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Dong L, Zhang Y, Fu B, Swart C, Jiang H, Liu Y, Huggett J, Wielgosz R, Niu C, Li Q, Zhang Y, Park SR, Sui Z, Yu L, Liu Y, Xie Q, Zhang H, Yang Y, Dai X, Shi L, Yin Y, Fang X. Reliable biological and multi-omics research through biometrology. Anal Bioanal Chem 2024; 416:3645-3663. [PMID: 38507042 DOI: 10.1007/s00216-024-05239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Metrology is the science of measurement and its applications, whereas biometrology is the science of biological measurement and its applications. Biometrology aims to achieve accuracy and consistency of biological measurements by focusing on the development of metrological traceability, biological reference measurement procedures, and reference materials. Irreproducibility of biological and multi-omics research results from different laboratories, platforms, and analysis methods is hampering the translation of research into clinical uses and can often be attributed to the lack of biologists' attention to the general principles of metrology. In this paper, the progresses of biometrology including metrology on nucleic acid, protein, and cell measurements and its impacts on the improvement of reliability and comparability in biological research are reviewed. Challenges in obtaining more reliable biological and multi-omics measurements due to the lack of primary reference measurement procedures and new standards for biological reference materials faced by biometrology are discussed. In the future, in addition to establishing reliable reference measurement procedures, developing reference materials from single or multiple parameters to multi-omics scale should be emphasized. Thinking in way of biometrology is warranted for facilitating the translation of high-throughput omics research into clinical practices.
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Affiliation(s)
- Lianhua Dong
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Yu Zhang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Boqiang Fu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Claudia Swart
- Physikalisch-Technische Bundesanstalt, 38116, Braunschweig, Germany
| | | | - Yahui Liu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Jim Huggett
- National Measurement Laboratory at LGC (NML), Teddington, Middlesex, UK
| | - Robert Wielgosz
- Bureau International Des Poids Et Mesures (BIPM), Pavillon de Breteuil, 92312, Sèvres Cedex, France
| | - Chunyan Niu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Qianyi Li
- BGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yongzhuo Zhang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Sang-Ryoul Park
- Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Zhiwei Sui
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Lianchao Yu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | | | - Qing Xie
- BGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongfu Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xinhua Dai
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Ye Yin
- BGI, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiang Fang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
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2
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Accurate quantification of SARS-CoV-2 RNA by isotope dilution mass spectrometry and providing a correction of reverse transcription efficiency in droplet digital PCR. Anal Bioanal Chem 2022; 414:6771-6777. [PMID: 35941317 PMCID: PMC9360635 DOI: 10.1007/s00216-022-04238-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/01/2022]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 505 million confirmed cases, including over 6 million deaths. Reference materials (RMs) of SARS-CoV-2 RNA played a crucial role in performance evaluation and quality control of testing laboratories. As the potential primary characterization method of RMs, reverse transcription digital PCR (RT-dPCR) measures the copy number of RNA, but the accuracy of reverse transcription (RT) efficiency has yet to be confirmed. This study established a method of enzymatic digestion followed by isotope dilution mass spectrometry (IDMS), which does not require an RT reaction, to quantify in vitro-transcribed SARS-CoV-2 RNA. RNA was digested to nucleotide monophosphate (NMP) within 15 min and analyzed by IDMS within 5 min. The consistency among the results of four different NMPs demonstrated the reliability of the proposed method. Compared to IDMS, the quantitative result of RT-dPCR turned out to be about 10% lower, possibly attributed to the incompleteness of the reverse transcription process. Therefore, the proposed approach could be valuable and reliable for quantifying RNA molecules and evaluating the RT efficiency of RT-based methods.
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Yamazaki J, Inoue I, Arakawa A, Karakawa S, Takahashi K, Nakayama A. Simultaneous quantification of oligo-nucleic acids and a ferritin nanocage by size-exclusion chromatography hyphenated to inductively coupled plasma mass spectrometry for developing drug delivery systems. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2219-2226. [PMID: 35616084 DOI: 10.1039/d2ay00068g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An analytical methodology, which can quantify nucleic acids, ferritin nanocages, and their complexes in a single injection, was established by means of size-exclusion chromatography hyphenated with inductively coupled plasma mass spectrometry (SEC-ICP-MS). In this study, several oligo-nucleic acids and ferritin (a human-derived cage-shaped protein) were used as model compounds of nucleic acid drugs (NAD) and drug delivery system (DDS) carriers, respectively. A fraction based on the nucleic acid-ferritin complex was completely distinguished from one based on free nucleic acids by SEC separation. The nucleic acids and ferritin were quantified based on the number of phosphorus and sulfur atoms, respectively. The quantification was carried out by an external calibration method using a series of elemental standard solutions without preparing designated standard materials for each drug candidate. The analytical performance, including sensitivity and accuracy, was evaluated to be appropriate for evaluating the medicines already launched in the market. As demonstrated in the latter part of this study, the encapsulation mechanism is possibly regulated by not only the averaged molecular size of nucleic acids but also the surface charge related to the number of (deoxy-) ribonucleotides. We believe that the methodology presented in this study has the potential to accelerate the development of new modalities based on NAD-DDS to realize therapies in the future.
