1
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Optimization and performance evaluation of double-stranded probe in real-time PCR. Anal Biochem 2022; 650:114711. [PMID: 35561816 DOI: 10.1016/j.ab.2022.114711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/18/2022] [Accepted: 05/01/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND TaqMan probe-based real-time PCR (qPCR/RT-qPCR) has been widely used in various fields because of its high sensitivity and specificity. However, TaqMan probes are associated with a relatively higher background signal, and hence negatively affect the detection results. METHODS Double-stranded probes (DSPs) were designed for the high sensitive detection of hepatitis B virus (HBV) DNA and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA using qPCR/RT-qPCR. DSPs consist of different lengths of positive and negative strands with complementary oligonucleotides. We systematically optimized DSP length, the free energy of hybridization (ΔG) between complementary oligonucleotides, and the length of sticky ends, and DSP performance was evaluated in comparison with other types of probes. RESULTS By using similar length positive and negative strands, controlling ΔG between complementary oligonucleotides to approximately -30 kcal/mol, and maintaining the sticky end length at 4-6 nt, the analytical performance of DSP was significantly improved. Compared with other types of probes, DSP is advantageous in fluorescence signal intensity and sensitivity. CONCLUSION DSPs can further improve the detection sensitivity and the detection rate of low-concentration samples in molecular diagnosis.
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2
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Vilchez Mercedes SA, Eder I, Ahmed M, Zhu N, Wong PK. Optimizing locked nucleic acid modification in double-stranded biosensors for live single cell analysis. Analyst 2022; 147:722-733. [DOI: 10.1039/d1an01802g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Double-stranded (ds) biosensors are homogeneous oligonucleotide probes for detection of nucleic acid sequences in biochemical assays and live cell imaging.
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Affiliation(s)
- Samuel A. Vilchez Mercedes
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ian Eder
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mona Ahmed
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ninghao Zhu
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Pak Kin Wong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Mechanical Engineering and Department of Surgery, The Pennsylvania State University, University Park, PA, 16802, USA
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3
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Maree L, Krügel M, Reinhardt B, Glass AJ. Evaluation of the Alinity m HIV-1 assay for the quantification of HIV-1 RNA plasma viral load in a high-throughput molecular laboratory in South Africa. J Clin Virol 2020; 132:104644. [DOI: 10.1016/j.jcv.2020.104644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/13/2020] [Indexed: 10/23/2022]
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4
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Addy PS, Zheng Y, Italia JS, Chatterjee A. A "Quenchergenic" Chemoselective Protein Labeling Strategy. Chembiochem 2019; 20:1659-1663. [PMID: 30740850 PMCID: PMC6663590 DOI: 10.1002/cbic.201800817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Indexed: 12/21/2022]
Abstract
Dynamic changes in protein structure can be monitored by using a fluorescent probe and a dark quencher. This approach is contingent upon the ability to precisely introduce a fluorophore/quencher pair into two specific sites of a protein of interest. Despite recent advances, there is continued demand for new and convenient approaches to site-selectively label proteins with such optical probes. We have recently developed a chemoselectively rapid azo-coupling reaction (CRACR) for site-specific protein labeling; it relies on rapid coupling between a genetically encoded 5-hydroxytryptophan residue and various aromatic diazonium ions. Herein, it is reported that the product of this conjugation reaction, a highly chromophoric biarylazo group, is a potent fluorescence quencher. The absorption properties of this azo product can be tuned by systematically altering the structure of the aryldiazonium species. A particular "quenchergenic" aryldiazonium has been identified that, upon conjugation, efficiently quenches the fluorescence of green fluorescent protein, which is a widely used genetically encoded fluorescent probe that can be terminally attached to target proteins. This fluorophore/quencher pair was used to evaluate the protein-labeling kinetics of CRACR, as well as to monitor the proteolysis of a fusion protein.
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Affiliation(s)
- Partha Sarathi Addy
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - Yunan Zheng
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - James S Italia
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, USA
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5
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Farzan VM, Kvach MV, Aparin IO, Kireev DE, Prikazchikova TA, Ustinov AV, Shmanai VV, Shipulin GA, Korshun VA, Zatsepin TS. Novel homo Yin-Yang probes improve sensitivity in RT-qPCR detection of low copy HIV RNA. Talanta 2019; 194:226-232. [DOI: 10.1016/j.talanta.2018.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 12/31/2022]
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6
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Rios L, Perera CL, Coronado L, Relova D, Álvarez AM, Ganges L, Díaz de Arce H, Núñez JI, Pérez LJ. Multi-Target Strategy for Pan/Foot-and-Mouth Disease Virus (FMDV) Detection: A Combination of Sequences Analysis, in Silico Predictions and Laboratory Diagnostic Evaluation. Front Vet Sci 2018; 5:160. [PMID: 30050913 PMCID: PMC6052897 DOI: 10.3389/fvets.2018.00160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/25/2018] [Indexed: 12/29/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting cloven-hoofed animals that causes severe economic losses. The disease is characterized by a vesicular condition and it cannot be differentiated from other vesicular diseases. Therefore, laboratory confirmation of any suspected FMD case is compulsory. Despite viral isolation in cell cultures has been considered for many years as the gold standard for FMD diagnosis, the advantages of real-time reverse transcription polymerase chain reaction (rRT-PCR) technology have motivated its use directly in clinical specimens for FMD diagnosis. The current work was aimed to develop and validate a molecular multi-check strategy using rRT-PCR (mMulti-rRT-PCR) based on SYBR-Green I for pan/foot-and-mouth disease virus (pan/FMDV) diagnosis. From in silico approaches, different primer pairs previously reported were selected and modified to reduce the likelihood of viral escape as well as potential failures in the pan/FMDV detection. The analytical parameters were evaluated using a high number of representative viral strains. The repeatability of the assay and its performance on field samples were also assessed. The mMulti-rRT-PCR was able to detect emergent FMDV strains that circulated in South America between the years 2006–2010 and on which the single rRT-PCRs failed when they were applied independently. The results obtained here showed that the proposed system is an accurate and rapid diagnosis method for sensitive and specific detection of FMDV. Thus, a validated mMulti-rRT-PCR assay based on SYBR-Green I detection coupled to melting curves resolution for pan/FMDV diagnosis on clinical samples is proposed. This study also highlights the need to incorporate the multi-target detection principle in the diagnosis of highly variable agents, specially, of those listed by OIE like FMDV.
