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Di Grandi D, Dayeh DM, Kaur K, Chen Y, Henderson S, Moon Y, Bhowmick A, Ihnat PM, Fu Y, Muthusamy K, Palackal N, Pyles EA. A single-nucleotide resolution capillary gel electrophoresis workflow for poly(A) tail characterization in the development of mRNA therapeutics and vaccines. J Pharm Biomed Anal 2023; 236:115692. [PMID: 37696189 DOI: 10.1016/j.jpba.2023.115692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023]
Abstract
The 3' poly(A) tail is an important component of messenger RNA (mRNA). The length of the poly(A) tail has direct impact on the stability and translation efficiency of the mRNA molecule and is therefore considered to be a critical quality attribute (CQA) of mRNA-based therapeutics and vaccines. Various analytical methods have been developed to monitor this CQA. Methods like ion-pair reversed-phase liquid chromatography (IPRP-LC) can be used to quantify the percentage of mRNA with poly(A) tail but fail to provide further information on the actual length of poly(A). High-resolution methods such as liquid chromatography coupled with mass spectrometry (LC-MS) or next generation sequencing (NGS) can separate poly(A) tail length by one nucleotide (n/n + 1 resolution) but are complicated to implement for release testing of manufactured mRNA. In this study, a workflow utilizing capillary gel electrophoresis (CGE) for characterizing the poly(A) tail length of mRNA was developed. The CGE method demonstrated resolution comparable with the LC-MS method. With UV detection and the addition of poly(A) length markers, this method can provide poly(A) tail length information and can also provide quantitation of each poly(A) length, making it a suitable release method to monitor the CQA of poly(A) tail length.
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Affiliation(s)
- Deanna Di Grandi
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Daniel M Dayeh
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Keerat Kaur
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Yizhuo Chen
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Steven Henderson
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Youmi Moon
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Arijit Bhowmick
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Peter M Ihnat
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Yue Fu
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA.
| | - Kathir Muthusamy
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA.
| | - Nisha Palackal
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Erica A Pyles
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
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2
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Holland LA, Casto-Boggess LD. Gels in Microscale Electrophoresis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:161-179. [PMID: 37314879 DOI: 10.1146/annurev-anchem-091522-080207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gel matrices are fundamental to electrophoresis analyses of biopolymers in microscale channels. Both capillary gel and microchannel gel electrophoresis systems have produced fundamental advances in the scientific community. These analytical techniques remain as foundational tools in bioanalytical chemistry and are indispensable in the field of biotherapeutics. This review summarizes the current state of gels in microscale channels and provides a brief description of electrophoretic transport in gels. In addition to the discussion of traditional polymers, several nontraditional gels are introduced. Advances in gel matrices highlighted include selective polymers modified to contain added functionality as well as thermally responsive gels formed through self-assembly. This review discusses cutting-edge applications to challenging areas of discovery in DNA, RNA, protein, and glycan analyses. Finally, emerging techniques that result in multifunctional assays for real-time biochemical processing in capillary and three-dimensional channels are identified.
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Affiliation(s)
- Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA;
| | - Laura D Casto-Boggess
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA;
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3
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Analysis of therapeutic nucleic acids by capillary electrophoresis. J Pharm Biomed Anal 2022; 219:114928. [PMID: 35853263 DOI: 10.1016/j.jpba.2022.114928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/04/2022] [Accepted: 07/02/2022] [Indexed: 12/19/2022]
Abstract
Nucleic acids are getting increased attention to fulfill unmet medical needs. The past five years have seen more than ten FDA approvals of nucleic acid based therapeutics. New analytical challenges have been posed in discovery, characterization, quality control and bioanalysis of therapeutic nucleic acids. Capillary electrophoresis (CE) has proven to be an efficient separation technique and has been widely used for analyzing oligonucleotides and nucleic acids. This review discusses the recent technical advances of CE in nucleic acid analysis such as polymeric matrices, separation conditions and detection methods, and the applications of CE to various therapeutic nucleic acids including antisense oligonucleotide (ASO), small interfering ribonucleic acid (siRNA), messenger RNA (mRNA), gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)-based gene and cell therapy, and other nucleic acid related therapeutics.
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4
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Kaczmarkiewicz A, Nuckowski Ł, Studzińska S, Buszewski B. Analysis of Antisense Oligonucleotides and Their Metabolites with the Use of Ion Pair Reversed-Phase Liquid Chromatography Coupled with Mass Spectrometry. Crit Rev Anal Chem 2019; 49:256-270. [PMID: 30612436 DOI: 10.1080/10408347.2018.1517034] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Antisense oligonucleotides (ASOs) have been widely investigated as a potential drugs because of their ability to bind with the target DNA or RNA strands, which may lead to inhibition of translational processes. This review presents currently approved oligonucleotide (OGN) drugs and summarizes their modification types, mechanisms of action, and application of ion pair reversed phase liquid chromatography for the analysis. Special attention was paid to the stationary phases selection for the separation of OGNs and the impact of different compositions of mobile phases on retention and signal intensity in mass spectrometry (MS). Moreover, the application of ion pair liquid chromatography coupled with MS for the separation and determination of metabolites of ASOs was described. The type of matrix, time of analysis, lower limits of quantification and detection, as well as precision, accuracy, and linearity of developed methods have been included as part of this contribution.