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Affiliation(s)
- Junko Yamazaki
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-8681, Japan.
| | - Ippei Inoue
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-8681, Japan.
| | - Akihiro Arakawa
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-8681, Japan.
| | - Sachise Karakawa
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-8681, Japan.
| | - Kazutoshi Takahashi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-8681, Japan.
| | - Akira Nakayama
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, 1-1, Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-8681, Japan.
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Ouranidis A, Vavilis T, Mandala E, Davidopoulou C, Stamoula E, Markopoulou CK, Karagianni A, Kachrimanis K. mRNA Therapeutic Modalities Design, Formulation and Manufacturing under Pharma 4.0 Principles. Biomedicines 2021; 10:50. [PMID: 35052730 PMCID: PMC8773365 DOI: 10.3390/biomedicines10010050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 12/12/2022] Open
Abstract
In the quest for a formidable weapon against the SARS-CoV-2 pandemic, mRNA therapeutics have stolen the spotlight. mRNA vaccines are a prime example of the benefits of mRNA approaches towards a broad array of clinical entities and druggable targets. Amongst these benefits is the rapid cycle "from design to production" of an mRNA product compared to their peptide counterparts, the mutability of the production line should another target be chosen, the side-stepping of safety issues posed by DNA therapeutics being permanently integrated into the transfected cell's genome and the controlled precision over the translated peptides. Furthermore, mRNA applications are versatile: apart from vaccines it can be used as a replacement therapy, even to create chimeric antigen receptor T-cells or reprogram somatic cells. Still, the sudden global demand for mRNA has highlighted the shortcomings in its industrial production as well as its formulation, efficacy and applicability. Continuous, smart mRNA manufacturing 4.0 technologies have been recently proposed to address such challenges. In this work, we examine the lab and upscaled production of mRNA therapeutics, the mRNA modifications proposed that increase its efficacy and lower its immunogenicity, the vectors available for delivery and the stability considerations concerning long-term storage.
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Affiliation(s)
- Andreas Ouranidis
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Department of Chemical Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Theofanis Vavilis
- Laboratory of Biology and Genetics, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Evdokia Mandala
- Fourth Department of Internal Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christina Davidopoulou
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Eleni Stamoula
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Catherine K Markopoulou
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anna Karagianni
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Kyriakos Kachrimanis
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Talap J, Zhao J, Shen M, Song Z, Zhou H, Kang Y, Sun L, Yu L, Zeng S, Cai S. Recent advances in therapeutic nucleic acids and their analytical methods. J Pharm Biomed Anal 2021; 206:114368. [PMID: 34571322 DOI: 10.1016/j.jpba.2021.114368] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022]
Abstract
Therapeutic nucleic acids are various chemically modified RNA or DNA with different functions, which mainly play roles at the gene level. Owing to its accurately targeting at pathogenic genes, nucleic acid based therapeutics have a wide range of application prospects. Recently, the improvement on chemical synthesis and delivery materials accelerated the development of therapeutic nucleic acids rapidly. Up to now, 17 nucleic acid based therapeutics approved by Food and Drug Administration (FDA) or European Medicines Agency (EMA). The development of therapeutics raised higher requirements for analytical methods, both in quality control and in clinical research. The first part of this review introduces different classes of therapeutic nucleic acids, including antisense oligonucleotide (ASO), RNA interference (RNAi) therapy, mRNA, aptamer and other classes which are under research. The second part reviews the therapeutic nucleic acids commercialized from 2019 to now. The third part discusses the analytical methods for nucleic acid based therapeutics, including liquid chromatography-based methods, capillary gel electrophoresis (CGE), hybridization enzyme-linked immunosorbent assay (ELISA) and other infrequently used methods. Finally, the advantages and shortcomings of these methods are summarized, and the future development of analysis methods are prospected.
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Affiliation(s)
- Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jing Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zihan Song
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
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6
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Niu C, Dong L, Gao Y, Zhang Y, Wang X, Wang J. Quantitative analysis of RNA by HPLC and evaluation of RT-dPCR for coronavirus RNA quantification. Talanta 2021; 228:122227. [PMID: 33773731 PMCID: PMC7898971 DOI: 10.1016/j.talanta.2021.122227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/31/2021] [Accepted: 02/13/2021] [Indexed: 01/23/2023]
Abstract
Nucleic acid detection and quantification have been known to be important at various fields, from genetically modified organisms and gene expression to virus detection. For DNA molecules, digital PCR has been developed as an absolute quantification method which is not dependent on external calibrators. While when it comes to RNA molecules, reverse transcription (RT) step must be taken before PCR amplification to obtain cDNA. With different kinds of reverse transcriptase (RTase) and RT reaction conditions being used in laboratory assays, the efficiency of RT process differs a lot which led variety in quantification results of RNA molecules. In this study, we developed HPLC method combined with enzymatic digestion of RNA to nucleotides for quantification of RNA without RT process. This method was metrologically traceable to four nuceloside monophosphate (NMP) Certification Reference Materials of National Institute of Metrology, China (NIMC) for insurance of accuracy. The established method was used to evaluate the reverse transcription digital polymerase chain reaction (RT-dPCR) of three target genes of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) RNA, including open reading frame 1ab (ORF1ab), nucleocapsid protein (N) and envelope protein (E) gene. Three available RT kits had been evaluated and disparities were observed for the RT efficiency varied from 9% to 182%. It is thus demonstrated that HPLC combined with enzymatic digestion could be a useful method to quantify RNA molecules and evaluate RT efficiency. It is suggested that RT process should be optimized and identified in RNA quantification assays.