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Affiliation(s)
- Liliam Rios
- Reiman Cancer Research Laboratory, Faculty of Medicine, University of New Brunswick, Saint John, NB, Canada
| | - Carmen L Perera
- Centro Nacional de Sanidad Agropecuaria, OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribean Region, San José de las Lajas, Cuba
| | - Liani Coronado
- Centro Nacional de Sanidad Agropecuaria, OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribean Region, San José de las Lajas, Cuba
| | - Damarys Relova
- Centro Nacional de Sanidad Agropecuaria, OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribean Region, San José de las Lajas, Cuba
| | - Ana M Álvarez
- Instituto Nacional de Investigaciones Agricolas, Maracay, Venezuela
| | - Llilianne Ganges
- OIE Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain.,IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autonoma de Barcelona, Barcelona, Spain
| | | | - José I Núñez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Lester J Pérez
- Dalhousie Medicine New Brunswick, Dalhousie University, Saint John, NB, Canada
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7
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Lee T, Wi JS, Oh A, Na HK, Lee J, Lee K, Lee TG, Haam S. Highly robust, uniform and ultra-sensitive surface-enhanced Raman scattering substrates for microRNA detection fabricated by using silver nanostructures grown in gold nanobowls. NANOSCALE 2018; 10:3680-3687. [PMID: 29323386 DOI: 10.1039/c7nr08066b] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Highly sensitive and reproducible surface enhanced Raman spectroscopy (SERS) requires not only a nanometer-level structural control, but also superb uniformity across the SERS substrate for practical imaging and sensing applications. However, in the past, increased reproducibility of the SERS signal was incompatible with increased SERS sensitivity. This work presents multiple silver nanocrystals inside periodically arrayed gold nanobowls (SGBs) via an electrochemical reaction at an overpotential of -3.0 V (vs. Ag/AgCl). The gaps between the silver nanocrystals serve as hot spots for SERS enhancement, and the evenly distributed gold nanobowls lead to a high device-to-device signal uniformity. The SGBs on the large sample surface exhibit an excellent SERS enhancement factor of up to 4.80 × 109, with excellent signal uniformity (RSD < 8.0 ± 2.5%). Furthermore, the SGBs can detect specific microRNA (miR-34a), which plays a widely acknowledged role as biomarkers in diagnosis and treatment of diseases. Although the small size and low abundance of miR-34a in total RNA samples hinder their detection, by utilizing the advantages of SGBs in SERS sensing, reliable and direct detection of human gastric cancer cells has been successfully accomplished.
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Affiliation(s)
- Taeksu Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 120-749, Republic of Korea.
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8
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Lee HJ, Go GH, Ro JJ, Kim BH. Detection of cofilin mRNA by hybridization-sensitive double-stranded fluorescent probes. RSC Adv 2018; 8:7514-7517. [PMID: 35539109 PMCID: PMC9078427 DOI: 10.1039/c7ra13349a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/10/2018] [Indexed: 12/13/2022] Open
Abstract
We have developed hybridization-sensitive fluorescent oligonucleotide probes that, in the presence of quencher strands, undergo efficient fluorescence quenching through the formation of partial DNA/DNA duplexes.
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Affiliation(s)
- Ha Jung Lee
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Gui Han Go
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Jong Jin Ro
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
| | - Byeang Hyean Kim
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Republic of Korea
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9
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Ki J, Jang E, Han S, Shin MK, Kang B, Huh YM, Haam S. Instantaneous pH-Boosted Functionalization of Stellate Gold Nanoparticles for Intracellular Imaging of miRNA. ACS APPLIED MATERIALS & INTERFACES 2017; 9:17702-17709. [PMID: 28524648 DOI: 10.1021/acsami.6b16452] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Various types of nanoprobes have recently been utilized to monitor living organisms by detecting and imaging intracellular biomarkers, such as microRNAs (miRs). We here present a simple one-pot method to prepare stellate gold nanoparticles functionalized with miR-detecting molecular beacons (SGNP-MBs); low pH conditions permitted the rapid-high loading of MBs on the surface of SGNPs. Compared to the conventional gold nanoparticle-based MBs, SGNPs carried a 4.5-fold higher load of MBs and exhibited a 6.4-fold higher cellular uptake. We demonstrated that SGNP-MBs were successfully internalized in human gastric cancer cell lines and could be used to accurately detect and image intracellular miRs in an miR-specific manner. Furthermore, the relative levels of intracellular miRs in three different cell lines expressing miR-10b (high, moderate, and low levels) could be monitored using SGNP-MBs. Consequently, these results indicated that SGNP-MBs could have applications as highly potent, efficient nanoprobes to assess intracellular miR levels in living cells.