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Affiliation(s)
- Anna Kaczmarkiewicz
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Łukasz Nuckowski
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Sylwia Studzińska
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Bogusław Buszewski
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
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5
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Wuethrich A, Quirino JP. A decade of microchip electrophoresis for clinical diagnostics - A review of 2008-2017. Anal Chim Acta 2018; 1045:42-66. [PMID: 30454573 DOI: 10.1016/j.aca.2018.08.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/30/2018] [Accepted: 08/03/2018] [Indexed: 01/10/2023]
Abstract
A core element in clinical diagnostics is the data interpretation obtained through the analysis of patient samples. To obtain relevant and reliable information, a methodological approach of sample preparation, separation, and detection is required. Traditionally, these steps are performed independently and stepwise. Microchip capillary electrophoresis (MCE) can provide rapid and high-resolution separation with the capability to integrate a streamlined and complete diagnostic workflow suitable for the point-of-care setting. Whilst standard clinical diagnostics methods normally require hours to days to retrieve specific patient data, MCE can reduce the time to minutes, hastening the delivery of treatment options for the patients. This review covers the advances in MCE for disease detection from 2008 to 2017. Miniaturised diagnostic approaches that required an electrophoretic separation step prior to the detection of the biological samples are reviewed. In the two main sections, the discussion is focused on the technical set-up used to suit MCE for disease detection and on the strategies that have been applied to study various diseases. Throughout these discussions MCE is compared to other techniques to create context of the potential and challenges of MCE. A comprehensive table categorised based on the studied disease using MCE is provided. We also comment on future challenges that remain to be addressed.
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Affiliation(s)
- Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Building 75, Brisbane, QLD, 4072, Australia
| | - Joselito P Quirino
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia.
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6
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Chen J, Ni Y, Liu C, Yamaguchi Y, Chen Q, Sekine S, Zhu X, Dou X. Rapid identification and quantitation for oral bacteria based on short-end capillary electrophoresis. Talanta 2016; 160:425-430. [DOI: 10.1016/j.talanta.2016.07.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/19/2016] [Accepted: 07/23/2016] [Indexed: 11/29/2022]
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7
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Tamizi E, Jouyban A. The potential of the capillary electrophoresis techniques for quality control of biopharmaceuticals-A review. Electrophoresis 2015; 36:831-58. [DOI: 10.1002/elps.201400343] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/27/2014] [Accepted: 11/27/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Elnaz Tamizi
- Biotechnology Research Center; Tabriz University of Medical Sciences; Tabriz Iran
| | - Abolghasem Jouyban
- Pharmacy Faculty and Drug Applied Research Center; Tabriz University of Medical Sciences; Tabriz Iran
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8
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Allan KE, Lenehan CE, Khodakov DA, Ellis AV. Rapid separation of synthetic oligonucleotides on polymer modified capillary surfaces using short-end injection capillary electrophoresis in free solution. Analyst 2014; 138:6954-61. [PMID: 24087827 DOI: 10.1039/c3an01422c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we use short-end electrokinetic injection capillary electrophoresis (CE) to investigate the free solution mobility of short strands of double-stranded oligonucleotides (dsODNs) on polymer modified capillaries. Single base pair (bp) resolution (Rs) of dsODNs ranging from 16-20 bp was achieved in free solution on an 8 cm capillary dynamically coated with poly(ethylpyrrolidine methacrylate-co-methyl methacrylate) (PEPyM-co-PMMA) random copolymer. Interestingly, separation of a dsODN mixture containing two 16 bp strands of different sequences resulted in partial resolution (0.52) implying that the free solution mobility of dsODNs was sequence dependent. The single bp resolution achieved for the complementary sequence strands (the sequence of all strands in the mixtures contained the same 16 bp sequence) was improved by up to 37% for separation of dsODNs containing non-complementary sequences. The 16 bp peak was not additive within each mixture, indicating the presence of ODN-ODN interactions. Investigation of these interactions (and ODN-buffer interactions) showed that they can be influenced by the ionic strength and conductivity of the background electrolyte (BGE). Increasing the ionic strength reduced the ODN-ODN interactions and improved the resolution, whereas, increasing the conductivity reduced ODN-buffer interactions, increasing the mobility, at the consequence of promoting ODN-ODN interactions, and hence decreasing the resolution.
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Affiliation(s)
- Kerrilee E Allan
- Flinders Centre for NanoScale Science and Technology, School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.
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9
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Yamaguchi K, Takeyasu N, Kaneta T. Determination of association constants between 5'-guanosine monophosphate gel and aromatic compounds by capillary electrophoresis. J Chromatogr A 2013; 1288:149-54. [PMID: 23522259 DOI: 10.1016/j.chroma.2013.02.090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/14/2013] [Accepted: 02/27/2013] [Indexed: 11/26/2022]
Abstract
Hydro gel formed by 5'-guanosine monophosphate (GMP) in the presence of a potassium ion is expected to exhibit interesting selectivity in capillary electrophoretic separations. Here, we estimated the conditional association constants between the hydro gel (G-gel) and aromatic compounds by capillary electrophoresis in order to investigate the separation selectivity that is induced by the G-gel. Several aromatic compounds were separated in a solution containing GMP and potassium ion at different concentrations. The association constants were calculated by correlating the electrophoretic mobilities of the analytes obtained experimentally using a concentration of G-gel. During semi-quantitative estimation, naphthalene derivatives had larger association constants (Kass=10.3-16.8) compared with those of benzene derivatives (Kass=3.91-5.31), which means that the binding sites of G-gel match better to a naphthalene ring than to a benzene ring. A hydrophobic interaction was also found when the association constants for alkyl resorcinol were compared with those of different hydrocarbon chains. The association constants of nucleobases and tryptophan ranged from 6.05 to 12.6, which approximated the intermediate values between benzene and naphthalene derivatives. Consequently, the selective interaction between G-gel and aromatic compounds was classified as one of three types: (1) an intercalation into stacked planar GMP tetramers; (2) a hydrophobic interaction with a long alkyl chain; or, (3) a small contribution of steric hindrance and/or hydrogen bonding with functional groups such as amino and hydroxyl groups.