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Affiliation(s)
- Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China.
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Yongzhuo Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Jing Wang
- Department of Metrological Services and Quality System, National Institute of Metrology, Beijing, 100013, China
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7
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Kwon HJ, Jeong JS, Bae YK, Choi K, Yang I. Stable Isotope Labeled DNA: A New Strategy for the Quantification of Total DNA Using Liquid Chromatography–Mass Spectrometry. Anal Chem 2019; 91:3936-3943. [DOI: 10.1021/acs.analchem.8b04940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Ji-Seon Jeong
- Department of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | | | | | - Inchul Yang
- Department of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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8
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Wu Y, Li J, Li X, Zhai S, Gao H, Li Y, Zhang X, Wu G. Development and strategy of reference materials for the DNA-based detection of genetically modified organisms. Anal Bioanal Chem 2019; 411:1729-1744. [DOI: 10.1007/s00216-019-01576-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/21/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
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9
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Yoo HB, Park SR, Dong L, Wang J, Sui Z, Pavšič J, Milavec M, Akgoz M, Mozioğlu E, Corbisier P, Janka M, Cosme B, de V Cavalcante JJ, Flatshart RB, Burke D, Forbes-Smith M, McLaughlin J, Emslie K, Whale AS, Huggett JF, Parkes H, Kline MC, Harenza JL, Vallone PM. International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction. Anal Chem 2016; 88:12169-12176. [PMID: 28193036 DOI: 10.1021/acs.analchem.6b03076] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Enumeration-based determination of DNA copy-concentration was assessed through an international comparison among national metrology institutes (NMIs) and designated institutes (DIs). Enumeration-based quantification does not require a calibration standard thereby providing a route to "absolute quantification", which offers the potential for reliable value assignments of DNA reference materials, and International System of Units (SI) traceability to copy number 1 through accurate counting. In this study, 2 enumeration-based methods, flow cytometric (FCM) counting and the digital polymerase chain reaction (dPCR), were compared to quantify a solution of the pBR322 plasmid at a concentration of several thousand copies per microliter. In addition, 2 orthogonal chemical-analysis methods based on nucleotide quantification, isotope-dilution mass spectrometry (IDMS) and capillary electrophoresis (CE) were applied to quantify a more concentrated solution of the plasmid. Although 9 dPCR results from 8 laboratories showed some dispersion (relative standard deviation [RSD] = 11.8%), their means were closely aligned with those of the FCM-based counting method and the orthogonal chemical-analysis methods, corrected for gravimetric dilution factors. Using the means of dPCR results, the RSD of all 4 methods was 1.8%, which strongly supported the validity of the recent enumeration approaches. Despite a good overall agreement, the individual dPCR results were not sufficiently covered by the reported measurement uncertainties. These findings suggest that some laboratories may not have considered all factors contributing to the measurement uncertainty of dPCR, and further investigation of this possibility is warranted.
