A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae
<div><table cellspacing="0" cellpadding="0" align="left"><tbody><tr><td align="left" valign="top"><p><strong><em>Background</em></strong><strong>:<em> </em></strong> ...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Tehran University of Medical Sciences
2016-09-01
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| Series: | Journal of Medical Bacteriology |
| Subjects: | |
| Online Access: | http://jmb.tums.ac.ir/index.php/jmb/article/view/211 |
| _version_ | 1811344839809171456 |
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| author | Farkhondeh Saba Moslem Papizadeh Javad Khansha Mahshid Sedghi Mehrnoosh Rasooli Mohammad Ali Amoozegar Mohammad Reza Soudi Seyed Abolhassan Shahzadeh Fazeli |
| author_facet | Farkhondeh Saba Moslem Papizadeh Javad Khansha Mahshid Sedghi Mehrnoosh Rasooli Mohammad Ali Amoozegar Mohammad Reza Soudi Seyed Abolhassan Shahzadeh Fazeli |
| author_sort | Farkhondeh Saba |
| collection | DOAJ |
| description | <div><table cellspacing="0" cellpadding="0" align="left"><tbody><tr><td align="left" valign="top"><p><strong><em>Background</em></strong><strong>:<em> </em></strong> Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR). Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol.</p><p> </p><p><strong><em>Methods</em></strong><strong>:<em> </em></strong> According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications.</p><p> </p><p><strong><em>Results</em></strong><strong>:<em> </em></strong><em> </em> This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s) of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.</p></td></tr></tbody></table></div><strong><em>Conclusion</em>:<em> </em></strong> Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality. |
| first_indexed | 2024-04-13T19:53:13Z |
| format | Article |
| id | doaj.art-e44342e04ce54d45b7bac4b00fb73141 |
| institution | Directory Open Access Journal |
| issn | 2251-8649 2322-2581 |
| language | English |
| last_indexed | 2024-04-13T19:53:13Z |
| publishDate | 2016-09-01 |
| publisher | Tehran University of Medical Sciences |
| record_format | Article |
| series | Journal of Medical Bacteriology |
| spelling | doaj.art-e44342e04ce54d45b7bac4b00fb731412022-12-22T02:32:26ZengTehran University of Medical SciencesJournal of Medical Bacteriology2251-86492322-25812016-09-0153-42228214A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green AlgaeFarkhondeh Saba0Moslem Papizadeh1Javad Khansha2Mahshid Sedghi3Mehrnoosh Rasooli4Mohammad Ali Amoozegar5Mohammad Reza Soudi6Seyed Abolhassan Shahzadeh Fazeli71 Microorganisms Bank, Iranian Biological Resource Center (IBRC), (ACECR), Tehran, Iran.1 Microorganisms Bank, Iranian Biological Resource Center (IBRC), (ACECR), Tehran, Iran.1 Microorganisms Bank, Iranian Biological Resource Center (IBRC), (ACECR), Tehran, Iran.1 Microorganisms Bank, Iranian Biological Resource Center (IBRC), (ACECR), Tehran, Iran.1 Microorganisms Bank, Iranian Biological Resource Center (IBRC), (ACECR), Tehran, Iran.2 Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran.3 National Laboratory of Industrial Microbiology, Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.4 Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in biology, University of Science and Culture, Tehran, Iran.<div><table cellspacing="0" cellpadding="0" align="left"><tbody><tr><td align="left" valign="top"><p><strong><em>Background</em></strong><strong>:<em> </em></strong> Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR). Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol.</p><p> </p><p><strong><em>Methods</em></strong><strong>:<em> </em></strong> According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications.</p><p> </p><p><strong><em>Results</em></strong><strong>:<em> </em></strong><em> </em> This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s) of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.</p></td></tr></tbody></table></div><strong><em>Conclusion</em>:<em> </em></strong> Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality.http://jmb.tums.ac.ir/index.php/jmb/article/view/211EukaryotesGenome (DNA) extractionIdentificationProkaryotesSequence |
| spellingShingle | Farkhondeh Saba Moslem Papizadeh Javad Khansha Mahshid Sedghi Mehrnoosh Rasooli Mohammad Ali Amoozegar Mohammad Reza Soudi Seyed Abolhassan Shahzadeh Fazeli A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae Journal of Medical Bacteriology Eukaryotes Genome (DNA) extraction Identification Prokaryotes Sequence |
| title | A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae |
| title_full | A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae |
| title_fullStr | A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae |
| title_full_unstemmed | A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae |
| title_short | A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae |
| title_sort | rapid and reproducible genomic dna extraction protocol for sequence based identification of archaea bacteria cyanobacteria diatoms fungi and green algae |
| topic | Eukaryotes Genome (DNA) extraction Identification Prokaryotes Sequence |
| url | http://jmb.tums.ac.ir/index.php/jmb/article/view/211 |
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