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Affiliation(s)
- Kaori Yamaguchi
- Department of Chemistry, Division of Earth, Life, and Molecular Sciences, Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka, Okayama 700-8530, Japan
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10
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Nai YH, Powell SM, Breadmore MC. Capillary electrophoretic system of ribonucleic acid molecules. J Chromatogr A 2012; 1267:2-9. [DOI: 10.1016/j.chroma.2012.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/03/2012] [Accepted: 08/06/2012] [Indexed: 11/25/2022]
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11
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Barron AE, Sunada WM, Blanch HW. Capillary electrophoresis of DNA in uncrosslinked polymer solutions: evidence for a new mechanism of DNA separation. Biotechnol Bioeng 2012; 52:259-70. [PMID: 18629893 DOI: 10.1002/(sici)1097-0290(19961020)52:2<259::aid-bit7>3.0.co;2-p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The electrophoretic separation of DNA molecules is usually performed in thin slabs of agarose or polyacrylamide gel. However, DNA separations can be achieved more rapidly and efficiently within a microbore fused silica capillary filled with an uncrosslinked polymer solution. An early assumption was that the mechanism of DNA separation in polymer solution-capillary electrophoresis (PS-CE) is the same as that postulated to occur in slab gel electrophoresis, i.e., that entangled polymer chains form a network of "pores" through which the DNA migrates. However, we have demonstrated that large DNA restriction fragments (2.0-23.1 kbp) can be separated by CE in extremely dilute polymer solutions, which contain as little as 6 parts per million [0.0006% (w/w)] of uncrosslinked hydroxyethyl cellulose (HEC) polymers. In such extremely dilute HEC solutions, far below the measured polymer entanglement threshold concentration, pore-based models of DNA electrophoresis do not apply. We propose a transient entanglement coupling mechanism for the electrophoretic separation of DNA in uncrosslinked polymer solutions, which is based on physical polymer/DNA interactions.
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Affiliation(s)
- A E Barron
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
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12
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Stranneheim H, Lundeberg J. Stepping stones in DNA sequencing. Biotechnol J 2012; 7:1063-73. [PMID: 22887891 PMCID: PMC3472021 DOI: 10.1002/biot.201200153] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/21/2012] [Accepted: 07/04/2012] [Indexed: 12/11/2022]
Abstract
In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid technological advances have enormously expanded sequencing opportunities and applications, but also imposed strains and challenges on steps prior to sequencing and in the downstream process of handling and analysis of these massive amounts of sequence data. Traditionally, sequencing has been limited to small DNA fragments of approximately one thousand bases (derived from the organism's genome) due to issues in maintaining a high sequence quality and accuracy for longer read lengths. Although many technological breakthroughs have been made, currently the commercially available massively parallel sequencing methods have not been able to resolve this issue. However, recent announcements in nanopore sequencing hold the promise of removing this read-length limitation, enabling sequencing of larger intact DNA fragments. The ability to sequence longer intact DNA with high accuracy is a major stepping stone towards greatly simplifying the downstream analysis and increasing the power of sequencing compared to today. This review covers some of the technical advances in sequencing that have opened up new frontiers in genomics.
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Affiliation(s)
- Henrik Stranneheim
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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13
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Cheng YQ, Yao B, Zhang HD, Fang J, Fang Q. An automated capillary electrophoresis system for high-speed separation of DNA fragments based on a short capillary. Electrophoresis 2012; 31:3184-91. [PMID: 22216429 DOI: 10.1002/elps.201000362] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A high-speed DNA fragment separation system was developed based on a short capillary and a slotted-vial array automated sample introduction system. The injection process of DNA sample in a short capillary was investigated systematically with three injection techniques including constant-field-strength, low-field-strength and translational spontaneous injections. Under the optimized conditions, picoliter-scale sample plugs (corresponding to ca. 20-μm plug length) were obtained, which ensure the high-speed and high-efficiency separation for DNA fragments with a short effective separation length. Other separation conditions including the sieving matrix concentration, separation field strength and effective separation length were also optimized. The present system was applied in the separation of ΦX174-Hae III digest DNA marker. With an effective separation length of 2.5 cm, the separation could be achieved in <100 s with plate heights ranging from 0.21 to 0.74 μm (corresponding to plate numbers from 4.86 × 10(6) to 1.36 × 10(6)/m). The repeatabilities for the migration time of the eleven fragments were between 0.4 and 1.1% RSD (n=8). By using the automated continuous injection method, the separation for four different DNA samples could be achieved within 250 s. The present system was further applied in the fast sizing of real DNA samples of PCR products.
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Affiliation(s)
- Yong-Qiang Cheng
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, PR China
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14
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Kaneta T, Ogura T, Yamato S, Imasaka T. Band broadening of DNA fragments isolated by polyacrylamide gel electrophoresis in capillary electrophoresis. J Sep Sci 2012; 35:431-5. [DOI: 10.1002/jssc.201100909] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Wu J, Zhao SL, Gao L, Wu J, Gao D. Separation of single-stranded DNA fragments at a 10-nucleotide resolution by stretching in microfluidic channels. LAB ON A CHIP 2011; 11:4036-4040. [PMID: 21997134 DOI: 10.1039/c1lc20600a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report a novel DNA separation method by tethering DNA chains to a solid surface and then stretching the DNA chains with an electric field. The anchor is such designed that the critical force to detach a DNA chain is independent of its size. Because the stretching force is proportional to the DNA net charge, a gradual increase of the electric field leads to size-based removal of the DNA strands from the surface and thus DNA separation. Here we show that this method, originally proposed for separation of long double-stranded DNA chains (>10,000 base pairs), is also applicable to single-stranded (ss) DNA fragments with less than 100 nucleotides (nt). Theoretical analysis indicates that the separation resolution is limited by the fluctuation forces on tethered DNA chains. By employing a microfluidic platform with narrow channels filled with a buffer of low ionic conductivity, we are able to apply a strong electric field to the DNA fragments with negligible Joule heating. Upon stepwise increments of the electric field, we demonstrate efficient separation of short ssDNA fragments at a 10-nt resolution.
