301
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Qian H, Li C, Lin Z, Zhang Y. Using thiophilic magnetic beads in purification of antibodies from human serum. Colloids Surf B Biointerfaces 2010; 75:342-8. [DOI: 10.1016/j.colsurfb.2009.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 07/15/2009] [Accepted: 09/09/2009] [Indexed: 10/20/2022]
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302
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Ma W, Chen W, Qiao R, Liu C, Yang C, Li Z, Xu D, Peng C, Jin Z, Xu C, Zhu S, Wang L. Rapid and sensitive detection of microcystin by immunosensor based on nuclear magnetic resonance. Biosens Bioelectron 2009; 25:240-3. [DOI: 10.1016/j.bios.2009.06.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/07/2009] [Accepted: 06/08/2009] [Indexed: 11/15/2022]
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303
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Comparative evaluation of two automated systems for nucleic acid extraction of BK virus: NucliSens easyMAG versus BioRobot MDx. J Virol Methods 2009; 162:208-12. [PMID: 19712698 DOI: 10.1016/j.jviromet.2009.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 08/04/2009] [Accepted: 08/17/2009] [Indexed: 12/17/2022]
Abstract
The objective of this study was to compare the performance of two automated nucleic acid extraction systems. Specifically, the NucliSens easyMAG system (bioMerieux, Marcy l'Etoile, France), which incorporates magnetic bead technology, was compared with the BioRobot MDx system (Qiagen GmbH, Hilden, Germany), which uses a silica membrane-based method of nucleic acid extraction. Nucleic acids from the BK virus (BKV DNA) were extracted from 98 plasma and 57 urine specimens using the Real-Q BKV quantitation kit (Biosewoom, Seoul, Korea). Failed PCR was defined as negative BKV DNA results having more than 36 threshold cycles of the internal control by the manufacturer's instruction. The PCR failure rate of nucleic acids isolated from plasma samples using the MDx system was similar to that of plasma samples processed using the easyMAG system (2.0% and 3.1%, respectively). The PCR failure rate of nucleic acids isolated from urine samples using the MDx system was higher than that of urine samples processed using the easyMAG system (33.3% and 12.5%, respectively). These data suggest that the PCR inhibitors present in urine specimens are removed more efficiently by the easyMAG system. Among amplified specimens, the discordant results obtained from the two systems revealed that the BKV DNA load ranged from 2.3 log10 copies/mL to 4.6 log10 copies/mL. Of the 25 urine specimens that yielded BKV DNA by both extraction systems, 15 specimens (60.0%) yielded higher BKV DNA loads by the easyMAG system, indicating that the easyMAG system extracted nucleic acid more efficiently than did the MDx system. In conclusion, the easyMAG method outperformed the MDx method when used to extract BKV DNA from urine samples. Magnetic bead-based extraction methods such as the easyMAG system are therefore preferable for the quantitation of viral DNA in urine.
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304
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Ming Z, Xianqing Z, Sen W, Chao C, Yali C. A simple method for purification of genomic DNA from whole blood using Fe3O4/Au composite particles as a carrier. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1000-1948(09)60044-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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305
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Ferguson BS, Buchsbaum SF, Swensen JS, Hsieh K, Lou X, Soh HT. Integrated Microfluidic Electrochemical DNA Sensor. Anal Chem 2009; 81:6503-8. [DOI: 10.1021/ac900923e] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian S. Ferguson
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, College of Creative Studies, Physics, University of California, Santa Barbara, California 93106, and Department of Materials, University of California, Santa Barbara, California 93106
| | - Steven F. Buchsbaum
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, College of Creative Studies, Physics, University of California, Santa Barbara, California 93106, and Department of Materials, University of California, Santa Barbara, California 93106
| | - James S. Swensen
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, College of Creative Studies, Physics, University of California, Santa Barbara, California 93106, and Department of Materials, University of California, Santa Barbara, California 93106
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, College of Creative Studies, Physics, University of California, Santa Barbara, California 93106, and Department of Materials, University of California, Santa Barbara, California 93106
| | - Xinhui Lou
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, College of Creative Studies, Physics, University of California, Santa Barbara, California 93106, and Department of Materials, University of California, Santa Barbara, California 93106
| | - H. Tom Soh
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, College of Creative Studies, Physics, University of California, Santa Barbara, California 93106, and Department of Materials, University of California, Santa Barbara, California 93106
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306
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Corchero JL, Villaverde A. Biomedical applications of distally controlled magnetic nanoparticles. Trends Biotechnol 2009; 27:468-76. [PMID: 19564057 DOI: 10.1016/j.tibtech.2009.04.003] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 04/14/2009] [Accepted: 04/24/2009] [Indexed: 11/19/2022]
Abstract
Nano-sized magnetic particles are increasingly being used across a wide spectrum of biomedical fields. Upon functionalization to enable specific binding, magnetic particles and their targets can be conveniently positioned in vitro and in vivo by the distal application of magnetic fields. Furthermore, such particles can be magnetically heated after reaching their in vivo targets, thus inducing localized cell death that has a considerable therapeutic value in, for instance, cancer therapy. In this context, innovative biomedical research has produced novel applications that have exciting clinical potential. Such applications include magnetically enhanced transfection, magnetically assisted gene therapy, magnetically induced hyperthermia and magnetic-force-based tissue engineering, and the principles and utilities of these applications will be discussed here.