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Affiliation(s)
- Hee-Bong Yoo
- Korea Research Institute of Standards and Science , Daejeon 34113, Republic of Korea.,University of Science and Technology , Daejeon 34141, Republic of Korea
| | - Sang-Ryoul Park
- Korea Research Institute of Standards and Science , Daejeon 34113, Republic of Korea.,University of Science and Technology , Daejeon 34141, Republic of Korea
| | - Lianhua Dong
- National Institute of Metrology , Beijing 100013, P.R. China
| | - Jing Wang
- National Institute of Metrology , Beijing 100013, P.R. China
| | - Zhiwei Sui
- National Institute of Metrology , Beijing 100013, P.R. China
| | - Jernej Pavšič
- National Institute of Biology , 1000 Ljubljana, Slovenia
| | - Mojca Milavec
- National Institute of Biology , 1000 Ljubljana, Slovenia
| | - Muslum Akgoz
- TUBITAK UME National Metrology Institute , Kocaeli 41470, Turkey
| | - Erkan Mozioğlu
- TUBITAK UME National Metrology Institute , Kocaeli 41470, Turkey
| | - Philippe Corbisier
- Institute for Reference Materials and Measurements, Joint Research Centre, European Commission , Geel 2440, Belgium
| | - Mátrai Janka
- Institute for Reference Materials and Measurements, Joint Research Centre, European Commission , Geel 2440, Belgium
| | - Bruno Cosme
- National Institute of Metrology, Quality and Technology , Xerém 25250-020, Brazil
| | | | | | - Daniel Burke
- National Measurement Institute Australia , Lindfield 2070, Australia
| | | | - Jacob McLaughlin
- National Measurement Institute Australia , Lindfield 2070, Australia
| | - Kerry Emslie
- National Measurement Institute Australia , Lindfield 2070, Australia
| | | | | | | | - Margaret C Kline
- National Institute of Standards and Technology , Gaithersburg, Maryland 20899-1070, United States
| | - Jo Lynne Harenza
- National Institute of Standards and Technology , Gaithersburg, Maryland 20899-1070, United States
| | - Peter M Vallone
- National Institute of Standards and Technology , Gaithersburg, Maryland 20899-1070, United States
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10
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Liang W, Xu L, Sui Z, Li Y, Li L, Wen Y, Li C, Ren S, Liu G. Quantification of plasmid DNA reference materials for Shiga toxin-producing Escherichia coli based on UV, HR-ICP-MS and digital PCR. Chem Cent J 2016; 10:55. [PMID: 27621755 PMCID: PMC5018943 DOI: 10.1186/s13065-016-0201-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 09/01/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The accuracy and metrology traceability of DNA quantification is becoming a critical theme in many fields, including diagnosis, forensic analysis, microorganism detection etc. Thus the research of DNA reference materials (RMs) and consistency of DNA quantification methods has attracted considerable research interest. RESULTS In this work, we developed 3 plasmid candidate RMs, containing 3 target genes of Escherichia coli O157:H7 (E. coli O157:H7) and other Shiga toxin-producing Escherichia coli (STEC): stx1, stx2, and fliC (h7) respectively. Comprehensive investigation of the plasmid RMs was performed for their sequence, purity, homogeneity and stability, and then the concentration was quantified by three different methods: ultraviolet spectrophotometer (UV), high resolution inductively coupled plasma mass spectrometry (HR-ICP-MS) and digital PCR. As a routinely applied method for DNA analysis, UV was utilized for the quantification (OD260) and purity analysis for the plasmids. HR-ICP-MS quantified the plasmid DNA through analysing the phosphorus in DNA molecules. Digital PCR distributed the DNA samples onto a microarray chip containing thousands of reaction chambers, and quantified the DNA copy numbers by analysing the number of positive signals without any calibration curves needed. CONCLUSIONS Based on the high purification of the DNA reference materials and the optimization of dPCR analysis, we successfully achieved good consistency between UV, HR-ICP-MS and dPCR, with relative deviations lower than 10 %. We then performed the co-quantification of 3 DNA RMs with three different methods together, and the uncertainties of their concentration were evaluated. Finally, the certified values and expanded uncertainties for 3 DNA RMs (pFliC, pStx1 and pStx2) were (1.60 ± 0.10) × 10(10) copies/μL, (1.53 ± 0.10) × 10(10) copies/μL and (1.70 ± 0.11) × 10(10) copies/μL respectively.Graphical abstractWe developed 3 plasmid candidate RMs, containing 3 target genes of Escherichia coli O157:H7 (E. coli O157:H7) and other Shiga toxin-producing Escherichia coli (STEC): stx1, stx2, and fliC (h7) respectively, and the quantification of three different methods (UV, dPCR, ICP) was studied.
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Affiliation(s)
- Wen Liang
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Li Xu
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Zhiwei Sui
- Division of Medical and Biological Measurement, National Institute of Metrology, No.18, Bei San Huan Dong Lu, Chaoyang District, Beijing, 100013 People’s Republic of China
| | - Yan Li
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Lanying Li
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Yanli Wen
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Chunhua Li
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Shuzhen Ren
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Gang Liu
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
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11
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A high-throughput flow injection inductively coupled plasma mass spectrometry method for quantification of oligonucleotides. Microchem J 2016. [DOI: 10.1016/j.microc.2015.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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12
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Shibayama S, Sakamaki H, Yamazaki T, Takatsu A. Metal free columns for determination of deoxynucleotide monophosphate by liquid chromatography/mass spectrometry and application to oligonucleotide. J Chromatogr A 2015; 1406:210-4. [PMID: 26141274 DOI: 10.1016/j.chroma.2015.06.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/10/2015] [Accepted: 06/14/2015] [Indexed: 02/06/2023]
Abstract
We have developed a highly sensitive method for the analysis of deoxynucleotide monophosphates (dNMPs), which involves the use of liquid chromatography/mass spectrometry (LC/MS) and a new metal-free column. The new column solves the problem that the phosphate group in dNMPs interacts with the metal portion of the device or column. After optimization of the analytical conditions, the limits of detection (LODs) of dNMPs were from 5.4ng/g to 6.3ng/g. Those values were 10 times lower than the LODs of previous methods. We applied the method to the determination of the base composition and the quantification of 20-mer oligonucleotide. Despite use of a very small sample amount of 14.5ng, we were able to determine the base composition, and the result was consistent with theoretical values. We were also able to quantify the mass fraction of oligonucleotide with 8.2% expanded uncertainty (k=2). By means of the developed method, we were able to analyze dNMPs with high sensitivity as well as determine the base composition and quantify the mass fraction of oligonucleotide despite use of a small amount of sample.