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Affiliation(s)
- Jiamin Wu
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
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16
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Wegman DW, Krylov SN. Direct Quantitative Analysis of Multiple miRNAs (DQAMmiR). Angew Chem Int Ed Engl 2011; 50:10335-9. [DOI: 10.1002/anie.201104693] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Indexed: 02/03/2023]
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Abstract
BACKGROUND Advances in the understanding of complex trait genetics have always been enabled by advances in genomic technology. Next-generation sequencing (NGS) is set to revolutionize the way complex trait genetics research is carried out. RESULTS NGS has multiple applications in the field of human genetics, but is accompanied by substantial study design, analysis and interpretation challenges. This review discusses key aspects of study design considerations, data handling issues and required analytical developments. We also highlight early successes in mapping genetic traits using NGS. CONCLUSION NGS opens the entire spectrum of genomic alterations for the genetic analysis of complex traits and there are early publications illustrating its power. Continuing development in analytical tools will allow the promise of NGS to be realized.
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Kaneta T, Ogura T, Imasaka T. Analysis of proteins in biological samples by capillary sieving electrophoresis with postcolumn derivatization/laser-induced fluorescence detection. Electrophoresis 2011; 32:1061-7. [DOI: 10.1002/elps.201000488] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/06/2010] [Accepted: 11/19/2010] [Indexed: 11/09/2022]
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20
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Zhang S, Jiang C, Jia L. Tetrabutylammonium phosphate-assisted separation of multiplex polymerase chain reaction products in non-gel sieving capillary electrophoresis. Anal Biochem 2011; 408:284-8. [DOI: 10.1016/j.ab.2010.09.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 09/13/2010] [Accepted: 09/15/2010] [Indexed: 10/19/2022]
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21
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Selection of aptamers for a non-DNA binding protein in the context of cell lysate. Anal Chim Acta 2010; 681:92-7. [PMID: 21035608 DOI: 10.1016/j.aca.2010.09.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 09/22/2010] [Accepted: 09/26/2010] [Indexed: 01/14/2023]
Abstract
Aptamer-facilitated Protein Isolation from Cells (AptaPIC) is a recently introduced method that allows, in particular, generation of aptamers for a protein target in a context of a crude cell lysate. The approach enables efficient, tag-free, affinity purification of target proteins which are not available in a pure form a priori, and for which no affinity ligands are available. In the proof-of-principle work, AptaPIC was used to develop aptamers for and purify MutS, a DNA mismatch repair protein. The DNA-binding nature of MutS raised concerns that AptaPIC was not a generic technique and could be inapplicable to protein targets that do not possess native nucleic acid-binding properties. Here we prove that these concerns are invalid. We used AptaPIC to generate pools of aptamers for human Platelet-Derived Growth Factor chain B (PDGF-B) protein, a non-DNA binding protein, in the context of a bacterial cell lysate, and subsequently purify it from the same lysate. Within a small number of rounds, the efficiencies of aptamer selection were similar in conventional Systematic Evolution of Ligands by Exponential Enrichment (SELEX) for pure protein and in AptaPIC for protein in the cell lysate. The conventional selection approach resulted in an aptamer pool with an EC(50) value of 2.0±0.1 μM, while the AptaPIC selection approach resulted in a pool with an EC(50) value of 3.9±0.4 μM. Our results clearly demonstrate that selection of aptamers for proteins in the cell lysate is not only realistic but also efficient.
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22
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Kaneta T, Yamamoto D, Imasaka T. Postcolumn derivatization of proteins in capillary sieving electrophoresis/laser-induced fluorescence detection. Electrophoresis 2009; 30:3780-5. [DOI: 10.1002/elps.200900314] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Microfluidic chip: Next-generation platform for systems biology. Anal Chim Acta 2009; 650:83-97. [DOI: 10.1016/j.aca.2009.04.051] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 04/16/2009] [Accepted: 04/27/2009] [Indexed: 12/30/2022]
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Abstract
Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA-sequencing methods have evolved from the labor-intensive slab gel electrophoresis, through automated multiCE systems using fluorophore labeling with multispectral imaging, to the "next-generation" technologies of cyclic-array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes were only possible with the advent of modern sequencing technologies that were a result of step-by-step advances with a contribution of academics, medical personnel and instrument companies. While next-generation sequencing is moving ahead at breakneck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of CE in DNA sequencing based in part of several of our articles in this journal.
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MESH Headings
- DNA/analysis
- DNA/genetics
- Electrophoresis, Capillary/history
- Electrophoresis, Capillary/instrumentation
- Electrophoresis, Capillary/methods
- Electrophoresis, Capillary/trends
- Electrophoresis, Microchip/instrumentation
- History, 20th Century
- History, 21st Century
- Humans
- Sequence Analysis, DNA/history
- Sequence Analysis, DNA/instrumentation
- Sequence Analysis, DNA/methods
- Sequence Analysis, DNA/trends
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Affiliation(s)
- Barry L Karger
- The Barnett Institute, Northeastern University, Boston, MA, USA
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Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008; 92:255-64. [PMID: 18703132 DOI: 10.1016/j.ygeno.2008.07.001] [Citation(s) in RCA: 665] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 07/04/2008] [Accepted: 07/09/2008] [Indexed: 12/17/2022]
Abstract
A new generation of sequencing technologies, from Illumina/Solexa, ABI/SOLiD, 454/Roche, and Helicos, has provided unprecedented opportunities for high-throughput functional genomic research. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted resequencing, discovery of transcription factor binding sites, and noncoding RNA expression profiling. This review discusses applications of next-generation sequencing technologies in functional genomics research and highlights the transforming potential these technologies offer.