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Affiliation(s)
- Jisun Ki
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Eunji Jang
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Seungmin Han
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Moo-Kwang Shin
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Byunghoon Kang
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University , Seoul 120-752, South Korea
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
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10
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Liu T, Wan Z, Liu J, Zhang L, Zhou Y, Lan K, Hu Y, Zhang C. A novel real-time reverse transcription-polymerase chain reaction assay with partially double-stranded linear DNA probe for sensitive detection of hepatitis C viral RNA. J Virol Methods 2016; 236:132-138. [PMID: 27451264 DOI: 10.1016/j.jviromet.2016.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 06/11/2016] [Accepted: 07/16/2016] [Indexed: 12/25/2022]
Abstract
The detection and quantification of HCV RNA is very helpful for the management and treatment of HCV related diseases. Detection of low HCV viral load is a great challenge in HCV RNA detection. Here, we developed a novel real-time RT-PCR assay with partially double-stranded linear DNA probe which can detect all HCV genotypes and improve the detection performance. The novel assay has a wide linear dynamic range of HCV RNA quantification (1×10(2)-1×10(11)IU/ml) and a limit of detection of 78IU/ml. The assay exhibits an excellent reproducibility with 2.52% and 1.33% coefficients of variations, for inter- and intra-assays, respectively. To evaluate the viability of the assay, a comparison with a commercial HCV RNA detection kit was performed using 106 serum samples. The lineared correlation coefficient between the novel assay and the commercial HCV RNA detection kit was 0.940. Meanwhile, the deviation between the two methods was tolerable. Therefore, the novel real-time RT-PCR assay was applicable for laboratory diagnosis and monitoring of HCV infection.
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Affiliation(s)
- Tianfu Liu
- Department of Hepatology, Lanzhou University Second Hospital, Lanzhou, Gansu, China; Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, Jiangsu, China
| | - Jia Liu
- Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Lingyi Zhang
- Department of Hepatology, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Yanheng Zhou
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Ke Lan
- Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Yihong Hu
- Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China.
| | - Chiyu Zhang
- Pathogen Diagnostic Center, CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China.
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11
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[Use of dried blood spots in early diagnosis of HIV-1 infection in children born to HIV-infected mothers as part of the prevention of mother-to-child transmission in Benin]. ACTA ACUST UNITED AC 2016; 109:155-9. [PMID: 27385037 DOI: 10.1007/s13149-016-0509-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
The goal of this study was to evaluate using the molecular diagnosis, infection transmission rate of HIV in children born to HIV-1 positive mothers as part of the prevention of mother-to-child transmission (PMTCT) in Benin. The sample consisted of 524 dried blood spots (DBS) of children born to HIV-1 positive mothers, from 30 sites (PMTCT) taken between October 2009 and June 2010. The diagnosis of HIV-1 was performed by the qualitative detection of viral nucleic acids (RNA and DNA) in DBS on filter paper using the Abbott RealTime(®) HIV-1 Qualitative assay. We found that 51 DBS were positive (9.7%) and 473 were negative (90.3%). The failure rate of PMTCT among 420 mothers who received antiretroviral prophylaxis was 6.7% (28/420). This failure rate was significantly higher among children born to infected mothers on antiretroviral monotherapy than on triple therapy (HAART). The results of our study enrich the data in the literature on highly active antiretroviral chemoprophylaxis to reduce the transmission of HIV-1 from mother to child.
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12
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Ebrahimi S, Kompany-Zareh M. Investigation of kinetics and thermodynamics of DNA hybridization by means of 2-D fluorescence spectroscopy and soft/hard modeling techniques. Anal Chim Acta 2016; 906:58-71. [DOI: 10.1016/j.aca.2015.11.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/27/2015] [Accepted: 11/30/2015] [Indexed: 01/23/2023]
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13
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Molecular Detection and Characterization of Hepatitis B Virus. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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O'Steen MR, Cornett EM, Kolpashchikov DM. Nuclease-containing media for resettable operation of DNA logic gates. Chem Commun (Camb) 2015; 51:1429-31. [PMID: 25493931 DOI: 10.1039/c4cc09283j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We designed and tested a system that allows DNA logic gates to respond multiple times to the addition of oligonucleotide inputs. After producing an output signal, the system spontaneously resets to the background state. This system does not require any operator action to achieve reset of a DNA logic gate, and may become useful for construction of reusable DNA-based computational devices.
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Affiliation(s)
- Martin R O'Steen
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA.
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15
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Zou J, Li N. Quantitative thermodynamic predication of interactions between nucleic acid and non-nucleic acid species using Microsoft excel. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2013; 111:755-762. [PMID: 23849929 DOI: 10.1016/j.cmpb.2013.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/05/2013] [Accepted: 06/14/2013] [Indexed: 06/02/2023]
Abstract
Proper design of nucleic acid sequences is crucial for many applications. We have previously established a thermodynamics-based quantitative model to help design aptamer-based nucleic acid probes by predicting equilibrium concentrations of all interacting species. To facilitate customization of this thermodynamic model for different applications, here we present a generic and easy-to-use platform to implement the algorithm of the model with Microsoft(®) Excel formulas and VBA (Visual Basic for Applications) macros. Two Excel spreadsheets have been developed: one for the applications involving only nucleic acid species, the other for the applications involving both nucleic acid and non-nucleic acid species. The spreadsheets take the nucleic acid sequences and the initial concentrations of all species as input, guide the user to retrieve the necessary thermodynamic constants, and finally calculate equilibrium concentrations for all species in various bound and unbound conformations. The validity of both spreadsheets has been verified by comparing the modeling results with the experimental results on nucleic acid sequences reported in the literature. This Excel-based platform described here will allow biomedical researchers to rationalize the sequence design of nucleic acid probes using the thermodynamics-based modeling even without relevant theoretical and computational skills.