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Affiliation(s)
- Sachie Shibayama
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8563, Japan.
| | - Hiroshi Sakamaki
- Chemicals Evaluation and Research Institute, 1600 Shimotakano, Sugito, Kitakatsushika, Saitama 345-0043, Japan
| | - Taichi Yamazaki
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8563, Japan
| | - Akiko Takatsu
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8563, Japan
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13
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Leclerc O, Fraisse PO, Labarraque G, Oster C, Pichaut JP, Baume M, Jarraud S, Fisicaro P, Vaslin-Reimann S. Method development for genomic Legionella pneumophila DNA quantification by inductively coupled plasma mass spectrometry. Anal Biochem 2013; 435:153-8. [PMID: 23333226 DOI: 10.1016/j.ab.2012.12.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/13/2022]
Abstract
The development of a method for the quantification of Legionella pneumophila genomic deoxyribonucleic acid is considered. The method is based on the quantification by inductively coupled plasma mass spectrometry (ICP-MS) of the mass fraction of phosphorus, stoichiometrically presented in the DNA molecules. Through the DNA sequencing data, it was possible to convert the ICP-MS analysis results into DNA genome units. L. pneumophila DNA samples were analyzed using ICP-sector field MS and ICP-quadrupole MS with a collision/reaction cell. Spectrophotometric measurements of the absorbance at 260nm and real-time PCR techniques were used to independently confirm the ICP-MS results. The comparison of the methods showed that the ICP-MS method provides better accuracy with respect to currently applied analytical techniques such as UV spectrophotometry, fluorescent dye methods, and real-time PCR. Moreover, with the use of calibration standards whose values are traceable to the International System of Units and the possibility of evaluating the contribution to the overall uncertainty of each step of the measurement procedure, the method enables long-term comparability of the measurement results. These advantages make the ICP-MS method suitable for nucleic acid investigation, from nucleotides to genomic DNA, as well as for the certification of the reference materials containing nucleic acids.
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Affiliation(s)
- Olga Leclerc
- Department of Medical and Inorganic Chemistry, Laboratoire National de Métrologie et d'Essais, Paris, France.
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14
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Application of High Performance Liquid Chromatography with Ultrasonic Splitting for DNA Quantification. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.3724/sp.j.1096.2011.01442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Dong L, Zang C, Wang J, Li L, Gao Y, Wu L, Li P. Lambda genomic DNA quantification using ultrasonic treatment followed by liquid chromatography-isotope dilution mass spectrometry. Anal Bioanal Chem 2012; 402:2079-88. [PMID: 22218463 DOI: 10.1007/s00216-011-5644-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/22/2011] [Accepted: 12/07/2011] [Indexed: 01/04/2023]
Abstract
Quantification of genomic DNA that is traceable to the SI was performed successfully by measuring the individual nucleotides. Specifically, ultrasound was used to shear lambda genomic DNA into fragments of less than 200 base pairs, followed by deoxyribonuclease Ι and phosphodiesterase Ι digestion and liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) quantification to estimate the mass fraction of the lambda DNA, based on the constituent deoxynucleotide monophosphates (dNMPs) within the molecule. Digital PCR (dPCR) was employed to quantify the same lambda DNA solution to provide independent data for comparing the performance of two quantitative methods. On the basis of the LC-IDMS measurement after ultrasonic treatment of the sample, the concentration of lambda DNA was 273.1 ± 9.8 μg/g (expanded uncertainty at the 95% confidence interval). This shows good agreement with the data from dPCR. Additionally, the result calculated on the basis of the sum of the concentrations of the four dNMPs is the same as that calculated on the basis of the sequence, which indicates that knowledge of the DNA sequence and length is unnecessary to measure the total DNA concentration when applying ultrasonic treatment-LC-IDMS.
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Affiliation(s)
- Lianhua Dong
- National Institute of Metrology, Beijing, China.
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16
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Dash K, Rastogi L, Arunachalam J. DNA quantification via traceable phosphorus measurement through microwave-assisted UV digestion-ion chromatography. Analyst 2012; 137:668-74. [DOI: 10.1039/c2an15883c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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17
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Development of salt-tolerance interface for an high performance liquid chromatography/inductively coupled plasma mass spectrometry system and its application to accurate quantification of DNA samples. Anal Chim Acta 2011; 713:23-9. [PMID: 22200303 DOI: 10.1016/j.aca.2011.11.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/13/2011] [Accepted: 11/17/2011] [Indexed: 11/22/2022]
Abstract
Accurate quantification of DNA is highly important in various fields. Determination of phosphorus by ICP-MS is one of the most effective methods for accurate quantification of DNA due to the fixed stoichiometry of phosphate to this molecule. In this paper, a smart and reliable method for accurate quantification of DNA fragments and oligodeoxythymidilic acids by hyphenated HPLC/ICP-MS equipped with a highly efficient interface device is presented. The interface was constructed of a home-made capillary-attached micronebulizer and temperature-controllable cyclonic spray chamber (IsoMist). As a separation column for DNA samples, home-made methacrylate-based weak anion-exchange monolith was employed. Some parameters, which include composition of mobile phase, gradient program, inner and outer diameters of capillary, temperature of spray chamber etc., were optimized to find the best performance for separation and accurate quantification of DNA samples. The proposed system could achieve many advantages, such as total consumption for small amount sample analysis, salt-tolerance for hyphenated analysis, high accuracy and precision for quantitative analysis. Using this proposed system, the samples of 20 bp DNA ladder (20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 300, 400, 500 base pairs) and oligodeoxythymidilic acids (dT(12-18)) were rapidly separated and accurately quantified.
