The Experts below are selected from a list of 6495 Experts worldwide ranked by ideXlab platform
Hyun Gyu Park - One of the best experts on this subject based on the ideXlab platform.
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A one-step and label-free, electrochemical DNA detection using metal ion-mediated Molecular Beacon probe
Elsevier, 2019Co-Authors: Songyi Baek, Ki Soo Park, Jun Ki Ahn, Byoung Yeon Won, Hyun Gyu ParkAbstract:We developed a one-step and label-free, electrochemical DNA detection method using metal ion-mediated Molecular Beacon (MB) probe specially designed to have target-specific sequence in its loop and Pb2+-binding aptamer in its stem. In the absence of target DNA, MB probe, after the interaction with Pb2+, forms the intraMolecular stem-loop hairpin structure, which limits Pb2+ to freely diffuse onto the electrode surface, leading to the low electrochemical signal. In contrast, the presence of target DNA that forms the hybridization complex with MB probe, breaks down the intraMolecular stem-loop structure of MB probe, and releases Pb2+ that is freely diffused onto the electrode surface to generate the high electrochemical signal. By employing this method, the target DNA from Chlamydia trachomatis, one of the major pathogens causing sexually transmitted disease was successfully detected with the high selectivity. Keywords: Molecular Beacon, G-quadruplex, Lead ion, Electrochemistry, Biosenso
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simple and universal platform for logic gate operations based on Molecular Beacon probes
Small, 2012Co-Authors: Ki Soo Park, Myung Wan Seo, Cheulhee Jung, Joonyoung Lee, Hyun Gyu ParkAbstract:A new platform technology is herein described with which to construct Molecular logic gates by employing the hairpin-structured Molecular Beacon probe as a basic work unit. In this logic gate operation system, single-stranded DNA is used as the input to induce a conformational change in a Molecular Beacon probe through a sequence-specific interaction. The fluorescent signal resulting from the opening of the Molecular Beacon probe is then used as the output readout. Importantly, because the logic gates are based on DNA, thus permitting input/output homogeneity to be preserved, their wiring into multi-level circuits can be achieved by combining separately operated logic gates or by designing the DNA output of one gate as the input to the other. With this novel strategy, a complete set of two-input logic gates is successfully constructed at the Molecular level, including OR, AND, XOR, INHIBIT, NOR, NAND, XNOR, and IMPLICATION. The logic gates developed herein can be reversibly operated to perform the set-reset function by applying an additional input or a removal strand. Together, these results introduce a new platform technology for logic gate operation that enables the higher-order circuits required for complex communication between various computational elements.
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dnazyme Molecular Beacon probes for target induced signal amplifying colorimetric detection of nucleic acids
Analytical Chemistry, 2011Co-Authors: Rongzhan Fu, Taihua Li, Hyun Gyu ParkAbstract:A novel DNAzyme Molecular Beacon (DNAzymeMB) strategy was developed for target-induced signal-amplifying colorimetric detection of target nucleic acids. The DNAzymeMB, which exhibits peroxidase activity in its free hairpin structure, was engineered to form a catalytically inactive hybrid through hybridization with a blocker DNA. The presence of target DNA leads to dissociation of the DNAzymeMB from the inactive hybrid through hybridization with the blocker DNA. This process results in recovery of the catalytically active DNAzymeMB, which can catalyze a colorimetric reaction that signals the presence of the target DNA. In addition, a primer was rationally designed to anneal to the blocker DNA of the blocker/target DNA duplex and displace the bound target DNA during the extension reaction. The released target DNA triggers the next cycle involving hybridization with blocker DNA, DNAzymeMB dissociation, primer extension, and target displacement. This unique amplifying strategy leads to the generation of multi...