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Affiliation(s)
- Olena Morozova
- BC Cancer Agency Genome Sciences Centre, Vancouver, BC, Canada
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26
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Abstract
Capillary electrophoresis (CE) is an alternative to conventional slab gel electrophoresis for the separation of DNA fragments. CE offers a number of advantages over slab gel separations in terms of speed, resolution, sensitivity, and data handling. Separation times are generally only a few minutes and the DNA is detected either by UV absorption or by fluorescent labeling. The quantity of DNA required for separation is in the nanogram range. Single-base resolution can be obtained on fragments up to several hundred base pairs. In the presence of appropriate standards, fragments can be accurately sized based on relative electrophoretic mobility. A protocol for the analysis of synthetic oligonucleotides in a flowable matrix is described in this unit.
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Affiliation(s)
- Alan Smith
- Stanford University, Stanford, California, USA
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27
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Zalewski DR, Schlautmann S, Schasfoort RBM, Gardeniers HJGE. Electrokinetic sorting and collection of fractions for preparative capillary electrophoresis on a chip. LAB ON A CHIP 2008; 8:801-809. [PMID: 18432352 DOI: 10.1039/b717785b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A microfabricated device capable of selecting and collecting multiple components from a mixture separated by capillary electrophoresis (CE) is described. This collection is automated and can be easily controlled by a set of rules defined by an operator, enabling fast and consistent operation. The device consists of an electrokinetically steered fluidic network that can be divided into three sections: a CE part, a fractions distribution region and a set of storage channels. Sample fractions leave the CE channel and are detected in the interfacial region by fluorescence intensity measurements. If an upcoming peak is detected, separation is withheld and the potentials are reconfigured to force the fraction into one of the collection channels, where they become available for further processing or analysis. The sequence of separation and collection is repeated until all the bands of interest are captured. A mixture of three fluorescent dyes (Rhodamine 6G, Rhodamine B and Fluorescein) was used to demonstrate the principle. The components were repeatedly separated by means of CE and pooled in their respective storage channels. In comparison to previous developments, the system presented in this paper offers automatic collection of all fractions in a single run. Furthermore, it is possible to run the system in a repetitive mode for accumulative pooling if more fractionated sample is required.
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Affiliation(s)
- Dawid R Zalewski
- MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, P.O Box 217, 7500AE, Enschede, The Netherlands.
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29
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Abstract
Capillary electrophoresis (CE) is an alternative to conventional slab gel electrophoresis for the separation of DNA fragments. CE offers a number of advantages over slab gel separations in terms of speed, resolution, sensitivity, and data handling. Separation times are generally only a few minutes and the DNA is detected either by UV absorption or by fluorescent labeling. The quantity of DNA required for separation is in the nanogram range. Single-base resolution can be obtained on fragments up to several hundred base pairs. In the presence of appropriate standards, fragments can be accurately sized based on relative electrophoretic mobility. A protocol for the analysis of synthetic oligonucleotides in a flowable matrix is described in this unit.
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Affiliation(s)
- Alan Smith
- Stanford University, Stanford, California, USA
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30
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12 CE in impurity profiling of drugs. CAPILLARY ELECTROPHORESIS METHODS FOR PHARMACEUTICAL ANALYSIS 2008. [DOI: 10.1016/s0149-6395(07)00012-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
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32
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Chen S, Xu Y, Xu F, Feng X, Du W, Luo Q, Liu BF. Separation and determination of amino acids by micellar electrokinetic chromatography coupling with novel multiphoton excited fluorescence detection. J Chromatogr A 2007; 1162:149-53. [PMID: 17560588 DOI: 10.1016/j.chroma.2007.05.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 05/14/2007] [Accepted: 05/14/2007] [Indexed: 11/29/2022]
Abstract
In this article, it was demonstrated that separation and determination of 20 amino acids were accomplished by micellar electrokinetic chromatography (MEKC) coupling with novel multiphoton excited fluorescence (MPEF) detection method. Different from MPEF achieved by expensive fs laser, continuous wave (CW) diode laser of ultra-low cost was uniquely employed in our MPEF system. Amino acids were fluorescently labeled with fluorescein isothiocyanate (FITC), and were subjected to sodium dodecyl sulfate (SDS)-based MEKC separation and CW-based MPEF detection. The result was compared with that by single photon excited fluorescence (SPEF), which indicated that MPEF had the advantages of better mass detectability and higher separation selectivity over SPEF. Quantitative analysis was performed and revealed linear dynamic range of over 2 orders of magnitude, with mass detection limit down to ymole level. To evaluate the reliability, this method was successfully applied for analyzing a commercial nutrition supplement liquid.
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Affiliation(s)
- Sheng Chen
- The Key Laboratory of Biomedical Photonics of MOE - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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33
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Chen H, Wu YH, Song DY, Zhang W, Dong XY, Li PW, Lu CM. On-line pre-concentration and UV determination of DNA fragments by dynamic coating capillary electrophoresis and its application to detection of genetically modified oilseed rape based on PCR. Microchem J 2007. [DOI: 10.1016/j.microc.2006.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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34
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Araya F, Huchet G, McGroarty I, Skellern GG, Waigh RD. Capillary electrophoresis for studying drug–DNA interactions. Methods 2007; 42:141-9. [PMID: 17472896 DOI: 10.1016/j.ymeth.2006.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 09/21/2006] [Accepted: 09/25/2006] [Indexed: 11/24/2022] Open
Abstract
The development of new drugs to treat disease by binding directly to DNA offers much promise but is reliant on methods to determine the relative affinity of the putative drug for different DNA sequences. Such methods should ideally be rapid and inexpensive as well as reliable. Use of capillary electrophoresis in simple silica columns offers such a method. The development of systems in which the solvent carries a soluble polymer allows the reliable separation of DNA oligomers, of 12-20 bp in length, which can then be titrated with the ligand in competition experiments. The results obtained are comparable with those obtained by footprinting and give direct graphical output, easily analysed for relative binding affinity.