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18
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Yin PG, Jiang L, Lang XF, Guo L, Yang S. Quantitative analysis of mononucleotides by isotopic labeling surface-enhanced Raman scattering spectroscopy. Biosens Bioelectron 2011; 26:4828-31. [PMID: 21723110 DOI: 10.1016/j.bios.2011.05.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 05/23/2011] [Accepted: 05/25/2011] [Indexed: 11/13/2022]
Abstract
A novel surface-enhanced Raman scattering (SERS) approach for accurate quantification of mononucleotides of deoxyribonucleic acid (DNA) is described. Reproducible SERS measurement was achieved by using isotopically labeled internal standard. By measuring the SERS spectra of mononucleotides and its isotope internal standard in combination with multivariate data analysis, the method was successfully applied to quantify mononucleotides. The independent validation of analyte concentrations gave a standard deviation of within 2%, which is comparable to HPLC result. Finally, a mixture of four mononucleotides of DNA was prepared to explore the possibility of quantifying the concentration of label-free, sequence-specific DNA strands by this approach. As compared to liquid chromatography/mass spectrometry (LC/MS), our method can be similarly precise but the SERS measurement is simple, rapid and potentially cheap.
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Affiliation(s)
- Peng-Gang Yin
- School of Chemistry and Environment, Beijing University of Aeronautics and Astronautics, Beijing, 100191, China.
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19
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Rapid and accurate determination of deoxyribonucleoside monophosphates from DNA using micellar electrokinetic chromatography with a cationic surfactant additive. Anal Bioanal Chem 2011; 400:2131-40. [DOI: 10.1007/s00216-011-4915-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 03/14/2011] [Accepted: 03/14/2011] [Indexed: 11/26/2022]
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20
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Fujii SI, Inagaki K, Chiba K, Takatsu A. Quantification of phosphorus in DNA using capillary electrophoresis hyphenated with inductively coupled plasma mass spectrometry. J Chromatogr A 2010; 1217:7921-5. [PMID: 21067764 DOI: 10.1016/j.chroma.2010.10.066] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/12/2010] [Accepted: 10/18/2010] [Indexed: 01/22/2023]
Abstract
We have analyzed phosphorus in an enzymatically digested DNA molecule using capillary electrophoresis (CE) hyphenated with inductively coupled plasma mass spectrometry (ICP-MS). The DNA concentration was quantified by the phosphorus value obtained in the CE-ICP-MS analysis. The CE-ICP-MS measurement, for which the interface device AIF-01 equipped three layered nebulizer was adopted, was achieved with limited μL/min nebulizing without loss of sample in the vaporizing chamber. The samples of nucleotides and free phosphate were separated well in the CE-ICP-MS measurement, and the calibration curve (0.1-10μg/mL) of the phosphorus showed a linear (R(2)=0.999) increase in intensity. After digestion of the 100-bp double-strand DNA sample to deoxyribonucleotide-5'-monophosphates (dNMPs) by phosphodiesterase-I, phosphorus was detected by CE-ICP-MS without further purification steps. In this study, we applied two calculation schemes of DNA analysis using a dNMP concentration obtained from CE-ICP-MS. Comparative CE-ICP-MS analysis with DNA digested to dNMPs showed that the assay gave an equal value obtained from the total DNA quantification using fluorescence detection. The detection limits of the DNA sample obtained from these species and phosphorus in nucleotides using CE-ICP-MS were 3.1-26ng/mL. These LOD values were equal to the conventional fluorescence determination of DNA.
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Affiliation(s)
- Shin-Ichiro Fujii
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8563, Japan.
