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...
Published in: | Frontiers in Zoology |
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Springer Science and Business Media LLC
2008
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Online Access: | http://dx.doi.org/10.1186/1742-9994-5-18 http://link.springer.com/content/pdf/10.1186/1742-9994-5-18.pdf http://link.springer.com/article/10.1186/1742-9994-5-18/fulltext.html https://link.springer.com/content/pdf/10.1186/1742-9994-5-18.pdf |
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crspringernat:10.1186/1742-9994-5-18 2023-05-15T14:08:02+02:00 DNA damage in preserved specimens and tissue samples: a molecular assessment Zimmermann, Juergen Hajibabaei, Mehrdad Blackburn, David C Hanken, James Cantin, Elizabeth Posfai, Janos Evans, Thomas C 2008 http://dx.doi.org/10.1186/1742-9994-5-18 http://link.springer.com/content/pdf/10.1186/1742-9994-5-18.pdf http://link.springer.com/article/10.1186/1742-9994-5-18/fulltext.html https://link.springer.com/content/pdf/10.1186/1742-9994-5-18.pdf en eng Springer Science and Business Media LLC http://creativecommons.org/licenses/by/2.0 CC-BY Frontiers in Zoology volume 5, issue 1 ISSN 1742-9994 Animal Science and Zoology Ecology, Evolution, Behavior and Systematics journal-article 2008 crspringernat https://doi.org/10.1186/1742-9994-5-18 2022-01-04T13:11:49Z 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 Springer Nature (via Crossref) Antarctic Frontiers in Zoology 5 1 |
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Springer Nature (via Crossref) |
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English |
topic |
Animal Science and Zoology Ecology, Evolution, Behavior and Systematics |
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Animal Science and Zoology Ecology, Evolution, Behavior and Systematics Zimmermann, Juergen Hajibabaei, Mehrdad Blackburn, David C Hanken, James Cantin, Elizabeth Posfai, Janos Evans, Thomas C DNA damage in preserved specimens and tissue samples: a molecular assessment |
topic_facet |
Animal Science and Zoology Ecology, Evolution, Behavior and Systematics |
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 |
Zimmermann, Juergen Hajibabaei, Mehrdad Blackburn, David C Hanken, James Cantin, Elizabeth Posfai, Janos Evans, Thomas C |
author_facet |
Zimmermann, Juergen Hajibabaei, Mehrdad Blackburn, David C Hanken, James Cantin, Elizabeth Posfai, Janos Evans, Thomas C |
author_sort |
Zimmermann, Juergen |
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 |
Springer Science and Business Media LLC |
publishDate |
2008 |
url |
http://dx.doi.org/10.1186/1742-9994-5-18 http://link.springer.com/content/pdf/10.1186/1742-9994-5-18.pdf http://link.springer.com/article/10.1186/1742-9994-5-18/fulltext.html https://link.springer.com/content/pdf/10.1186/1742-9994-5-18.pdf |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Frontiers in Zoology volume 5, issue 1 ISSN 1742-9994 |
op_rights |
http://creativecommons.org/licenses/by/2.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/1742-9994-5-18 |
container_title |
Frontiers in Zoology |
container_volume |
5 |
container_issue |
1 |
_version_ |
1766280055721295872 |