed different detection modes: 'turn-on' and 'turn-off'. As for the 'turn-on' sensor, the intramolecular stem-loop structure ensured a low background signal, and the co-amplification of detection signal by dual DNAzymes (Cu(2+)-specific DNAzyme and G-quadruplex DNAzyme) provided a high sensitivity. This sensor enabled the selective detection of aqueous Cu(2+) with a detection limit of 3.9 nM. Visual detection was possible. Although the 'turn-off' sensor gave lower detection sensitivity than the 'turn-on' one, the characteristics of cost-effectiveness and ease of operation made it an important implement to reduce the possibility of pseudo-positive or pseudo-negative results. Combining the ability of Hg(2+) ion to stabilize T-T base mismatch, above dual DNAzymes-based strategy was further used for Hg(2+) sensor design. The proposed sensor allowed the specific detection of Hg(2+) ion with a detection of 4.8 nM. Visual detection was also possible.
    PLoS ONE 09/2013; 8(9):e73012. DOI:10.1371/journal.pone.0073012 · 3.53 Impact Factor
  • De-Ming Kong
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    ABSTRACT: G-quadruplex DNAzymes are peroxidase-like complexes formed by nucleic acid G-quadruplexes and hemin. Compared with natural enzymes, G-quadruplex DNAzyme offers many advantages, thus making it a promising tool in the design of biosensors and chemical sensors. Many biosensors and chemical sensors based on G-quadruplex DNAzymes have been reported. A number of factors may affect the performance of G-quadruplex DNAzyme-based sensors. Here we focus on some aspects to be taken into account when designing a G-quadruplex DNAzyme-based sensor. These include the G-quadruplex-forming G-rich sequence, solution components, the reaction substrate, and enrichment strategy for G-quadruplex DNAzyme. We also provide an outlook for further research on G-quadruplex DNAzyme-based sensors.
    Methods 07/2013; 64(3). DOI:10.1016/j.ymeth.2013.07.013 · 3.22 Impact Factor
  • Yang Cai, Nan Li, De-Ming Kong, Han-Xi Shen
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    ABSTRACT: Due to the inherent higher sensitivity of fluorescence detection than colorimetric detection, it is necessary to screen out a suitable fluorogenic substrate for G-quadruplex DNAzymes to improve the sensitivities of G-quadruplex DNAzyme-based sensors. Herein, seven candidates were tested to determine the possibilities of them as fluorogenic substrates. Among these candidates, tyramine hydrochloride gave the maximum signal-to-background ratio for the sensing systems with and without G-quadruplexes, and thus was recommended as the fluorogenic substrate for the sensors that are developed on the basis of target-triggered G-quadruplex formation or destruction. 10-acetyl-3,7-dihydroxyphenoxazine gave the maximum fluorescence signal change between the sensing systems without and with H2O2, thus was recommended as the fluorogenic substrate for the sensors targeting the detection of H2O2 or H2O2-related analytes. In a model system of G-quadruplex DNAzyme-based Cu(2+) sensor, fluorescence detection using tyramine hydrochloride as fluorogenic substrate could decrease the detection limit from 4nM to 0.7nM compared with the colorimetric detection.
    Biosensors & Bioelectronics 05/2013; 49C:312-317. DOI:10.1016/j.bios.2013.05.034 · 6.45 Impact Factor
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    Li-Na Zhu, Bin Wu, De-Ming Kong
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    ABSTRACT: Ligands targeting telomeric G-quadruplexs are considered good candidates for anticancer drugs. However, current studies on G-quadruplex ligands focus exclusively on the interactions of ligands and monomeric G-quadruplexes under dilute conditions. Living cells are crowded with biomacromolecules, and the ∼200-nucleotide G-rich single-stranded overhang of human telomeric DNA has the potential to fold into multimeric G-quadruplex structures containing several G-quadruplex units. Studies on interactions between ligands and multimeric G-quadruplexes under molecular crowding conditions could provide a new route for screening specific telomeric G-quadruplex-targeting ligands. Herein, TMPipEOPP, a cationic porphyrin derivative designed by us, was demonstrated as a promising multimeric telomeric G-quadruplex ligand under molecular crowding conditions. It could highly specifically recognize G-quadruplexes. It could also promote the formation of G-quadruplexes and stabilize them. Detailed studies showed that TMPipEOPP interacted with monomeric G-quadruplexes in sandwich-like end-stacking mode of quadruplex/TMPipEOPP/quadruplex and interacted with multimeric human telomeric G-quadruplexes by intercalating into the pocket between two adjacent G-quadruplex units. The pocket size greatly affected TMPipEOPP binding. A larger pocket was advantageous for the intercalation of TMPipEOPP. This work provides new insights into the ligand-binding properties of multimeric G-quadruplexes under molecular crowding conditions and introduces a new route for screening anticancer drugs targeting telomeric G-quadruplexes.
