DNA Damage in Preserved Specimens and Tissue Samples: A Molecular Assessment
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-...
Published in: | Frontiers in Zoology |
---|---|
Main Authors: | , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BioMed Central
2008
|
Subjects: | |
Online Access: | http://nrs.harvard.edu/urn-3:HUL.InstRepos:4458173 https://doi.org/10.1186/1742-9994-5-18 |
id |
ftharvardudash:oai:dash.harvard.edu:1/4458173 |
---|---|
record_format |
openpolar |
spelling |
ftharvardudash:oai:dash.harvard.edu:1/4458173 2023-05-15T13:57:56+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., Jr. 2008 application/pdf http://nrs.harvard.edu/urn-3:HUL.InstRepos:4458173 https://doi.org/10.1186/1742-9994-5-18 en_US eng BioMed Central doi:10.1186/1742-9994-5-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579423/pdf/ Frontiers in Zoology Zimmermann, Juergen, Mehrdad Hajibabaei, David C. Blackburn, James Hanken, Elizabeth Cantin, Janos Posfai, and Thomas C. Evans Jr. 2008. DNA damage in preserved specimens and tissue samples: a molecular assessment. Frontiers in Zoology 5:18. 1742-9994 http://nrs.harvard.edu/urn-3:HUL.InstRepos:4458173 Journal Article 2008 ftharvardudash https://doi.org/10.1186/1742-9994-5-18 2022-04-04T12:42:27Z 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. Organismic and Evolutionary Biology Version of Record Article in Journal/Newspaper Antarc* Antarctic Harvard University: DASH - Digital Access to Scholarship at Harvard Antarctic Frontiers in Zoology 5 1 |
institution |
Open Polar |
collection |
Harvard University: DASH - Digital Access to Scholarship at Harvard |
op_collection_id |
ftharvardudash |
language |
English |
description |
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. Organismic and Evolutionary Biology Version of Record |
format |
Article in Journal/Newspaper |
author |
Zimmermann, Juergen Hajibabaei, Mehrdad Blackburn, David C Hanken, James Cantin, Elizabeth Posfai, Janos Evans, Thomas C., Jr. |
spellingShingle |
Zimmermann, Juergen Hajibabaei, Mehrdad Blackburn, David C Hanken, James Cantin, Elizabeth Posfai, Janos Evans, Thomas C., Jr. DNA Damage in Preserved Specimens and Tissue Samples: A Molecular Assessment |
author_facet |
Zimmermann, