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Zhao C, Xu W, Gao W. A real-time quantitative PCR based on molecular beacon for detecting Brucella infection. ARQ BRAS MED VET ZOO 2020. [DOI: 10.1590/1678-4162-11133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | - W. Xu
- Southeast University, China
| | - W. Gao
- Southeast University, China
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2
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Tomas D, Fan M, Zhu S, Klijn A. Use of biochemical miniaturized galleries, rRNA based lateral flow assay and Real Time PCR for Cronobacter spp. confirmation. Food Microbiol 2018; 76:189-195. [DOI: 10.1016/j.fm.2018.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/04/2018] [Accepted: 05/21/2018] [Indexed: 10/16/2022]
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3
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Wills MKB, Kirby AM, Lloyd VK. Detecting the Lyme Disease Spirochete, Borrelia Burgdorferi, in Ticks Using Nested PCR. J Vis Exp 2018. [PMID: 29443061 PMCID: PMC5912355 DOI: 10.3791/56471] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lyme disease is a serious vector-borne infection that is caused by the Borrelia burgdorferi sensu lato family of spirochetes, which are transmitted to humans through the bite of infected Ixodes ticks. The primary etiological agent in North America is Borrelia burgdorferi sensu stricto. As geographic risk regions expand, it is prudent to support robust surveillance programs that can measure tick infection rates, and communicate findings to clinicians, veterinarians, and the general public. The molecular technique of nested polymerase chain reaction (nPCR) has long been used for this purpose, and it remains a central, inexpensive, and robust approach in the detection of Borrelia in both ticks and wildlife. This article demonstrates the application of nPCR to tick DNA extracts to identify infected specimens. Two independent B. burgdorferi targets, genes encoding Flagellin B (FlaB) and Outer surface protein A (OspA), have been used extensively with this technique. The protocol involves tick collection, DNA extraction, and then an initial round of PCR to detect each of the two Borrelia-specific loci. Subsequent polymerase chain reaction (PCR) uses the product of the first reaction as a new template to generate smaller, internal amplification fragments. The nested approach improves upon both the specificity and sensitivity of conventional PCR. A tick is considered positive for the pathogen when inner amplicons from both Borrelia genes can be detected by agarose gel electrophoresis.
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Affiliation(s)
| | | | - Vett K Lloyd
- Department of Biology, Mount Allison University;
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4
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LNA-modified isothermal oligonucleotide microarray for differentiating bacilli of similar origin. J Biosci 2015; 39:795-804. [PMID: 25431409 DOI: 10.1007/s12038-014-9485-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Oligonucleotide microarray has been one of the most powerful tools in the 'Post-Genome Era' for its high sensitivity, high throughput and parallel processing capability. To achieve high detection specificity, we fabricated an isothermal microarray using locked nucleic acid (LNA)-modified oligonucleotide probes, since LNA has demonstrated the advanced ability to enhance the binding affinity toward their complementary nucleotides. After designing the nucleotide sequences of these oligonucleotide probes for gram-positive bacilli of similar origin (Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus megaterium and Bacillus circulans), we unified the melting temperatures of these oligonucleotide probes by modifying some nucleotides using LNA. Furthermore, we optimized the experimental procedures of hydrating microarray slides, blocking side surface as well as labelling the PCR products. Experimental results revealed that KOD Dash DNA polymerase could efficiently incorporate Cy3-dCTP into the PCR products, and the LNA-isothermal oligonucleotide microarray were able to distinguish the bacilli of similar origin with a high degree of accuracy and specificity under the optimized experimental condition.
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Wu GQ, Liu NN, Xue XL, Cai LT, Zhang C, Qu QR, Yan XJ. Multiplex Real-time PCR for RRM1, XRCC1, TUBB3 and TS mRNA for Prediction of Response of Non-small Cell Lung Cancer to Chemoradiotherapy. Asian Pac J Cancer Prev 2014; 15:4153-8. [DOI: 10.7314/apjcp.2014.15.10.4153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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6
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Homogeneous duplex polymerase chain reaction assay using switchable lanthanide fluorescence probes. Anal Biochem 2013; 436:16-21. [DOI: 10.1016/j.ab.2013.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/07/2013] [Accepted: 01/12/2013] [Indexed: 11/20/2022]
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7
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Jacroux T, Rieck DC, Cui R, Ouyang Y, Dong WJ. Enzymatic amplification of DNA/RNA hybrid molecular beacon signaling in nucleic acid detection. Anal Biochem 2013; 432:106-14. [PMID: 23000602 PMCID: PMC3522425 DOI: 10.1016/j.ab.2012.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 11/22/2022]
Abstract
A rapid assay operable under isothermal or nonisothermal conditions is described, where the sensitivity of a typical molecular beacon (MB) system is improved by using thermostable RNase H to enzymatically cleave an MB composed of a DNA stem and an RNA loop (R/D-MB). On hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7× above background) due to an opening of the probe and a concomitant reduction in the Förster resonance energy transfer efficiency. The addition of thermostable RNase H resulted in the cleavage of the RNA loop, which eliminated energy transfer. The cleavage step also released bound target DNA, enabling it to bind to another R/D-MB probe and rendering the approach a cyclic amplification scheme. Full processing of R/D-MBs maximized the fluorescence signal to the fullest extent possible (12.9× above background), resulting in an approximately 2- to 2.8-fold increase in the signal-to-noise ratio observed isothermally at 50 °C following the addition of RNase H. The probe was also used to monitor real-time polymerase chain reactions by measuring enhancement of donor fluorescence on R/D-MB binding to amplified pUC19 template dilutions. Hence, the R/D-MB-RNase H scheme can be applied to a broad range of nucleic acid amplification methods.
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Affiliation(s)
- Thomas Jacroux
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Daniel C. Rieck
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Rong Cui
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
| | - Yexin Ouyang
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
| | - Wen-Ji Dong
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
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8
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Mishra S, Ghosh S, Mukhopadhyay R. Maximizing mismatch discrimination by surface-tethered locked nucleic acid probes via ionic tuning. Anal Chem 2013; 85:1615-23. [PMID: 23268627 DOI: 10.1021/ac3028382] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several investigations on DNA-based nucleic acid sensors performed in the past few years point toward the requirement of an alternative nucleic acid that can detect target DNA strands more efficiently, i.e., with higher sensitivity and selectivity, and can be more robust compared to the DNA sensor probes. Locked nucleic acid (LNA), a conformationally restricted DNA analogue, is potentially a better alternative than DNA, since it is nuclease-resistant, it can form a more stable duplex with DNA in a sequence-specific manner, and it interacts less with substrate surface due to presence of a rigid backbone. In this work, we probed solid-phase dehybridization of ssDNA targets from densely packed fully modified ssLNA probes immobilized onto a gold(111) surface by fluorescence-based measurement of the "on-surface" melting temperatures. We find that mismatch discrimination can be clearly improved by applying the surface-tethered LNA probes, in comparison to the corresponding DNA probes. We show that concentration as well as type of cation (monovalent and polyvalent) can significantly influence thermal stability of the surface-confined LNA-DNA duplexes, the nature of concentration dependence contradicting the solution phase behavior. Since the ionic setting influenced the fully matched duplexes more strongly than the singly mismatched duplexes, the mismatch discrimination ability of the surface-confined LNA probes could be controlled by ionic modulations. To our knowledge, this is the first report on ionic regulation of melting behavior of surface-confined LNA-DNA duplexes.
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Affiliation(s)
- Sourav Mishra
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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Kolpashchikov DM. An elegant biosensor molecular beacon probe: challenges and recent solutions. SCIENTIFICA 2012; 2012:928783. [PMID: 24278758 PMCID: PMC3820487 DOI: 10.6064/2012/928783] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/10/2012] [Indexed: 05/02/2023]
Abstract
Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.
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Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
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Huang J, Su X, Li Z. Enzyme-Free and Amplified Fluorescence DNA Detection Using Bimolecular Beacons. Anal Chem 2012; 84:5939-43. [DOI: 10.1021/ac3004727] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jiahao Huang
- Department of Mechanical Engineering, The Hong Kong University of Science and Technology,
Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public Health and
Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories,
Hong Kong
| | - Zhigang Li
- Department of Mechanical Engineering, The Hong Kong University of Science and Technology,
Clear Water Bay, Kowloon, Hong Kong
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Detection of Raw Pork Targeting Porcine-Specific Mitochondrial Cytochrome B Gene by Molecular Beacon Probe Real-Time Polymerase Chain Reaction. FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-011-9260-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Satterfield BC, Bartosiewicz M, West JAA, Caplan MR. Surpassing specificity limits of nucleic acid probes via cooperativity. J Mol Diagn 2010; 12:359-67. [PMID: 20304941 DOI: 10.2353/jmoldx.2010.090056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The failure to correctly identify single nucleotide polymorphisms (SNPs) significantly contributes to the misdiagnosis of infectious disease. Contrary to the strategy of creating shorter probes to improve SNP differentiation, we created larger probes that appeared to increase selectivity. Specifically, probes with enhanced melting temperature differentials (>13x improvement) to SNPs were generated by linking two probes that consist of both a capture sequence and a detection sequence; these probes act cooperatively to improve selectivity over a wider range of reaction conditions. These cooperative probe constructs (Tentacle probes) were then compared by modeling thermodynamic and hybridization characteristics to both Molecular Beacons (stem loop DNA probes) and Taqman probes (a linear oligonucleotide). The biophysical models reveal that cooperative probes compared with either Molecular beacons or Taqman probes have enhanced specificity. This was a result of increased melting temperature differentials and the concentration-independent hybridization revealed between wild-type and variant sequences. We believe these findings of order of magnitude enhanced melting temperature differentials with probes possessing concentration independence and more favorable binding kinetics have the potential to significantly improve molecular diagnostic assay functionality.
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Affiliation(s)
- Brent C Satterfield
- Arcxis Biotechnologies, 6920 Koll Center Pkwy, Suite 215, Pleasanton, CA 94566, USA
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Ye Q, Zhuang H, Zhou C, Wang Q. Real-time fluorescent quantitative immuno-PCR method for determination of fluoranthene in water samples with a molecular beacon. J Environ Sci (China) 2010; 22:796-800. [PMID: 20608519 DOI: 10.1016/s1001-0742(09)60179-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A reliable and sensitive competitive real-time fluorescent quantitative immuno-PCR (RTFQ-IPCR) assay using a molecular beacon was developed for the determination of trace fluoranthene (FL) in the environment. Under optimized assay conditions, FL can be determined in the concentration range from 1 fg/mL to 100 ng/mL, withy = 0.194x + 7.859, and a correlation coefficient of 0.967 was identified, with a detection limit of 0.6 fg/mL. Environmental water samples were successfully analyzed, recovery was between 90% and 116%, with intra-day relative standard deviation (RSD) of 6.7%-12.8% and inter-day RSD of 8.4%-15.2%. The results obtained from RTFQ-IPCR were confirmed by ELISA, showing good accuracy and suitability to analyze FL in field samples. As a highly sensitive method, the molecular beacon-based RTFQ-IPCR is acceptable and promising for providing reliable test results to make environmental decisions.
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Affiliation(s)
- Qiyan Ye
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
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Zhuang H, Ye Q, Chen H. Detection of PCB77 by Antibody-Coated Competitive Fluorescent Quantitative Immuno-PCR Using Molecular Beacon. ANAL LETT 2009. [DOI: 10.1080/00032710903201891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Ye QY, Zhuang HS, Zhou C. Detection of trace anthracene in soil samples with real-time fluorescence quantitative immuno-PCR using a molecular beacon probe. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2009; 28:386-391. [PMID: 21784031 DOI: 10.1016/j.etap.2009.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Revised: 06/09/2009] [Accepted: 06/13/2009] [Indexed: 05/31/2023]
Abstract
We developed a highly sensitive and robust real-time fluorescence quantitative immuno-PCR (RTFQ-IPCR) method which uses molecular beacon (MB) probe to detect trace anthracene in the environment. This method was performed on serial dilutions of known anthracene concentrations equivalent to 10-fold dilutions of 10fg/mL to 100pg/mL. We obtained a linear relationship between 10fg/mL and 100pg/mL, with y=0.684x+13.221. A correlation coefficient of 0.994 was also identified, with a detection limit of 4.5fg/mL. After investigating the presence of anthracene in soil samples via RTFQ-IPCR, the obtained concentrations were confirmed by ELISA to be correct and believable, with the recovery ratio ranging from 82% to 112.5%. Based on its sensitivity and reproducibility, MB-based RTFQ-IPCR was found to be acceptable for use in on-site field tests to provide rapid, quantitative, and reliable test results for making environmental decisions.