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Affiliation(s)
- Fitsumbirhan Araya
- Department of Pharmaceutical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, UK
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35
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Sjödahl J, Lindberg P, Roeraade J. Separation of oligonucleotides in N-methyl-formamide-based polymer matrices by capillary electrophoresis. J Sep Sci 2007; 30:104-9. [PMID: 17313148 DOI: 10.1002/jssc.200600228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
N-Methylformamide (NMF)-based matrices for capillary electrophoretic separation of nucleic acids have been developed. The use of an organic solvent as liquid base for the separation matrices allowed a hydrophobic polymer, C16-derivatized 2-hydroxyethyl cellulose (HEC), to be employed as structural element in the sieving medium. With a matrix consisting of 5% w/v of this polymer dissolved in NMF containing 50 mM ammonium acetate, p(dA)12-18 and p(dA)40-60 oligonucleotides were baseline separated. The addition of ammonium acetate to the buffer and separation matrix resulted in enhanced separation efficiency. Furthermore, it was possible to tailor the sieving performance of the separation medium by the use of a binary mixture of C16-derivatized HEC and PVP. Differences in sieving behavior of the various matrices evaluated are discussed.
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Affiliation(s)
- Johan Sjödahl
- Department of Analytical Chemistry, KTH School of Chemical Science and Engineering, Stockholm, Sweden.
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36
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Du W, Chen S, Xu Y, Chen Z, Luo Q, Liu BF. Multiphoton excitation fluorescence: A versatile detection method for capillary electrophoresis. J Sep Sci 2007; 30:906-15. [PMID: 17536736 DOI: 10.1002/jssc.200600477] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multiphoton excitation is a relatively old concept in quantum optics. But using multiphoton excitation fluorescence (MPEF) for bioanalysis is still in its infancy. Recently, MPEF has been introduced into the microseparation field, particularly CE, as a novel detection method. In this paper, MPEF detection for CE is reviewed, including MPEF fundamentals, approaches to achieving MPEF, detector configurations and applications in biological and environmental analyses. Emphasis will be placed on some recent advances of CE-MPEF in our laboratory. Challenges and future prospects are also discussed.
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Affiliation(s)
- Wei Du
- Key Laboratory of Biomedical Photonics of MOE, Hubei Bioinformatics, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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37
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Abstract
A nanostructured copolymer matrix has successfully separated oligonucleotides with high resolution by CE using a very short separation channel which simulates the real microchip condition for the first time. The triblock copolymer, E(45)B(14)E(45) (B20-5000) with E, B, and subscript denoting oxyethylene, oxybutylene, and segment length, respectively, has a unique temperature-dependent viscosity-adjustable property and a dynamic coating ability in 1xTBE buffer (89 mM Tris, 89 mM boric acid, 2 mM EDTA in Milli-Q water). The B-block is hydrophilic at low temperatures, e.g., 4 degrees C, and the polymer solution has a very low viscosity of about 100 cP in a 32.5% w/v solution. At room temperatures, the B-block becomes hydrophobic due to a breakdown of hydrogen bonds between B-blocks and water, and the polymer matrix forms a body-centered cubic structure at high concentrations. Oligonucleotide sizing markers ranging from 8 to 32 base could be successfully separated with one-base resolution in a 1.5 cm long separation channel by E(45)B(14)E(45) in its gel-like state.
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Affiliation(s)
- Jun Zhang
- Department of Chemistry, Stony Brook University, NY 11794-3400, USA
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38
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Marsters JC, Ng P, Jhurani P, Yasser M, Bischofberger N. 5′-Phosphorylation of Oligonucleotides with Phosphorous Acid in Automated DNA Synthesis. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319008046064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Wan F, He W, Zhang J, Ying Q, Chu B. Scale-up development of high-performance polymer matrix for DNA sequencing analysis. Electrophoresis 2006; 27:3712-23. [PMID: 16960843 DOI: 10.1002/elps.200600299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Linear polyacrylamide (LPA) has been widely used as a replaceable separation matrix in CE. An increase in the molecular weight of the separation medium favors the separation of larger DNA fragments. In order to obtain ultrahigh-molecular-weight (UHMW) LPA, a "frozen" method was developed to synthesize the LPA homopolymer. This approach has three major advantages when compared with other existing routes of LPA synthesis: (i) long LPA chains could be obtained easily, with their average molecular weight (MW) being in the high 10 MDa range; (ii) the desired MW could be adjusted over a broad range by controlling the temperature and the concentration of initiators during synthesis; (iii) the product solution contains only a tiny amount of impurity besides the solvent and LPA. Both static and dynamic laser light scattering measurements were carried out to characterize the synthesized LPA in the buffer solution. The DNA sequencing matrix prepared from LPA using this method was studied and the results were compared with the newly developed commercial product POP7 from Applied Biosystems. It should be noted that this approach can be applied to synthesize other water-soluble polymers, resulting in UHMW products because the chain transfer constant is smaller at lower temperatures.