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Affiliation(s)
- José Luis Corchero
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, 08196 Barcelona, Spain
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307
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Duford DA, Peng DD, Salin ED. Magnetically Driven Solid Sample Preparation for Centrifugal Microfluidic Devices. Anal Chem 2009; 81:4581-4. [PMID: 19422186 DOI: 10.1021/ac9006733] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David A. Duford
- Department of Chemistry, McGill University 801, Sherbrooke Street West, Montreal, Quebec, Canada, H3A 2K6
| | - Dan D. Peng
- Department of Chemistry, McGill University 801, Sherbrooke Street West, Montreal, Quebec, Canada, H3A 2K6
| | - Eric D. Salin
- Department of Chemistry, McGill University 801, Sherbrooke Street West, Montreal, Quebec, Canada, H3A 2K6
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308
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Functionalized gold nanoparticles: Synthesis, structure and colloid stability. J Colloid Interface Sci 2009; 331:251-62. [DOI: 10.1016/j.jcis.2008.12.002] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 11/24/2008] [Accepted: 12/02/2008] [Indexed: 11/19/2022]
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309
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Qian H, Lin Z, Xu H, Chen M. The efficient and specific isolation of the antibodies from human serum by thiophilic paramagnetic polymer nanospheres. Biotechnol Prog 2009; 25:376-83. [DOI: 10.1002/btpr.105] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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310
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Cheng C, Wen Y, Xu X, Gu H. Tunable synthesis of carboxyl-functionalized magnetite nanocrystal clusters with uniform size. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b910832g] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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311
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Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. J Biomed Biotechnol 2009; 2009:574398. [PMID: 20011662 PMCID: PMC2789530 DOI: 10.1155/2009/574398] [Citation(s) in RCA: 313] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 11/05/2009] [Indexed: 12/30/2022] Open
Abstract
Extraction of DNA, RNA, and protein is the basic method used in molecular biology. These biomolecules can be isolated from any biological material for subsequent downstream processes, analytical, or preparative purposes. In the past, the process of extraction and purification of nucleic acids used to be complicated, time-consuming, labor-intensive, and limited in terms of overall throughput. Currently, there are many specialized methods that can be used to extract pure biomolecules, such as solution-based and column-based protocols. Manual method has certainly come a long way over time with various commercial offerings which included complete kits containing most of the components needed to isolate nucleic acid, but most of them require repeated centrifugation steps, followed by removal of supernatants depending on the type of specimen and additional mechanical treatment. Automated systems designed for medium-to-large laboratories have grown in demand over recent years. It is an alternative to labor-intensive manual methods. The technology should allow a high throughput of samples; the yield, purity, reproducibility, and scalability of the biomolecules as well as the speed, accuracy, and reliability of the assay should be maximal, while minimizing the risk of cross-contamination.
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Affiliation(s)
- Siun Chee Tan
- School of Postgraduate Studies & Research, Division of Pharmacy, International Medical University, No. 126, Jalan 19/155B, Bukit Jalil, 57000 Kuala Lumpur, Malaysia.