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Affiliation(s)
- Qi-Yan Ye
- College of Environmental Science and Engineering, Donghua University, 2999 North Renming Road, Songjiang, Shanghai 201620, China
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Ram S, Vajpayee P, Shanker R. Enterotoxigenic Escherichia coli in sewage-impacted waters and aquatic weeds: quantitative PCR for culture-independent enumeration. J Appl Microbiol 2009; 108:1007-1014. [PMID: 19735327 DOI: 10.1111/j.1365-2672.2009.04501.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM To develop quantitative PCR for culture-independent enumeration of enterotoxigenic Escherichia coli (ETEC) in sewage-impacted waters and aquatic weeds. METHODS AND RESULTS Two fluorescent probes (TaqMan and FRET) based on two different real-time PCR chemistries were designed in highly conserved region of LT1 gene encoding heat labile enterotoxin. Both the assays could detect 2 CFU ml(-1) from serially diluted (two-fold and ten-fold) culture of reference strain (E. coli MTCC 723). FRET performed better in terms of CT value and PCR efficiency than TaqMan. The presence of 10(6) CFU ml(-1) of nonpathogenic E. coli reduced the detection limit two-fold with both the probes. However, the performance for two chemistries in various environmental samples was significantly (student's t-test, P<0.05) different. CONCLUSION It could be inferred from this study that real-time PCR chemistries (TaqMan and FRET) could detect very few copies of target DNA in pure cultures, but may give varied response in the presence of nonspecific DNA and natural inhibitors present in environmental sample matrices. SIGNIFICANCE AND IMPACT OF THE STUDY The assays can be used for pre-emptive monitoring of aquatic weeds (a potential nonpoint source), surface and potable waters to prevent waterborne outbreaks caused by ETEC.
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Affiliation(s)
- S Ram
- Indian Institute of Toxicology Research (C.S.I.R.), PO Box 80, Mahatma Gandhi Marg, Lucknow-226001, UP, India
| | - P Vajpayee
- Indian Institute of Toxicology Research (C.S.I.R.), PO Box 80, Mahatma Gandhi Marg, Lucknow-226001, UP, India
| | - R Shanker
- Indian Institute of Toxicology Research (C.S.I.R.), PO Box 80, Mahatma Gandhi Marg, Lucknow-226001, UP, India
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Oh KJ, Cash KJ, Plaxco KW. Beyond molecular beacons: optical sensors based on the binding-induced folding of proteins and polypeptides. Chemistry 2009; 15:2244-51. [PMID: 19191230 DOI: 10.1002/chem.200701748] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Many polypeptides and small proteins can be readily engineered such that they only fold upon binding a specific target ligand. This approach couples target recognition with a considerable change in polymer structure and dynamics. Recent years have seen the development of a number of biosensors that couple these large changes to readily measurable optical (fluorescent) outputs. These sensors afford the detection of a wide variety of macromolecular targets including proteins, polypeptides, and nucleic acids. Here we describe the design of such biosensors, from the first iterations as protein engineering experiments, to the development of biosensors targeting a range of protein and nucleic acid targets.