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Affiliation(s)
- Jiaqi Zou
- Department of Mechanical and Aerospace Engineering, University of Miami, Coral Gables, FL 33124, USA
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16
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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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17
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Kim E, Yang J, Park J, Kim S, Kim NH, Yook JI, Suh JS, Haam S, Huh YM. Consecutive targetable smart nanoprobe for molecular recognition of cytoplasmic microRNA in metastatic breast cancer. ACS NANO 2012; 6:8525-8535. [PMID: 22947044 DOI: 10.1021/nn300289u] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report smart nanoprobe, hyaluronic acid (HA)-based nanocontainers containing miR-34a beacons (bHNCs), for the intracellular recognition of miR-34a levels in metastatic breast cancer cells, which is distinct from the imaging of biomarkers such of cell membrane receptors such as HER2. In this study, we demonstrate that a nanoscale vesicle that couples a targeting endocytic route, CD44, and a molecular imaging probe enables the efficient detection of specific miRNAs. Furthermore, bHNCs showed no cytotoxicity and high stability due to the anchored HA molecules on the surface of nanocontainers, and enables the targeted delivery of beacons via CD44 receptor-mediated endocytosis. In vitro and in vivo optical imaging using bHNCs also allow the measurement of miR-34a expression levels due to the selective recognition of the beacons released from the internalized bHNCs. We believe that the technique described herein can be further developed as a cancer diagnostic as well as a miRNA-based therapy of metastatic cancer.
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Affiliation(s)
- Eunjung Kim
- Department of Chemical and Biomolecular Engineering, Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul, Republic of Korea
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18
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Jangam SR, Agarwal AK, Sur K, Kelso DM. A point-of-care PCR test for HIV-1 detection in resource-limited settings. Biosens Bioelectron 2012. [PMID: 23202333 DOI: 10.1016/j.bios.2012.10.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A low-cost, fully integrated sample-to-answer, quantitative PCR (qPCR) system that can be used for detection of HIV-1 proviral DNA in infants at the point-of-care in resource-limited settings has been developed and tested. The system is based on a novel DNA extraction method, which uses a glass fiber membrane, a disposable assay card that includes on-board reagent storage, provisions for thermal cycling and fluorescence detection, and a battery-operated portable analyzer. The system is capable of automated PCR mix assembly using a novel reagent delivery system and performing qPCR. HIV-1 and internal control targets are detected using two spectrally separated fluorophores, FAM and Quasar 670. In this report, a proof-of-concept of the platform is demonstrated. Initial results with whole blood demonstrate that the test is capable of detecting HIV-1 in blood samples containing greater than 5000 copies of HIV-1. In resource-limited settings, a point-of-care HIV-1 qPCR test would greatly increase the number of test results that reach the infants caregivers, allowing them to pursue anti-retroviral therapy.
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Affiliation(s)
- Sujit R Jangam
- Center for Innovation in Global Health Technologies, Biomedical Engineering, 2145 Sheridan Road E310, Northwestern University, Evanston, IL 60208-3107, USA.
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19
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Tang YW, Ou CY. Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections. Emerg Microbes Infect 2012; 1:e19. [PMID: 26038427 PMCID: PMC3630918 DOI: 10.1038/emi.2012.15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/08/2012] [Accepted: 05/21/2012] [Indexed: 12/31/2022]
Abstract
Substantive and significant advances have been made in the last two decades in the characterization of human immunodeficiency virus (HIV) infections using molecular techniques. These advances include the use of real-time measurements, isothermal amplification, the inclusion of internal quality assurance protocols, device miniaturization and the automation of specimen processing. The result has been a significant increase in the availability of results to a high level of accuracy and quality. Molecular assays are currently widely used for diagnostics, antiretroviral monitoring and drug resistance characterization in developed countries. Simple and cost-effective point-of-care versions are also being vigorously developed with the eventual goal of providing timely healthcare services to patients residing in remote areas and those in resource-constrained countries. In this review, we discuss the evolution of these molecular technologies, not only in the context of the virus, but also in the context of tests focused on human genomics and transcriptomics.
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Affiliation(s)
- Yi-Wei Tang
- Memorial Sloan-Kettering Cancer Center , New York, NY 10065, USA
| | - Chin-Yih Ou
- Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
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20
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Hötzer B, Medintz IL, Hildebrandt N. Fluorescence in nanobiotechnology: sophisticated fluorophores for novel applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2297-326. [PMID: 22678833 DOI: 10.1002/smll.201200109] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 02/22/2012] [Indexed: 05/26/2023]
Abstract
Nanobiotechnology is one of the fastest growing and broadest-ranged interdisciplinary subfields of the nanosciences. Countless hybrid bio-inorganic composites are currently being pursued for various uses, including sensors for medical and diagnostic applications, light- and energy-harvesting devices, along with multifunctional architectures for electronics and advanced drug-delivery. Although many disparate biological and nanoscale materials will ultimately be utilized as the functional building blocks to create these devices, a common element found among a large proportion is that they exert or interact with light. Clearly continuing development will rely heavily on incorporating many different types of fluorophores into these composite materials. This review covers the growing utility of different classes of fluorophores in nanobiotechnology, from both a photophysical and a chemical perspective. For each major structural or functional class of fluorescent probe, several representative applications are provided, and the necessary technological background for acquiring the desired nano-bioanalytical information are presented.