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312
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Nishio K, Masaike Y, Ikeda M, Narimatsu H, Gokon N, Tsubouchi S, Hatakeyama M, Sakamoto S, Hanyu N, Sandhu A, Kawaguchi H, Abe M, Handa H. Development of novel magnetic nano-carriers for high-performance affinity purification. Colloids Surf B Biointerfaces 2008; 64:162-9. [DOI: 10.1016/j.colsurfb.2008.01.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
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313
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Zeng L, Huang J, Zhang Y, Qiu G, Tong J, Chen D, Zhou J, Luo X. An effective method of DNA extraction for bioleaching bacteria from acid mine drainage. Appl Microbiol Biotechnol 2008; 79:881-8. [PMID: 18481056 DOI: 10.1007/s00253-008-1491-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 04/04/2008] [Accepted: 04/05/2008] [Indexed: 11/26/2022]
Abstract
An effective and versatile method for microorganism lysis and direct extraction of DNA from bioleaching bacteria was developed using pure cultures and an acid mine drainage (AMD) sediment sample. In the described method, microorganisms are treated at three different incubation temperatures: boiling water incubation for 6-10 min, followed by 60 +/- 5 degrees C for 30 min, then 72 degrees C for 30 min. The extracted DNA is purified using a phenol/chloroform/alcohol mixture and precipitated in absolute alcohol. The 16S ribosomal RNA (rRNA) and gyrB genes of the pure cultures were amplified using the polymerase chain reaction (PCR) and differentiated using repetitive intergenic DNA sequences amplification (Rep-PCR). For the AMD sediment sample, the 16S rRNA and gyrB genes of the amplicons were digested with Hin6I and MspI, and the restriction fragment length polymorphism analysis patterns were used as a fingerprint to discern community diversity. The results indicated that this method is a versatile, reproducible, effective, and rapid technique for routine DNA extraction from bioleaching bacteria. The low cost of this method also makes it attractive for large-scale studies.
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Affiliation(s)
- Leping Zeng
- Xiang-Ya School of Medicine, Central South University, Changsha, China
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314
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Ribeiro-Silva A, Zhang H, Jeffrey SS. RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies. BMC Mol Biol 2007; 8:118. [PMID: 18154675 PMCID: PMC2233637 DOI: 10.1186/1471-2199-8-118] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2007] [Accepted: 12/21/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The development of protocols for RNA extraction from paraffin-embedded samples facilitates gene expression studies on archival samples with known clinical outcome. Older samples are particularly valuable because they are associated with longer clinical follow up. RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue is problematic due to chemical modifications and continued degradation over time. We compared quantity and quality of RNA extracted by four different protocols from 14 ten year old and 14 recently archived (three to ten months old) FFPE breast cancer tissues. Using three spin column purification-based protocols and one magnetic bead-based protocol, total RNA was extracted in triplicate, generating 336 RNA extraction experiments. RNA fragment size was assayed by reverse transcription-polymerase chain reaction (RT-PCR) for the housekeeping gene glucose-6-phosphate dehydrogenase (G6PD), testing primer sets designed to target RNA fragment sizes of 67 bp, 151 bp, and 242 bp. RESULTS Biologically useful RNA (minimum RNA integrity number, RIN, 1.4) was extracted in at least one of three attempts of each protocol in 86-100% of older and 100% of recently archived ("months old") samples. Short RNA fragments up to 151 bp were assayable by RT-PCR for G6PD in all ten year old and months old tissues tested, but none of the ten year old and only 43% of months old samples showed amplification if the targeted fragment was 242 bp. CONCLUSION All protocols extracted RNA from ten year old FFPE samples with a minimum RIN of 1.4. Gene expression of G6PD could be measured in all samples, old and recent, using RT-PCR primers designed for RNA fragments up to 151 bp. RNA quality from ten year old FFPE samples was similar to that extracted from months old samples, but quantity and success rate were generally higher for the months old group. We preferred the magnetic bead-based protocol because of its speed and higher quantity of extracted RNA, although it produced similar quality RNA to other protocols. If a chosen protocol fails to extract biologically useful RNA from a given sample in a first attempt, another attempt and then another protocol should be tried before excluding the case from molecular analysis.
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Affiliation(s)
- Alfredo Ribeiro-Silva
- Department of Surgery, Stanford University School of Medicine, MSLS Bldg Room P214; 1201 Welch Road, Stanford, CA 94305-5494, USA.
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