    Nucleic Acids Research 02/2013; 41(7). DOI:10.1093/nar/gkt103 · 9.11 Impact Factor
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    ABSTRACT: The bioresponsive detection of DNA or proteins and the controlled release of drug molecules are two important research areas for both experimental studies and practical applications. However, the real incorporation of these two functions into one system is still untouched. Being different from the widely reported mesoporous silica nanoparticles that were used as the support, herein we report a smart system based on hybrid phosphonate-TiO(2) mesoporous nanostructures capped with fluorescein labeled oligonucleotides, which can realize simultaneous and highly-efficient biomolecule sensing and controlled drug release. The fluorescence of the labeled oligonucleotides is first quenched by the phosphonate-TiO(2) materials, which are related to the fluorescence resonance energy transfer mechanism. The addition of complementary DNA strands or protein target leads to the displacement of the capped DNA due to hybridization or protein-aptamer reactions. The opening of the pores can further cause the release of entrapped drugs as well as the restoration of dye fluorescence. The present method is proven to have high selectivity towards specific ssDNA and proteins.
    The Analyst 01/2013; 138(4):1084-1090. DOI:10.1039/c2an36631b · 3.91 Impact Factor
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    ABSTRACT: A previously reported Cu(2+)-dependent DNAzyme/substrate complex was reconstructed in this work, which makes possible the use of an intramolecular stem-loop structure and is, therefore, a good choice for the design of Cu(2+) sensors. To demonstrate this, a fluorescent sensor was designed on the basis of the reconstructed complex. In this sensor, the fluorophore/quencher pair was caged tightly in an intramolecular double-helix structure; thus, the background signal was greatly suppressed. Cu(2+)-dependent cleavage of the complex could cause the release of the fluorophore, leading to restoration of the fluorescence signal. High quenching efficiency provides the sensor with three important characteristics: high sensitivity, high temperature variation tolerance and high ionic strength tolerance. The proposed sensor allows specific detection of aqueous Cu(2+) down to a limit of 0.6nM, and the performance is independent of temperature and ionic strength in the range of 4-40°C and 0.8-3.0M NaCl, respectively. This work identifies a good choice for sensor design on the basis of DNAzymes containing triple-helix structures.
    Biosensors & Bioelectronics 10/2012; 42C:225-228. DOI:10.1016/j.bios.2012.10.070 · 6.45 Impact Factor
  • Qi Zhang, Yang Cai, Hui Li, De-Ming Kong, Han-Xi Shen
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    ABSTRACT: A universal label-free metal ion sensor design strategy was developed on the basis of a metal ion-specific DNA/RNA-cleaving DNAzyme and a G-quadruplex DNAzyme. In this strategy, the substrate strand of the DNA/RNA-cleaving DNAzyme was designed as an intramolecular stem-loop structure, and a G-rich sequence was caged in the double-stranded stem and could not form catalytically active G-quadruplex DNAzyme. The metal ion-triggered cleavage of the substrate strand could result in the release of the G-rich sequence and subsequent formation of a catalytic G-quadruplex DNAzyme. The self-blocking mechanism of the G-quadruplex DNAzyme provided the sensing system with a low background signal. The signal amplifications of both the DNA/RNA-cleaving DNAzyme and the G-quadruplex DNAzyme provided the sensing system with a high level of sensitivity. This sensor design strategy can be used for metal ions with reported specific DNA/RNA-cleaving DNAzymes and extended for metal ions with unique properties. As examples, dual DNAzymes-based Cu(2+), Pb(2+) and Hg(2+) sensors were designed. These "turn-on" colorimetric sensors can simply detect Cu(2+), Pb(2+) and Hg(2+) with high levels of sensitivity and selectivity, with detection limits of 4 nM, 14 nM and 4 nM, respectively.
    Biosensors & Bioelectronics 06/2012; 38(1):331-6. DOI:10.1016/j.bios.2012.06.011 · 6.45 Impact Factor

Publication Stats

726 Citations
231.89 Total Impact Points


  • 2002–2015
    • Nankai University
      • • State Key Laboratory of Medicinal Chemical Biology
      • • Research Center for Analytical Sciences
      • • Department of Chemistry
      T’ien-ching-shih, Tianjin Shi, China