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Affiliation(s)
- Benjamin Hötzer
- NanoBioPhotonics, Institut d'Electronique Fondamentale, Université Paris-Sud, 91405 Orsay Cedex, France
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21
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Karasi J, Dziezuk F, Quennery L, Förster S, Reischl U, Colucci G, Schoener D, Seguin-Devaux C, Schmit J. High correlation between the Roche COBAS® AmpliPrep/COBAS® TaqMan® HIV-1, v2.0 and the Abbott m2000 RealTime HIV-1 assays for quantification of viral load in HIV-1 B and non-B subtypes. J Clin Virol 2011; 52:181-6. [DOI: 10.1016/j.jcv.2011.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 06/01/2011] [Accepted: 07/05/2011] [Indexed: 10/17/2022]
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Huang S, Erickson B, Mak WB, Salituro J, Abravaya K. A novel RealTime HIV-1 Qualitative assay for the detection of HIV-1 nucleic acids in dried blood spots and plasma. J Virol Methods 2011; 178:216-24. [PMID: 21968095 DOI: 10.1016/j.jviromet.2011.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 09/10/2011] [Accepted: 09/19/2011] [Indexed: 12/17/2022]
Abstract
Abbott RealTime HIV-1 Qualitative is an in vitro real-time PCR assay for detecting HIV-1 nucleic acids in human plasma and dried blood spots (DBS). The assay was designed to be used in diagnosis of HIV-1 infections in pediatric and adult patients, with an emphasis on the applicability in resource-limited settings. Use of DBS facilitates specimen collection from remote areas and transportation to testing laboratories. Small sample input requirement facilitates testing of specimens with limited collection volume. The Abbott RealTime HIV-1 Qualitative assay is capable of detecting HIV-1 group M subtypes A-H, group O and group N samples. HIV-1 virus concentrations detected with 95% probability were 80 copies/mL of plasma using the plasma protocol, and 2469 copies/mL of whole blood using the DBS protocol. The assay detected HIV-1 infection in 13 seroconversion panels an average 10.5 days earlier than an HIV-1 antibody test and 4.9 days earlier than a p24 antigen test. For specimens collected from 6 weeks to 18 months old infants born to HIV-1 positive mothers, assay results using both the DBS and plasma protocols agreed well with the Roche Amplicor HIV-1 DNA Test version 1.5 (95.5% agreement for DBS and 97.8% agreement for plasma).
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Affiliation(s)
- Shihai Huang
- Abbott Molecular Inc., 1300 E Touhy Avenue, Des Plaines, IL 60018-3315, USA.
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Scott LE, Crump JA, Msuya E, Morrissey AB, Venter WF, Stevens WS. Abbott RealTime HIV-1 m2000rt viral load testing: manual extraction versus the automated m2000sp extraction. J Virol Methods 2011; 172:78-80. [PMID: 21172389 PMCID: PMC3164890 DOI: 10.1016/j.jviromet.2010.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 12/06/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
Abstract
The Abbott RealTime HIV-1 assay is a real-time nucleic acid amplification assay available for HIV-1 viral load quantitation. The assay has a platform for automated extraction of viral RNA from plasma or dried blood spot samples, and an amplification platform with real time fluorescent detection. Overall, this study found no clinically relevant differences in viral load, if samples were extracted manually.
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Affiliation(s)
- Lesley E Scott
- University of the Witwatersrand, Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, 7 York Rd Parktown, Johannesburg 2000, South Africa.
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Comparative evaluation of the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 version 2 test using the TaqMan 48 analyzer and the Abbott RealTime HIV-1 assay. J Clin Microbiol 2010; 49:377-9. [PMID: 20980564 DOI: 10.1128/jcm.01285-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acceptable precision was achieved in a comparison study of the Abbott RealTime (RT) and Roche CAP/CTM-48 V2 HIV-1 assays, but viral load quantification was under- and overestimated, respectively, compared to the 2nd HIV-1 WHO International Standard. The same quantification patterns were observed for patient cohorts from Africa and the United States.
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Sur K, McFall SM, Yeh ET, Jangam SR, Hayden MA, Stroupe SD, Kelso DM. Immiscible phase nucleic acid purification eliminates PCR inhibitors with a single pass of paramagnetic particles through a hydrophobic liquid. J Mol Diagn 2010; 12:620-8. [PMID: 20581047 DOI: 10.2353/jmoldx.2010.090190] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extraction and purification of nucleic acids from complex biological samples for PCR are critical steps because inhibitors must be removed that can affect reaction efficiency and the accuracy of results. This preanalytical processing generally involves capturing nucleic acids on microparticles that are then washed with a series of buffers to desorb and dilute out interfering substances. We have developed a novel purification method that replaces multiple wash steps with a single pass of paramagnetic particles (PMPs) though an immiscible hydrophobic liquid. Only two aqueous solutions are required: a lysis buffer, in which nucleic acids are captured on PMPs, and an elution buffer, in which they are released for amplification. The PMPs containing the nucleic acids are magnetically transported through a channel containing liquid wax that connects the lysis chamber to the elution chamber in a specially designed cartridge. Transporting PMPs through the immiscible phase yielded DNA and RNA as pure as that obtained after extensive wash steps required by comparable purification methods. Our immiscible-phase process has been applied to targets in whole blood, plasma, and urine and will enable the development of faster and simpler purification systems.
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Affiliation(s)
- Kunal Sur
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, Illinois 60208, USA
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Zhang N, Appella DH. Advantages of peptide nucleic acids as diagnostic platforms for detection of nucleic acids in resource-limited settings. J Infect Dis 2010; 201 Suppl 1:S42-5. [PMID: 20225945 DOI: 10.1086/650389] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Peptide nucleic acids are a class of nondegradable oligonucleotide mimics that can be used as probes for nucleic acid sequences and could convey the necessary stability to be a diagnostic tool for use in a resource-limited setting. In this review, there is a brief introduction to the field of peptide nucleic acids and their potential benefits as probes for DNA and RNA sequences, followed by highlights of ways by which peptide nucleic acids could benefit a number of established diagnostic tools for human immunodeficiency virus detection.