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dnazyme Molecular Beacon probes for target induced signal amplifying colorimetric detection of nucleic acids
Analytical Chemistry, 2011Co-Authors: Soo Suk Lee, Hyun Gyu ParkAbstract:A novel DNAzyme Molecular Beacon (DNAzymeMB) strategy was developed for target-induced signal-amplifying colorimetric detection of target nucleic acids. The DNAzymeMB, which exhibits peroxidase activity in its free hairpin structure, was engineered to form a catalytically inactive hybrid through hybridization with a blocker DNA. The presence of target DNA leads to dissociation of the DNAzymeMB from the inactive hybrid through hybridization with the blocker DNA. This process results in recovery of the catalytically active DNAzymeMB, which can catalyze a colorimetric reaction that signals the presence of the target DNA. In addition, a primer was rationally designed to anneal to the blocker DNA of the blocker/target DNA duplex and displace the bound target DNA during the extension reaction. The released target DNA triggers the next cycle involving hybridization with blocker DNA, DNAzymeMB dissociation, primer extension, and target displacement. This unique amplifying strategy leads to the generation of multiple numbers of active DNAzymeMB molecules from a single target molecule and gives a detection limit down to 1 pM, a value that is nearly 3 or 5 orders of magnitude lower than those of previously reported DNAzyme Molecular Beacon-based DNA detection methods.
Weihong Tan - One of the best experts on this subject based on the ideXlab platform.
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a targeted self delivered and photocontrolled Molecular Beacon for mrna detection in living cells
Journal of the American Chemical Society, 2013Co-Authors: Liping Qiu, Jianhui Jiang, Mingxu You, Da Han, Tao Chen, Guizhi Zhu, Weihong TanAbstract:The spatiotemporal dynamics of specific mRNA molecules are difficult to image and detect inside living cells, and this has been a significant challenge for the chemical and biomedical communities. To solve this problem, we have developed a targeted, self-delivered, and photocontrolled aptamer-based Molecular Beacon (MB) for intracellular mRNA analysis. An internalizing aptamer connected via a double-stranded DNA structure was used as a carrier probe (CP) for cell-specific delivery of the MB designed to signal target mRNA. A light activation strategy was employed by inserting two photolabile groups in the CP sequence, enabling control over the MB’s intracellular function. After the probe was guided to the target cell via specific binding of aptamer AS1411 to nucleolin on the cell membrane, light illumination released the MB for mRNA monitoring. Consequently, the MB is able to perform live-cell mRNA imaging with precise spatiotemporal control, while the CP acts as both a tracer for intracellular distributio...
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A novel sensitive and selective ligation-based ATP assay using a Molecular Beacon.
The Analyst, 2013Co-Authors: Zhiwen Tang, Xiaohai Yang, Kemin Wang, Weihong TanAbstract:In this paper, a novel, facile fluorometric ATP assay with high sensitivity and excellent selectivity has been reported. This approach utilizes a Molecular Beacon, T4 DNA ligase and two short oligonucleotides. In the presence of ATP, the T4 DNA ligase catalyzes the ligation reaction and the ligation product restores the fluorescence of the Molecular Beacon. Owing to the high sensitivity of the Molecular Beacon and T4 DNA ligase's high substrate dependence, this novel ATP assay demonstrates exceptional selectivity and high sensitivity down to 0.14 nM in homogeneous solution. Cellular ATP concentrations in several cell lines have been determined by measuring the lysate sample containing 8.0 × 10(3) cells.
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Molecular Beacon based junction probes for efficient detection of nucleic acids via a true target triggered enzymatic recycling amplification
Analytical Chemistry, 2011Co-Authors: Rongmei Kong, Weihong Tan, Yan Huang, Xiaobing Zhang, Liangliang Zhang, Guoli ShenAbstract:This work reports the development of a new Molecular Beacon-based junction sensing system with highly sensitive DNA detection and a strong capability to identify SNPs. The single linear probe typically labels the midsection of the oligonucleotide, but our next-generation junction sensing system uses a hairpin-structured MB with labels on each end of the oligonucleotide to maintain the cleaving activity of our newly designed ssDNA-cleaved endonuclease, Nt.BbvCI, rather than the typical dsDNA-cleaved endonuclease. These design improvements guarantee a true and efficient target-triggered enzymatic recycling amplification process in our sensing system. They also afford a faster and more sensitive response toward target DNA than the first-generation junction sensing system.
