DNA damage in preserved specimens and tissue samples: a molecular assessment
Abstract The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing form...
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ftdoajarticles:oai:doaj.org/article:055c8c36549b449d8ccbdbd2db48478f 2023-05-15T13:54:46+02:00 DNA damage in preserved specimens and tissue samples: a molecular assessment Cantin Elizabeth Hanken James Blackburn David C Hajibabaei Mehrdad Zimmermann Juergen Posfai Janos Evans Thomas C 2008-10-01T00:00:00Z https://doi.org/10.1186/1742-9994-5-18 https://doaj.org/article/055c8c36549b449d8ccbdbd2db48478f EN eng BMC http://www.frontiersinzoology.com/content/5/1/18 https://doaj.org/toc/1742-9994 doi:10.1186/1742-9994-5-18 1742-9994 https://doaj.org/article/055c8c36549b449d8ccbdbd2db48478f Frontiers in Zoology, Vol 5, Iss 1, p 18 (2008) Zoology QL1-991 article 2008 ftdoajarticles https://doi.org/10.1186/1742-9994-5-18 2022-12-30T21:38:07Z Abstract The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing formaldehyde-fixed, paraffin-embedded tissue. Efforts to obtain genetic information from these sources are often hampered by an inability to amplify the desired DNA as a consequence of DNA damage. Previous studies have described techniques for improved DNA extraction from such samples or focused on the effect of damaging agents – such as light, oxygen or formaldehyde – on free nucleotides. We present ongoing work to characterize lesions in DNA samples extracted from preserved specimens. The extracted DNA is digested to single nucleosides with a combination of DNase I, Snake Venom Phosphodiesterase, and Antarctic Phosphatase and then analyzed by HPLC-ESI-TOF-MS. We present data for moth specimens that were preserved dried and pinned with no additional preservative and for frog tissue samples that were preserved in either ethanol, or formaldehyde, or fixed in formaldehyde and then preserved in ethanol. These preservation methods represent the most common methods of preserving animal specimens in museum collections. We observe changes in the nucleoside content of these samples over time, especially a loss of deoxyguanosine. We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks. Article in Journal/Newspaper Antarc* Antarctic Directory of Open Access Journals: DOAJ Articles Antarctic Frontiers in Zoology 5 1 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
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Zoology QL1-991 |
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Zoology QL1-991 Cantin Elizabeth Hanken James Blackburn David C Hajibabaei Mehrdad Zimmermann Juergen Posfai Janos Evans Thomas C DNA damage in preserved specimens and tissue samples: a molecular assessment |
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Zoology QL1-991 |
description |
Abstract The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing formaldehyde-fixed, paraffin-embedded tissue. Efforts to obtain genetic information from these sources are often hampered by an inability to amplify the desired DNA as a consequence of DNA damage. Previous studies have described techniques for improved DNA extraction from such samples or focused on the effect of damaging agents – such as light, oxygen or formaldehyde – on free nucleotides. We present ongoing work to characterize lesions in DNA samples extracted from preserved specimens. The extracted DNA is digested to single nucleosides with a combination of DNase I, Snake Venom Phosphodiesterase, and Antarctic Phosphatase and then analyzed by HPLC-ESI-TOF-MS. We present data for moth specimens that were preserved dried and pinned with no additional preservative and for frog tissue samples that were preserved in either ethanol, or formaldehyde, or fixed in formaldehyde and then preserved in ethanol. These preservation methods represent the most common methods of preserving animal specimens in museum collections. We observe changes in the nucleoside content of these samples over time, especially a loss of deoxyguanosine. We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks. |
format |
Article in Journal/Newspaper |
author |
Cantin Elizabeth Hanken James Blackburn David C Hajibabaei Mehrdad Zimmermann Juergen Posfai Janos Evans Thomas C |
author_facet |
Cantin Elizabeth Hanken James Blackburn David C Hajibabaei Mehrdad Zimmermann Juergen Posfai Janos Evans Thomas C |
author_sort |
Cantin Elizabeth |
title |
DNA damage in preserved specimens and tissue samples: a molecular assessment |
title_short |
DNA damage in preserved specimens and tissue samples: a molecular assessment |
title_full |
DNA damage in preserved specimens and tissue samples: a molecular assessment |
title_fullStr |
DNA damage in preserved specimens and tissue samples: a molecular assessment |
title_full_unstemmed |
DNA damage in preserved specimens and tissue samples: a molecular assessment |
title_sort |
dna damage in preserved specimens and tissue samples: a molecular assessment |
publisher |
BMC |
publishDate |
2008 |
url |
https://doi.org/10.1186/1742-9994-5-18 https://doaj.org/article/055c8c36549b449d8ccbdbd2db48478f |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Frontiers in Zoology, Vol 5, Iss 1, p 18 (2008) |
op_relation |
http://www.frontiersinzoology.com/content/5/1/18 https://doaj.org/toc/1742-9994 doi:10.1186/1742-9994-5-18 1742-9994 https://doaj.org/article/055c8c36549b449d8ccbdbd2db48478f |
op_doi |
https://doi.org/10.1186/1742-9994-5-18 |
container_title |
Frontiers in Zoology |
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5 |
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1 |
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1766260870640304128 |