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Affiliation(s)
- Kenneth J Oh
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
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Saidac DS, Marras SAE, Parveen N. Detection and quantification of Lyme spirochetes using sensitive and specific molecular beacon probes. BMC Microbiol 2009; 9:43. [PMID: 19239692 PMCID: PMC2670302 DOI: 10.1186/1471-2180-9-43] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 02/24/2009] [Indexed: 11/10/2022] Open
Abstract
Background Lyme disease, caused by Borrelia burgdorferi, affects a large number of people in both the USA and Europe. The mouse is a natural host for this spirochete and is widely used as a model system to study Lyme pathogenesis mechanisms. Since disease manifestations often depend upon the spirochete burden in a particular tissue, it is critical to accurately measure the bacterial number in infected tissues. The current methods either lack sensitivity and specificity (SYBR Green), or require independent analysis of samples in parallel to quantitate host and bacterial DNA (TaqMan). We have developed a novel molecular beacon-based convenient multiplex real-time quantitative PCR assay to identify and detect small numbers of B. burgdorferi in infected mouse tissues. Results We show here that molecular beacons are effective, sensitive and specific probes for detecting and estimating wide-ranging numbers of B. burgdorferi in the presence of mouse DNA. In our assays, the spirochete recA and the mouse nidogen gene amplicons were detected simultaneously using molecular beacons labeled with different fluorophores. We further validated the application of these probes by quantifying the wild-type strain and bgp-defective mutant of B. burgdorferi. The bgp-defective mutant shows a ten-fold reduction in the level of spirochetes present in various tissues. Conclusion The high sensitivity and specificity of molecular beacons makes them superior probes for the detection of small numbers of B. burgdorferi. Furthermore, the use of molecular beacons can be expanded for the simultaneous detection and quantification of multiple pathogens in the infected hosts, including humans, and in the arthropod vectors.
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Affiliation(s)
- Diana S Saidac
- Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, NJ 07103-3535, USA.
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Ye Q, Zhuang H, Zhou C. Detection of naphthalene by real-time immuno-PCR using molecular beacon. Mol Cell Probes 2008; 23:29-34. [PMID: 19028563 DOI: 10.1016/j.mcp.2008.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 10/22/2008] [Accepted: 10/22/2008] [Indexed: 10/21/2022]
Abstract
A rapid and quantitative technique is urgently needed in detecting toxicological and carcinogenic polycyclic aromatic hydrocarbons (PAHs) in the environment. Using a molecular beacon (MB), this study aimed at detecting the presence of naphthalene through an assay developed via a highly sensitive and robust, real-time fluorescent quantitative immuno-PCR (FQ-IPCR), which was then performed on serial dilutions of known naphthalene concentrations equivalent to 10-fold dilutions of 1-10(4) fg/mL. A correlation coefficient of 0.996 was identified, and a linear relationship between 1 fg/mL and 10 pg/mL, with y = 1.392x + 11.188, was obtained. A trace amount (1 fg/mL) of naphthalene congeners could be detected using this method. Five water samples were then used for validation, the results of which were further confirmed through a conventional enzyme-linked immuno sorbent assay (ELISA). Based on sensitivity and reproduction, the MB-based FQ-IPCR technique is a promising tool for monitoring environmental endocrine disruptors.
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Affiliation(s)
- Qiyan Ye
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
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Takács T, Jeney C, Kovács L, Mózes J, Benczik M, Sebe A. Molecular beacon-based real-time PCR method for detection of 15 high-risk and 5 low-risk HPV types. J Virol Methods 2008; 149:153-62. [DOI: 10.1016/j.jviromet.2007.12.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 12/07/2007] [Accepted: 12/13/2007] [Indexed: 11/26/2022]
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Abstract
Locked nucleic acids (LNA) show remarkable affinity and specificity against native DNA targets. Effects of LNA modifications on mismatch discrimination were studied as a function of sequence context and identity of the mismatch using ultraviolet (UV) melting experiments. A triplet of LNA residues centered on the mismatch was generally found to have the largest discriminatory power. An exception was observed for G–T mismatches, where discrimination decreased when the guanine nucleotide at the mismatch site or even the flanking nucleotides were modified. Fluorescence experiments using 2-aminopurine suggest that LNA modifications enhance base stacking of perfectly matched base pairs and decrease stabilizing stacking interactions of mismatched base pairs. LNAs do not change the amount of counterions (Na+) that are released when duplexes denature. New guidelines are suggested for design of LNA probes, which significantly improve mismatch discrimination in comparison with unmodified DNA probes.
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Affiliation(s)
| | | | | | - Richard Owczarzy
- To whom correspondence should be addressed. Tel: +1 319 626 8459; Fax: +1 319 626 8444;
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