De-Ming Kong

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

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Publications (48)215.92 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. · 6.45 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. · 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; · 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; · 6.38 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; · 8.81 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.
    J. Mater. Chem. B. 02/2014; 2(11).
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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.
    J. Mater. Chem. A. 01/2014; 2(7).
  • 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. · 6.45 Impact Factor
  • PLoS ONE 10/2013; 8(10). · 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; · 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. · 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; · 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. · 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; · 8.81 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. · 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. · 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. · 6.45 Impact Factor
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    ABSTRACT: G-quadruplex DNAzymes are peroxidase-like complexes formed by nucleic acid G-quadruplexes and hemin. Various chemical sensors and biosensors have been developed, based on such DNAzymes. Here we report a novel, specific nucleic acid detection method utilizing the isothermal amplification strategy of G-quadruplex DNAzymes. In this method, an unlabeled oligonucleotide probe was used. The probing sequence of the oligonucleotide was in the form of a stem-loop structure. A G-rich sequence, containing three GGG repeats, was linked to the 5'-end of the stem-loop structure. In the presence of target, the probing sequence hybridized to the target, and a G(n) (n≥2) repeat was extended from its 3'-end. This G(n) repeat, together with the three GGG repeats at the 5'-end, folded into a G-quadruplex, and displayed enhanced peroxidase acitivity upon hemin binding. Utilizing the dynamic binding interaction between the probe and its target, the enrichment of G-quadruplex DNAzymes was achieved. Using this method, simple, rapid and cost-effective nucleic acid detection could be achieved. This method displayed high target-length tolerance and good detection specificity; one-base mismatch could be judged easily, even by visual inspection. This method may be used as an auxiliary tool for amplified detection of specific DNA targets in some situations, in which isothermal detection is desirable.
    Analytica chimica acta 06/2012; 729:67-72. · 4.31 Impact Factor
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    ABSTRACT: The discovery of uncommon DNA structures and speculation about their potential functions in genes has brought attention to specific DNA structure recognition. G-quadruplexes are four-stranded nucleic acid structures formed by G-rich DNA (or RNA) sequences. G-rich sequences with a high potential to form G-quadruplexes have been found in many important genomic regions. Porphyrin derivatives with cationic side arm substituents are important G-quadruplex-binding ligands. For example, 5,10,15,20-Tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphyrin (TMPyP4), interacts strongly with G-quadruplexes, but has poor selectivity for G-quadruplex versus duplex DNA. To increase the G-quadruplex recognition specificity, a new cationic porphyrin derivative, 5,10,15,20-tetra-{4-[2-(1-methyl-1-piperidinyl)ethoxy]phenyl} porphyrin (TMPipEOPP), with large side arm substituents was synthesized, and the interactions between TMPipEOPP and different DNA structures were compared. The results show that G-quadruplexes cause large changes in the UV-Vis absorption and fluorescence spectra of TMPipEOPP, but duplex and single-stranded DNAs do not, indicating that TMPipEOPP can be developed as a highly specific optical probe for discriminating G-quadruplex from duplex and single-stranded DNA. Visual discrimination is also possible. Job plot and Scatchard analysis suggest that a complicated binding interaction occurs between TMPipEOPP and G-quadruplexes. At a low [G-quadruplex]/[TMPipEOPP] ratio, one G-quadruplex binds two TMPipEOPP molecules by end-stacking and outside binding modes. At a high [G-quadruplex]/[TMPipEOPP] ratio, two G-quadruplexes bind to one TMPipEOPP molecule in a sandwich-like end-stacking mode.
    PLoS ONE 05/2012; 7(5):e35586. · 3.53 Impact Factor
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    ABSTRACT: The scavenging of 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) radical cation (ABTS(+)) by antioxidants has been widely used in antioxidant capacity assay. Because of ABTS(+) disproportionation, however, this radical cannot be prepared on a large scale and stored long-term, making it unsuitable for high-throughput detection and screening of antioxidants. We developed a modified "post-additional" antioxidant capacity assay. This method possessed two remarkable features: First, instead of natural peroxidases, an artificial enzyme, G-quadruplex DNAzyme, was used for the preparation of ABTS(+), thus greatly reducing the cost of the assay, and eliminating the strict demand for the storage of enzymes. Second, an ABTS(+) stabilizer, adenosine triphosphate (ATP), was used. In the presence of ATP, the disproportionation of ABTS(+) was effectively inhibited, and the lifetime of this radical cation was prolonged about 6-fold (12 days versus 2 days), making the large-scale preparation of ABTS(+) possible. Utilizing this method, the antioxidant capacities of individual antioxidants and real samples can be quantified and compared easily. In addition, this method can be developed as a high-throughput screening method for antioxidants. The screening results could even be judged by the naked eye, eliminating the need for expensive instruments.
    Biosensors & Bioelectronics 03/2012; 35(1):407-12. · 6.45 Impact Factor

Publication Stats

453 Citations
215.92 Total Impact Points


  • 2002–2014
    • Nankai University
      • • State Key Laboratory of Medicinal Chemical Biology
      • • Research Center for Analytical Sciences
      • • Department of Chemistry
      T’ien-ching-shih, Tianjin Shi, China
  • 2012
    • Tianjin University
      • Department of Chemistry
      Tianjin, Tianjin Shi, China