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design of a novel Molecular Beacon modification of the stem with artificially genetic alphabet
Chemical Communications, 2008Co-Authors: Pinpin Sheng, Weihong Tan, Zunyi Yang, Youngmi Kim, Steven A BennerAbstract:A Molecular Beacon that incorporates components of an artificially expanded genetic information system (AEGIS) in its stem is shown not to be opened by unwanted stem invasion by adventitious standard DNA; this should improve the “darkness” of the Beacon in real-world applications.
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Molecular Beacon based array for sensitive dna analysis
Analytical Biochemistry, 2004Co-Authors: Gang Yao, Weihong TanAbstract:Molecular Beacon (MB) DNA probes provide a new way for sensitive label-free DNA/protein detection in homogeneous solution and biosensor development. However, a relatively low fluorescence enhancement after the hybridization of the surface-immobilized MB hinders its effective biotechnological applications. We have designed new Molecular Beacon probes to enable a larger separation between the surface and the surface-bound MBs. Using these MB probes, we have developed a DNA array on avidin-coated cover slips and have improved analytical sensitivity. A home-built wide-field optical setup was used for imaging the array. Our results show that linker length, pH, and ionic strength have obvious effects on the performance of the surface-bound MBs. The fluorescence enhancement of the new MBs after hybridization has been increased from 2 to 5.5. The MB-based DNA array could be used for DNA detection with high sensitivity, enabling simultaneous multiple-target bioanalysis in a variety of biotechnological applications.
Salvatore A. E. Marras - One of the best experts on this subject based on the ideXlab platform.
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Use of Sloppy Molecular Beacon Probes for Identification of Mycobacterial Species
Journal of clinical microbiology, 2009Co-Authors: Hiyam El-hajj, Fred Russell Kramer, Salvatore A. E. Marras, Sanjay Tyagi, Elena Shashkina, Mini Kamboj, Timothy E. Kiehn, Michael S. Glickman, David AllandAbstract:We report here the use of novel "sloppy" Molecular Beacon probes in homogeneous PCR screening assays in which thermal denaturation of the resulting probe-amplicon hybrids provides a characteristic set of amplicon melting temperature (T(m)) values that identify which species is present in a sample. Sloppy Molecular Beacons possess relatively long probe sequences, enabling them to form hybrids with amplicons from many different species despite the presence of mismatched base pairs. By using four sloppy Molecular Beacons, each possessing a different probe sequence and each labeled with a differently colored fluorophore, four different T(m) values can be determined simultaneously. We tested this technique with 27 different species of mycobacteria and found that each species generates a unique, highly reproducible signature that is unaffected by the initial bacterial DNA concentration. Utilizing this general paradigm, screening assays can be designed for the identification of a wide range of species.
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Design and optimization of Molecular Beacon real-time polymerase chain reaction assays.
Methods in molecular biology (Clifton N.J.), 2005Co-Authors: Jacqueline A. M. Vet, Salvatore A. E. MarrasAbstract:During the last few years, several innovative technologies have become available for performing sensitive and accurate genetic analyses. These techniques use fluorescent detection strategies in combination with nucleic acid amplification protocols. Most commonly used is the real-time polymerase chain reaction (PCR). To achieve the maximum potential of a real-time PCR assay, several parameters must be evaluated and optimized independently. This chapter describes the different steps necessary for establishing a Molecular Beacon real-time PCR assay: (1) target design, (2) primer design, (3) optimization of the amplification reaction conditions using SYBR Green, (4) Molecular Beacon design, and (5) Molecular Beacon synthesis and characterization. The last section provides an example of a multiplex quantitative real-time PCR.