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Affiliation(s)
- Ning Zhang
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
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28
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Pau CP, Wells SK, Rudolph DL, Owen SM, Granade TC. A rapid real-time PCR assay for the detection of HIV-1 proviral DNA using double-stranded primer. J Virol Methods 2009; 164:55-62. [PMID: 19948189 DOI: 10.1016/j.jviromet.2009.11.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 11/18/2009] [Accepted: 11/23/2009] [Indexed: 11/25/2022]
Abstract
In this study, a rapid real-time PCR assay to detect HIV-1 proviral DNA in whole blood was developed using a novel double-stranded primer that does not require a target-specific fluorescent probe or intercalating dye systems. Co-amplification of a human gene RNase P served as the internal control to monitor the efficiency of the DNA extraction and PCR amplification. The HIV-1 amplification efficiency was 100% and could amplify 1 copy of HIV-1 DNA 64% of the time and all attempts to amplify 4 copies were successful in less than 51 min. All 22 HIV-1 sero-positive and 20 sero-negative whole blood specimens tested were classified correctly by this assay. In addition, 22 cultured PBMC specimens infected with various HIV-1 subtypes or CRF (A=2, AC=1, B=4, C=3, D=3, AE=2, F=1, BF=2, G=4) were amplified equally well with a similar threshold cycle (C(t)) number (22.9+/-1.2). The high amplification efficiency and short PCR cycles were in part due to the short target sequence amplified by eliminating the probe-binding sequence between the primers. This assay may be useful as an alternative confirmation test in a variety of HIV testing venues.
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Affiliation(s)
- Chou-Pong Pau
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, United States.
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Muradrasoli S, Mohamed N, Belák S, Czifra G, Herrmann B, Berencsi G, Blomberg J. Broadly targeted triplex real-time PCR detection of influenza A, B and C viruses based on the nucleoprotein gene and a novel "MegaBeacon" probe strategy. J Virol Methods 2009; 163:313-22. [PMID: 19879296 PMCID: PMC7172653 DOI: 10.1016/j.jviromet.2009.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Revised: 09/19/2009] [Accepted: 10/20/2009] [Indexed: 11/19/2022]
Abstract
A PCR assay that covers animal and human influenza A, B and C viruses, i.e., most of Orthomyxoviridae, is needed. Influenza types are distinguished based on differences in the nucleoprotein (NP) present in the virus. Conserved NP regions were therefore used to design a TaqMan-based triplex reverse transcription real-time PCR method. Variability of influenza A within the probe target region mandated the development of a novel molecular beacon, the "Mega" molecular beacon (MegaBeacon; MegB), for the detection of influenza A with this method. MegaBeacon is a mismatch-tolerant molecular beacon that is also a TaqMan probe. The triplex method (3QPCR-MegB) was evaluated with influenza A isolates covering 18 HxNx combinations, two influenza B isolates, and five Japanese influenza C isolates, as well as influenza A, B and C synthetic DNA targets. One to ten viral RNA and cDNA genome equivalents were detected per PCR reaction for influenza A, B and C. Seventy-one human nasopharyngeal aspirates from respiratory infections yielded 30 influenza A, 11 influenza B and 0 influenza C with 3QPCR-MegB, where immunofluorescence (IF) found 28 influenza A and 10 influenza B. 3QPCR-MegB was more mismatch-tolerant than a variant PCR with an influenza A TaqMan probe (3QPCR) and is a sensitive and rational method to detect influenza viruses of animal and human origin. MegaBeacon probes hold promise for variable target nucleic acids.
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Affiliation(s)
- Shaman Muradrasoli
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
| | - Nahla Mohamed
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
| | - Sándor Belák
- Department of Virology, National Veterinary Institute and Swedish University of Agricultural Sciences, Ultuna, Uppsala, Sweden
| | - György Czifra
- Department of Virology, National Veterinary Institute and Swedish University of Agricultural Sciences, Ultuna, Uppsala, Sweden
| | - Björn Herrmann
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
| | | | - Jonas Blomberg
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
- Corresponding author at: Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Academic Hospital, 751 85 Uppsala, Sweden. Tel.: +46 18 6115593; fax: +46 18 551012.
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Rapid, point-of-care extraction of human immunodeficiency virus type 1 proviral DNA from whole blood for detection by real-time PCR. J Clin Microbiol 2009; 47:2363-8. [PMID: 19644129 DOI: 10.1128/jcm.r00092-09] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR detection of human immunodeficiency virus type 1 (HIV-1) proviral DNA is the method recommended for use for the diagnosis of HIV-1 infection in infants in limited-resource settings. Currently, testing must be performed in central laboratories, which are usually located some distance from health care facilities. While the collection and transportation of samples, such as dried blood spots, has improved test accessibility, the results are often not returned for several weeks. To enable PCR to be performed at the point of care while the mothers wait, we have developed a vertical filtration method that uses a separation membrane and an absorbent pad to extract cellular DNA from whole blood in less than 2 min. Cells are trapped in the separation membrane as the specimen is collected, and then a lysis buffer is added. The membrane retains the DNA, while the buffer washes away PCR inhibitors, which get wicked into the absorbent blotter pad. The membrane containing the entrapped DNA is then added to the PCR mixture without further purification. The method demonstrates a high degree of reproducibility and analytical sensitivity and allows the quantification of as few as 20 copies of HIV-1 proviral DNA from 100 microl of blood. In a blinded study with 182 longitudinal samples from infants (ages, 0 to 72 weeks) obtained from the Women and Infants Transmission Study, our assay demonstrated a sensitivity of 99% and a specificity of 100%.