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Affiliation(s)
- Fen Wan
- Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
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40
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Barron AE, Blanch HW. DNA Separations by Slab Gel, and Capillary Electrophoresis: Theory and Practice. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/03602549508014343] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Sun P, Hartwick RA. The Effect of Electric Fields on the Dispersion of Oligonucleotides Using a Multi-Point Detection Method in Capillary Gel Electrophoresis. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/10826079408013464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- P. Sun
- a Department of Chemistry , State University of New York at Binghamton , Binghamton , New York , 13902
| | - R. A. Hartwick
- a Department of Chemistry , State University of New York at Binghamton , Binghamton , New York , 13902
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42
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Guttman A, Sperling E, Mazsaroff I. Performance and Economics in Micropreparative Capillary Electrophoresis of Oligosaccharides. J LIQ CHROMATOGR R T 2006. [DOI: 10.1080/10826079608005490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Chemoselective enzymatic preparation of N-hydroxyalkylacrylamides, monomers for hydrophilic polymer matrices. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcatb.2006.01.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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Zhang J, Gassmann M, He W, Wan F, Chu B. Reversible thermo-responsive sieving matrix for oligonucleotide separation. LAB ON A CHIP 2006; 6:526-33. [PMID: 16572215 DOI: 10.1039/b515557f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A reversible thermo-responsive gel system, consisting of Pluronic copolymer mixture of F87 and F127, has been used to successfully carry out the separation of oligonucleotides, for the first time, by microchip-based capillary electrophoresis. Pluronic triblock copolymers F87 (E(61)P(40)E(61)) and F127 (E(99)P(69)E(99)), with E, P, and subscript denoting oxyethylene, oxypropylene, and segment length respectively, have a unique temperature dependent viscosity-adjustable property and a dynamic coating ability in aqueous solution, including 1 x TBE buffer. The mixture solution has a reversible thermo-responsive property and its sol-gel transition temperature can be adjusted ranging from about 17 degrees C to 38 degrees C by varying the relative weight ratio of F87 and F127 at an optimized concentration of approximately 30% (w/v) for oligonucleotide separations. Oligonucleotide sizing markers ranging from 8 to 32 base could be successfully separated in a 1.5 cm long separation channel by the mixture solution in its gel-like state. A 30% (w/v) with a F87/F127 weight ratio of 1 ratio 2 which has a "sol-gel" transition point of about 26 degrees C shows the best sieving ability. The sieving ability of the mixture solution was further confirmed in an Agilent Bioanalyzer 2100 system. Fast separation of oligonucleotides has been achieved within 40 s with one base resolution.
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Affiliation(s)
- Jun Zhang
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
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45
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Chen S, Liu BF, Fu L, Xiong T, Liu T, Zhang Z, Huang ZL, Lu Q, Zhao YD, Luo Q. Continuous wave-based multiphoton excitation fluorescence for capillary electrophoresis. J Chromatogr A 2006; 1109:160-6. [PMID: 16325835 DOI: 10.1016/j.chroma.2005.11.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Revised: 11/04/2005] [Accepted: 11/08/2005] [Indexed: 11/29/2022]
Abstract
It was reported that a novel detection method, continuous wave (CW)-based multiphoton excitation (MPE) fluorescence detection with diode laser (DL), has been firstly proposed for capillary electrophoresis (CE). Special design of end-column detection configuration proved to be superior to on-column type, considering the detection sensitivity. Three different kinds of fluorescent tags that were widely used as molecular label in bio-analysis, such as small-molecule dye, fluorescent protein and nano particle or also referred to as quantum dot (QD), have been evaluated as samples for the constructed detection scheme. Quantitative analyses were also performed using rhodamine species as tests, which revealed dynamic linear range over two orders of magnitude, with detection limit down to zeptomole-level. Simultaneous detection of fluorescent dyestuffs with divergent excitation and emission wavelengths in a broad range showed advantage of this scheme over conventional laser-induced fluorescence (LIF) detection. Further investigations on CW-MPE fluorescence detection with diode laser for capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) separations of fluorescein isothiocyanate (FITC) labeled amino acids indicated good prospect of this detection approach in various micro or nano-column liquid phase separation technologies.
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Affiliation(s)
- Sheng Chen
- Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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46
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Liu BF, Xu B, Zhang G, Du W, Luo Q. Micro-separation toward systems biology. J Chromatogr A 2005; 1106:19-28. [PMID: 16236294 DOI: 10.1016/j.chroma.2005.09.066] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 09/14/2005] [Accepted: 09/21/2005] [Indexed: 10/25/2022]
Abstract
Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.
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Affiliation(s)
- Bi-Feng Liu
- The Key Laboratory of Biomedical Photonics of MOE - Hubei Bioinformatics, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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47
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Zhu J, Feng YL. Size exclusive capillary electrophoresis separation of DNA oligonucleotides in small size linear polyacrylamide polymer solution. J Chromatogr A 2005; 1081:19-23. [PMID: 16013592 DOI: 10.1016/j.chroma.2005.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mobility of analytes in capillary electrophoresis using polymer gels and solutions is usually described as having an inverse relationship with the molecular size (mobility decreases as molecular size increases). The most commonly used models for predicting such mobility are the Ogston model and the Reptation model. However, in this study a new separation phenomenon was observed in which the mobility of DNA oligonucleotides increased with molecular size in a capillary electrophoresis phase (CEP) coated capillary column. The polymer system used was a 11% linear polyacrylamide (Mr = 1500) solution. The log-transformed number of base pairs (log N) of three double stranded oligonucleotides had an inverse linear relationship (r2 > 0.9981) with their migration time in the capillary column. Such a relationship is similar to that observed with size exclusive chromatography.
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Affiliation(s)
- Jiping Zhu
- Chemistry Research Division, Health Canada, AL 0800C, Building 8, Tunney's Pasture, Ottawa, Ont., Canada K1A 0L2.