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Rapid Identification of Candida dubliniensis Using a Species-Specific Molecular Beacon
Journal of clinical microbiology, 2000Co-Authors: Steven Park, Salvatore A. E. Marras, Sanjay Tyagi, Timothy E. Kiehn, May Wong, Emily W. Cross, Vishnu Chaturvedi, David S. PerlinAbstract:Candida dubliniensis is an opportunistic fungal pathogen that has been linked to oral candidiasis in AIDS patients, although it has recently been isolated from other body sites. DNA sequence analysis of the internal transcribed spacer 2 (ITS2) region of rRNA genes from reference Candida strains was used to develop Molecular Beacon probes for rapid, high-fidelity identification of C. dubliniensis as well as C. albicans. Molecular Beacons are small nucleic acid hairpin probes that brightly fluoresce when they are bound to their targets and have a significant advantage over conventional nucleic acid probes because they exhibit a higher degree of specificity with better signal-to-noise ratios. When applied to an unknown collection of 23 strains that largely contained C. albicans and a smaller amount of C. dubliniensis, the species-specific probes were 100% accurate in identifying both species following PCR amplification of the ITS2 region. The results obtained with the Molecular Beacons were independently verified by random amplified polymorphic DNA analysis-based genotyping and by restriction enzyme analysis with enzymes BsmAI and NspBII, which cleave recognition sequences within the ITS2 regions of C. dubliniensis and C. albicans, respectively. Molecular Beacons are promising new probes for the rapid detection of Candida species.
Lei Liu - One of the best experts on this subject based on the ideXlab platform.
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multiplexed discrimination of microrna single nucleotide variants through triplex Molecular Beacon sensors
Chemical Communications, 2018Co-Authors: Bingyuan Guo, Yingying Sheng, Yun Zhang, Jin Wang, Shuchuan Peng, Lei LiuAbstract:Herein, we develop a new nanopore sensing strategy for the selective detection of microRNAs and single nucleotide variants (SNVs) based on triplex Molecular Beacon sensors. This sensing system shows very high specificity in discriminating microRNA SNVs and can be applied for the simultaneous detection of several microRNAs of the same family in a mixture.
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analyte triggered dna probe release from a triplex Molecular Beacon for nanopore sensing
Angewandte Chemie, 2018Co-Authors: Bingyuan Guo, Yingying Sheng, Ke Zhou, Quansheng Liu, Lei LiuAbstract:A new nanopore sensing strategy based on triplex Molecular Beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming Molecular Beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the Molecular Beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point-of-care diagnostics with a portable nanopore kit in the future.
Meiping Zhao - One of the best experts on this subject based on the ideXlab platform.
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universal Molecular Beacon based tracer system for real time polymerase chain reaction
Analytical Chemistry, 2006Co-Authors: Yong Huang, Yuan Guan, Meiping ZhaoAbstract:DNA diagnostic has been moving from expensive, low-throughput, multistep methods to inexpensive, higher throughput, closed-tube, and automated methods. Fluorescence is the favored signaling technology for such assays. In this method, we describe a universal Molecular Beacon (U-MB) as the fluorescent tracer in the real-time PCR technique. A 5'-universal template primer (5'-UT primer) has been designed with a tail in complementary to the loop and 5'-side arm sequence of U-MB at the 5'-end of forward target specific primer. As PCR cycles increase, a new DNA fragment with a 5'-UT primer tail is synthesized, which is used as the template for next PCR cycle. As the reverse primer extends to the 5'-UT primer tail, the U-MB hybridized is displaced and the fluorescence from the fluorophore of the U-MB is quenched, indicating that the allele-specific PCR is in progress. This tracing system combined with an allele-specific reverse primer and vent (exo-) DNA polymerase, a polymerase that lacks 3'- to 5'-exonuclease activity, was used for the detection of point mutations of base G in codon 259 (AGA) of exon 7 of p53 gene on a panel of breast cancer individuals.