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31
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Performance of the new Roche Cobas AmpliPrep-Cobas TaqMan version 2.0 human immunodeficiency virus type 1 assay. J Clin Microbiol 2009; 47:3400-2. [PMID: 19656975 DOI: 10.1128/jcm.00727-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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32
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Kolpashchikov DM. Triple-Stem DNA Probe: A New Conformationally Constrained Probe for SNP Typing. Chembiochem 2009; 10:1443-5. [DOI: 10.1002/cbic.200900264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Huang Q, Li Q. Characterization of the 5′ to 3′ nuclease activity of Thermus aquaticus DNA polymerase on fluorogenic double-stranded probes. Mol Cell Probes 2009; 23:188-94. [DOI: 10.1016/j.mcp.2009.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 03/25/2009] [Accepted: 04/09/2009] [Indexed: 11/27/2022]
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Gidwani V, Riahi R, Zhang DD, Wong PK. Hybridization kinetics of double-stranded DNA probes for rapid molecular analysis. Analyst 2009; 134:1675-81. [PMID: 20448937 DOI: 10.1039/b906077d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This study reports the hybridization kinetics of double-stranded DNA probes for rapid molecular analysis. Molecular binding schemes based on double-stranded DNA probes have been developed for quantitative detection of various biomolecules, such as nucleic acids and DNA binding proteins recently. The thermodynamic competition between the target and the competitor in binding to the probe provides a highly specific mechanism for molecular detection. The kinetics of the double-stranded DNA probe, on the other hand, represent another key aspect toward its general applicability for a wide set of biomedical applications. Herein we report a systematic investigation of the kinetics of double-stranded DNA probes. The signal-to-background ratio and assay time of the double-stranded DNA probes are optimized at a high ionic strength (over 100 mM NaCl). Both the donor probe and the quencher probe sequences are shown to be important in the hybridization kinetics. A long sticky end of the probe is able to dramatically accelerate the kinetics of the assay. To provide a quantitative description of the kinetics, a two-stage binding model is developed to describe the major features of the kinetics of the assay. The sensitivity of the kinetic model and the dominant affinity constants are studied. The study provides a general guideline for the design of the probes for reducing the total assay time. With an appropriate design of the probes, the assay can be finished within minutes at room temperature.
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Affiliation(s)
- Vinay Gidwani
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona, USA
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35
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Pyne MT, Konnick EQ, Phansalkar A, Hillyard DR. Evaluation of the Abbott investigational use only realtime HIV-1 assay and comparison to the Roche Amplicor HIV-1 monitor test, version 1.5. J Mol Diagn 2009; 11:347-54. [PMID: 19460935 DOI: 10.2353/jmoldx.2009.080166] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abbott Molecular's m2000 system and RealTime HIV-1 assay (RealTime) were evaluated for sensitivity, reproducibility, linearity, ability to detect diverse HIV-1 subtypes/groups, and correlation to the Roche AMPLICOR HIV-1 MONITOR Test, Version 1.5 (Amplicor). The limit of detection was determined using the second International World Health Organization Standard and Viral Quality Assurance standard material. Serial dilutions of four patient samples were used to determine inter- and intra-assay reproducibility and linearity. Samples representing HIV-1 groups M, N, and O were evaluated in the RealTime, Amplicor, and Siemens Versant HIV-1 branched chain DNA 3.0 (Versant) assays. Archived Amplicor-tested samples were tested with the 1 ml, 0.5 ml, and 0.6 ml versions of the RealTime assay. Probit analysis predicts a limit of detection of 21.94 IU/ml using the World Health Organization Standard and 26.54 copies/ml using Viral Quality Assurance material with the 1 ml assay. Linearity and reproducibility were very good between approximately 1.60 to 6.0 log(10) copies/ml. All three assays produced similar measurements for all Group M subtypes tested; the RealTime assay was the only assay that detected all three Group O samples tested. Correlation with the Amplicor assay was good, although the RealTime assay measured between 0.342 and 0.716 log(10) copies/ml lower on average, depending on the input volume. The automated RealTime assay exhibits excellent sensitivity, dynamic range, reproducibility, and group/subtype detection, albeit with consistently lower values than Amplicor.
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Affiliation(s)
- Michael T Pyne
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA.
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Evaluation of the Abbott m2000 RealTime human immunodeficiency virus type 1 (HIV-1) assay for HIV load monitoring in South Africa compared to the Roche Cobas AmpliPrep-Cobas Amplicor, Roche Cobas AmpliPrep-Cobas TaqMan HIV-1, and BioMerieux NucliSENS EasyQ HIV-1 assays. J Clin Microbiol 2009; 47:2209-17. [PMID: 19420172 DOI: 10.1128/jcm.01761-08] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The implementation of antiretroviral therapy demands the need for increased access to viral load (VL) monitoring. Newer real-time VL testing technologies are faster and have larger dynamic ranges and fully automated extraction to benefit higher throughputs in resource-poor environments. The Abbott RealTime human immunodeficiency virus type 1 (HIV-1) assay was evaluated as a new option for testing for HIV-1 subtype C in South Africa, and its performance was compared to the performance of existing assays (the Cobas AmpliPrep-Cobas TaqMan HIV-1, version 1, assay; the AmpliPrep-Cobas Monitor standard HIV-1 assay; and the NucliSENS EasyQ-EasyMag HIV-1 assay) in a high-throughput laboratory. The total precision of the RealTime HIV-1 assay was acceptable over all viral load ranges. This assay compared most favorably with the Cobas AmpliPrep-Cobas TaqMan HIV-1 assay (R(2) = 0.904), with a low standard deviation of difference being detected (0.323 copies/ml). The bias against comparator assays ranged from -0.001 copies/ml to -0.228 copies/ml. Variability in the reporting of VLs for a 20-member subtype panel compared to the variability of other assays was noted with subtypes G and CRF02-AG. The RealTime HIV-1 assay can test 93 samples per day with minimal manual preparation, less staff, and the minimization of contamination through automation. This assay is suitable for HIV-1 subtype C VL quantification in South Africa.