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21
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Burke DG, Griffiths K, Kassir Z, Emslie K. Accurate Measurement of DNA Methylation That Is Traceable to the International System of Units. Anal Chem 2009; 81:7294-301. [DOI: 10.1021/ac901116f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Daniel G. Burke
- National Measurement Institute, Australia, 1 Suakin Street, Pymble, NSW 2073, Australia
| | - Kate Griffiths
- National Measurement Institute, Australia, 1 Suakin Street, Pymble, NSW 2073, Australia
| | - Zena Kassir
- National Measurement Institute, Australia, 1 Suakin Street, Pymble, NSW 2073, Australia
| | - Kerry Emslie
- National Measurement Institute, Australia, 1 Suakin Street, Pymble, NSW 2073, Australia
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22
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Kline MC, Duewer DL, Travis JC, Smith MV, Redman JW, Vallone PM, Decker AE, Butler JM. Production and certification of NIST Standard Reference Material 2372 Human DNA Quantitation Standard. Anal Bioanal Chem 2009; 394:1183-92. [PMID: 19377837 DOI: 10.1007/s00216-009-2782-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 03/27/2009] [Accepted: 03/30/2009] [Indexed: 12/22/2022]
Abstract
Modern highly multiplexed short tandem repeat (STR) assays used by the forensic human-identity community require tight control of the initial amount of sample DNA amplified in the polymerase chain reaction (PCR) process. This, in turn, requires the ability to reproducibly measure the concentration of human DNA, [DNA], in a sample extract. Quantitative PCR (qPCR) techniques can determine the number of intact stretches of DNA of specified nucleotide sequence in an extremely small sample; however, these assays must be calibrated with DNA extracts of well-characterized and stable composition. By 2004, studies coordinated by or reported to the National Institute of Standards and Technology (NIST) indicated that a well-characterized, stable human DNA quantitation certified reference material (CRM) could help the forensic community reduce within- and among-laboratory quantitation variability. To ensure that the stability of such a quantitation standard can be monitored and that, if and when required, equivalent replacement materials can be prepared, a measurement of some stable quantity directly related to [DNA] is required. Using a long-established conventional relationship linking optical density (properly designated as decadic attenuance) at 260 nm with [DNA] in aqueous solution, NIST Standard Reference Material (SRM) 2372 Human DNA Quantitation Standard was issued in October 2007. This SRM consists of three quite different DNA extracts: a single-source male, a multiple-source female, and a mixture of male and female sources. All three SRM components have very similar optical densities, and thus very similar conventional [DNA]. The materials perform very similarly in several widely used gender-neutral assays, demonstrating that the combination of appropriate preparation methods and metrologically sound spectrophotometric measurements enables the preparation and certification of quantitation [DNA] standards that are both maintainable and of practical utility.
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Affiliation(s)
- Margaret C Kline
- Biochemical Science Division, National Institute of Standards and Technology, 100 Bureau Drive, MS 8311, Gaithersburg, MD 20899-8311, USA.
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23
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Kinumi T, Narukawa T, Fujii SI, Eyama S, Saeki M, Takatsu A. Quantification of oligonucleotide containing sequence failure product: comparison of isotope dilution mass spectrometry with other quantification methods. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:399-407. [PMID: 19395775 DOI: 10.1255/ejms.986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
There is an increasing demand to develop a method for accurate quantification of DNA. Because current methods such as the ultraviolet (UV) absorption-based method are only capable of relative quantification, the quantification result depends completely on the reference material. To achieve accurate quantification of DNA, we have performed isotope dilution mass spectrometry (ID MS)-based quantification of oligonucleotides. We chose a 20-mer synthetic oligonucleotide as the analyte with a longer sequence failure product. Oligonucleotides sometimes contain sequence failure products, which are difficult to remove. It is important to quantify a target product in such mixture. After evaluating the content of the sequence failure product, the analyte spiked with stable isotopically labeled deoxynucleotide monophosphates (dNMPs) was digested by enzyme to its constituent dNMPs or deoxynucleosides, and quantified by liquid chromatography-mass spectrometry. The obtained mass fractions of the 20-mer oligonucleotide showed a good agreement with the results based on phosphate analysis by inductively coupled plasma-optical emission spectrometry and ion chromatography. UV absorption, the general method for DNA quantification, resulted in underestimation. On the other hand, the mass fraction obtained by the gravimetric method was overestimated. This study shows that the ID MS method can determine the precise mass fraction of the target oligonucleotide with the sequence failure product and possesses potential as the primary method for the certification of DNA as a reference material.
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Affiliation(s)
- Tomoya Kinumi
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8563, Japan.
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24
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Holden MJ, Rabb SA, Tewari YB, Winchester MR. Traceable phosphorus measurements by ICP-OES and HPLC for the quantitation of DNA. Anal Chem 2007; 79:1536-41. [PMID: 17297952 DOI: 10.1021/ac061463b] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Measurement of the phosphorus content of nucleotides and deoxyribonucleic acid (DNA) offers an approach to the quantitation of nucleic acids that is traceable to the SI. Such measurements can be an alternative to the commonly used spectroscopic tools that are not traceable. Phosphorus measurements of thymidine 5'-monophosphate (TMP) and acid-digested plasmid and genomic DNA preparations were made using high-performance inductively coupled plasma optical emission spectroscopy (HP-ICP-OES) and high-performance liquid chromatography (HPLC) and compared for bias and uncertainty. A prerequisite for quality measurement is the purity of the materials. Quantitation with the two platforms was comparable for the TMP. However, the HPLC values had larger uncertainties and were all statistically different from the gravimetric values at the 95% confidence level. When using ICP-OES, the digestion of the nucleotide monophosphate can be eliminated, thus simplifying the procedure. The differences between the results obtained by using the two platforms, when measuring genomic or plasmid DNA, were dependent on the mass fraction of the digest. ICP-OES measurement of phosphorus provides a highly accurate quantitation for both nucleotide monophosphates and DNA with expanded uncertainties of less than 0.1%. Currently, ICP-OES requires a significant sample size restricting its usefulness for the quantitation of DNA but represents a valuable tool for certification of reference materials. HPLC requires smaller amounts of material to perform the analysis but is less useful for certification of reference materials because of lower accuracy and 10-fold higher expanded uncertainties.