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48
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Hart EA, Patton WC, Jacobson JD, King A, Corselli J, Chan PJ. Luteal phase serum cell-free DNA as a marker of failed pregnancy after assisted reproductive technology. J Assist Reprod Genet 2005; 22:213-7. [PMID: 16047583 PMCID: PMC3455499 DOI: 10.1007/s10815-005-4924-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
PURPOSE DNA-damaging factors have been reported in patients that failed to achieve pregnancy after assisted reproductive technologies (ART). The hypothesis was that increased circulating cell-free DNA released by damaged cells could predict unfavorable conditions leading to failed ART treatment. The objective was to compare the relative concentrations of cell-free DNA in the luteal phase sera of nonpregnant versus pregnant patients. METHODS Frozen-thawed sera (30 IVF cases) were obtained 1 week after embryo transfer. There were 16 pregnant and 14 nonpregnant cases and controls consisting of male sera (n = 8 cases). Modified isocratic capillary electrophoresis was performed and the images analyzed for cell-free DNA. RESULTS Circulating cell-free DNA were identified in the sera of all patients. The serum concentrations of high (12 kb) and low (1 kb) molecular weight cell-free DNA were similar for both nonpregnant and pregnant patients. Male control sera had higher cell-free DNA concentrations compared with females. Evaluation of sera from a control case showed no fluctuations in cell-free DNA concentrations throughout specific days of the menstrual cycle. CONCLUSIONS The results do not support the use of the luteal phase cell-free DNA concentration as a marker for failed pregnancies. The equal concentrations of high and low molecular weight cell-free DNA and ladder band-like gel patterns suggested cell apoptosis as the source of DNA.
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Affiliation(s)
- Elaine A. Hart
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, California 92350
| | - William C. Patton
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, California 92350
| | - John D. Jacobson
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, California 92350
| | - Alan King
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, California 92350
| | - Johannah Corselli
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, California 92350
| | - Philip J. Chan
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, California 92350
- Department of Physiology and Pharmacology, Loma Linda University School of Medicine, Loma Linda, California 92350
- Loma Linda University Center for Fertility and In Vitro Fertilization, 11370 Anderson Street, Suite 3950, Loma Linda, California 92354
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Chou JS, Jacobson JD, Patton WC, King A, Chan PJ. Modified isocratic capillary electrophoresis detection of cell-free DNA in semen. J Assist Reprod Genet 2005; 21:397-400. [PMID: 15672952 PMCID: PMC3455857 DOI: 10.1007/s10815-004-7527-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE The objectives were: i) to analyze semen for the presence of cell-free DNA and ii) to determine the association between sperm parameters and cell-free DNA. METHODS Cell-free DNA in semen (N = 25 cases) were detected using the modified capillary gel electrophoresis (CE) procedure. SYBR-Gold was used to stain high (12 Kb) and low (1 Kb) molecular weight DNA fragments and the images analyzed. RESULTS The quantity of low-molecular weight cell-free DNA was positively correlated to rapid progression, curvilinear velocity (>40 microm/s), normal strict morphology and capacitation index. High-molecular weight cell-free DNA intensity index was negatively correlated to post-wash hyperactivation. Sperm concentration was not related to cell-free DNA quantity. The sperm freezing process did not increase cell-free DNA but reduced the more labile low-molecular weight cell-free DNA. CONCLUSIONS Cell-free DNA present in semen was correlated to important sperm parameters linked to normal sperm function. The data suggested the possible use of cell-free DNA as a marker of semen quality. This study reports on the novel finding of cell-free DNA released along with sperm during each ejaculation.
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Affiliation(s)
- Jennifer S. Chou
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, CA U.S.A
| | - John D. Jacobson
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, CA U.S.A
| | - William C. Patton
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, CA U.S.A
| | - Alan King
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, CA U.S.A
| | - Philip J. Chan
- Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, CA U.S.A
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50
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Kan CW, Fredlake CP, Doherty EAS, Barron AE. DNA sequencing and genotyping in miniaturized electrophoresis systems. Electrophoresis 2004; 25:3564-88. [PMID: 15565709 DOI: 10.1002/elps.200406161] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Advances in microchannel electrophoretic separation systems for DNA analyses have had important impacts on biological and biomedical sciences, as exemplified by the successes of the Human Genome Project (HGP). As we enter a new era in genomic science, further technological innovations promise to provide other far-reaching benefits, many of which will require continual increases in sequencing and genotyping efficiency and throughput, as well as major decreases in the cost per analysis. Since the high-resolution size- and/or conformation-based electrophoretic separation of DNA is the most critical step in many genetic analyses, continual advances in the development of materials and methods for microchannel electrophoretic separations will be needed to meet the massive demand for high-quality, low-cost genomic data. In particular, the development (and commercialization) of miniaturized genotyping platforms is needed to support and enable the future breakthroughs of biomedical science. In this review, we briefly discuss the major sequencing and genotyping techniques in which high-throughput and high-resolution electrophoretic separations of DNA play a significant role. We review recent advances in the development of technology for capillary electrophoresis (CE), including capillary array electrophoresis (CAE) systems. Most of these CE/CAE innovations are equally applicable to implementation on microfabricated electrophoresis chips. Major effort is devoted to discussing various key elements needed for the development of integrated and practical microfluidic sequencing and genotyping platforms, including chip substrate selection, microchannel design and fabrication, microchannel surface modification, sample preparation, analyte detection, DNA sieving matrices, and device integration. Finally, we identify some of the remaining challenges, and some of the possible routes to further advances in high-throughput DNA sequencing and genotyping technologies.
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Affiliation(s)
- Cheuk-Wai Kan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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