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Ruelle J, Jnaoui K, Lefèvre I, Lamarti N, Goubau P. Comparative evaluation of the VERSANT® HIV-1 RNA 1.0 kinetic PCR molecular system (kPCR) for the quantification of HIV-1 plasma viral load. J Clin Virol 2009; 44:297-301. [DOI: 10.1016/j.jcv.2009.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 01/14/2009] [Indexed: 10/21/2022]
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Peng X, Chen H, Draney DR, Volcheck W, Schutz-Geschwender A, Olive DM. A nonfluorescent, broad-range quencher dye for Förster resonance energy transfer assays. Anal Biochem 2009; 388:220-8. [PMID: 19248753 DOI: 10.1016/j.ab.2009.02.024] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Revised: 02/09/2009] [Accepted: 02/17/2009] [Indexed: 10/21/2022]
Abstract
We report here a novel, water-soluble, nonfluorescent dye that efficiently quenches fluorescence from a broad range of visible and near-infrared (NIR) fluorophores in Förster resonance energy transfer (FRET) systems. A model FRET-based caspase-3 assay system was used to test the performance of the quencher dye. Fluorogenic caspase-3 substrates were prepared by conjugating the quencher, IRDye QC-1, to a GDEVDGAK peptide in combination with fluorescein (emission maximum approximately 540 nm), Cy3 (approximately 570 nm), Cy5 (approximately 670 nm), IRDye 680 (approximately 700 nm), IRDye 700DX (approximately 690 nm), or IRDye 800CW (approximately 790 nm). The Förster distance R(0) values are calculated as 41 to 65A for these dye/quencher pairs. The fluorescence quenching efficiencies of these peptides were determined by measuring the fluorescence change on complete cleavage by recombinant caspase-3 and ranged from 97.5% to 98.8%. The fold increase in fluorescence on caspase cleavage of the fluorogenic substrates ranged from 40 to 83 depending on the dye/quencher pair. Because IRDye QC-1 effectively quenches both the NIR fluorophores (e.g., IRDye 700DX, IRDye 680, IRDye 800CW) and the visible fluorophores (e.g., fluorescein, Cy3, Cy5), it should find broad applicability in FRET assays using a wide variety of fluorescent dyes.
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Schutten M. Comparison of the Abbott Realtime HIV-1 and HCV viral load assays with commercial competitor assays. Expert Rev Mol Diagn 2008; 8:369-77. [PMID: 18598219 DOI: 10.1586/14737159.8.4.369] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The introduction of commercially available quantitative HIV-1 RNA detection methods at the end of the last century has had a significant impact on the management of patients requiring treatment. Similarly for hepatitis C virus (HCV), clinical decision-making with respect to initiation and prolonging therapy is largely based on data from viral load assays. The methods developed in the early 1990s and further improved since then still have significant drawbacks. For example, they are labor intensive, have a small dynamic range and are contamination sensitive. The development of real-time detection techniques for reverse transcription PCR has in part solved these problems. In the present review the advantages and disadvantages of the recently marketed Abbott Realtime HCV and HIV-1 viral load assays relative to their competitors will be discussed.
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Affiliation(s)
- Martin Schutten
- Department of Virology, s-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands.
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Wang Z, Gidwani V, Sun Z, Zhang DD, Wong PK. Development of a Molecular Assay for Rapid Screening of Chemopreventive Compounds Targeting Nrf2. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.jala.2008.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Emerging molecular studies have shown that the transcription factor NF-E2-related factor (Nrf2) plays an essential role in cancer chemoprevention. Here, we report the development of a molecular biosensor for rapid detection of antioxidant-responsive element (ARE)-bound Nrf2 protein. The development will provide a molecular assay for high-throughput screening of chemopreventive compounds. Specifically, a double-stranded DNA probe is designed based on the ARE sequence. One of the DNA strands is labeled with a fluorophore on the 5′ end and the complementary strand is labeled with a quencher on the 3′ end. A single-stranded DNA competitor is also designed. The existence of the Nrf2 stabilizes the fluorescent probes and delays the competitor from separating the fluorophore-quencher complex. Therefore, the concentration of the Nrf2 proteins can be measured quantitatively based on the fluorescence intensity. The molecular binding scheme was demonstrated using purified p50 and the detection of endogenous Nrf2 was demonstrated using whole-cell lysates treated with sulforaphane. The assay can easily be incorporated into an automated platform for high-throughput screening of chemopreventive compounds targeting Nrf2.
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Meserve D, Wang Z, Zhang DD, Wong PK. A double-stranded molecular probe for homogeneous nucleic acid analysis. Analyst 2008; 133:1013-9. [PMID: 18645642 DOI: 10.1039/b804853c] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This paper reports the design and optimization of a double-stranded molecular probe for homogeneous detection of specific nucleotide sequences. The probes are labeled with either a fluorophore or a quencher such that the probe hybridization brings the two labels into close proximity, and this diminishes the fluorescence signal in the absence of a target. In the presence of a target, the fluorophore probe is thermodynamically driven to unzip from its hybridized form and bind with the target. An equilibrium analysis, which successfully describes all the major features of the assay without any fitting parameter, is performed to generalize the design of the probe. Several key parameters affecting the performance of the assay are examined. We show that the dynamic range and the signal-to-noise ratio of the assay can be optimized by the probe concentration, the quencher-to-fluorophore ratio, and the probe strand sequence. By proper design of the sequence, the probe discriminates single nucleotide mismatches in a single step without any separation step or measurement of melting profile.
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Affiliation(s)
- Daniel Meserve
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, Arizona, USA
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