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Affiliation(s)
- Marcia J Holden
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899-8311, USA. marcia.holden@ nist.gov
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25
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.
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26
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Yang I, Han MS, Yim YH, Hwang E, Park SR. A strategy for establishing accurate quantitation standards of oligonucleotides: quantitation of phosphorus of DNA phosphodiester bonds using inductively coupled plasma-optical emission spectroscopy. Anal Biochem 2005; 335:150-61. [PMID: 15519582 DOI: 10.1016/j.ab.2004.08.038] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Indexed: 10/26/2022]
Abstract
A novel approach for quantitation of DNA (oligonucleotides) with an unprecedented accuracy of approximately 1% is reported. Quantitation of DNA is commonly performed by measuring UV absorption or fluorescence from dyes intercalated into DNA. Both methods need accurate quantitation standards to yield more comparable results between laboratories. For establishing technically authentic standards for DNA quantitation, a new measurement approach carrying an inherent capability of absolute quantitation is demanded. The proposed approach is based on the stoichiometric existence of phosphorus (P) in DNA. The quantity of P from the phosphodiester backbone of a purified oligonucleotide was accurately determined using inductively coupled plasma-optical emission spectroscopy (ICP-OES) with yttrium internal standard via acid digestion. The number of moles of oligonucleotides was then calculated from that of P using the stoichiometry. The major issues regarding the validity of the suggested approach were (i) effective removal of extra P sources, (ii) quantitative recovery of P through the digestion process, and (iii) oligomeric purity of the target oligonucleotide. These issues were investigated experimentally using various analytical techniques such as matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), capillary electrophoresis, electrical conductometry, UV spectrometry, and gravimetry. In conclusion, it is feasible to certify pure oligonucleotide reference materials with uncertainties less than 1% using the proposed approach.
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Affiliation(s)
- Inchul Yang
- Division of Chemical Metrology and Materials Evaluation, Korea Research Institute of Standards and Science, 1 Doryong-dong, Yuseong-gu, Daejon 305-340, Republic of Korea
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27
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Shimelis O, Zhou X, Li G, Giese RW. Phenolic extraction of DNA from mammalian tissues and conversion to deoxyribonucleoside-5'-monophosphates devoid of ribonucleotides. J Chromatogr A 2005; 1053:143-9. [PMID: 15543980 DOI: 10.1016/j.chroma.2004.04.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Towards a goal of detecting scaled-up DNA adducts as altered deoxynucleotides by mass spectrometry, we have set up a practical and general method for isolating DNA-derived deoxyribonucleoside-5'-monophosphates devoid of ribonucleotides starting with a 1 g sample of mammalian tissue. The method is practical because costs have been minimized, and it is general because it can be applied to a more difficult sample such as mouse skin or non-fresh calf liver. The procedure, consisting of a series of steps that were largely gleaned and tuned from prior literature, proceeds as follows: (1) homogenize the tissue in sodium dodecyl sulfate; (2) digest with ribonuclease A, ribonuclease TI, alpha-amylase and proteinase K; (3) partition between water and phenol; (4) precipitate the DNA with ethanol followed by redissolving and dialysis; and (5) digest with nuclease P1 and phosphodiesterase I followed by ultrafiltration and boric acid gel chromatography. The yellow to brown color of DNA from difficult tissues only persisted up to the ultrafiltration step. Apparently this DNA was contaminated with iron-containing proteins. Residual ribonucleotides were not observable (<0.1%) by HPLC in the final sample. Without boric acid gel chromatography, residual contamination by ribonucleotides was about 1% even when the DNA was purified before digestion by phenol partitioning followed by use of a Genomic Tip kit from Qiagen.
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Affiliation(s)
- Olga Shimelis
- Department of Pharmaceutical Sciences in the Bouve College of Health Sciences, Barnett Institute and Chemistry Department, Northeastern University, Boston, MA 02115, USA
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28
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Kandimalla ER, Pandey RK, Agrawal S. Hybridization-based fluorescence assay allows quantitation of single-stranded oligodeoxynucleotides in low nanomolar range. Anal Biochem 2004; 328:93-5. [PMID: 15081915 DOI: 10.1016/j.ab.2004.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Indexed: 11/24/2022]
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29
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:1298-1307. [PMID: 12489092 DOI: 10.1002/jms.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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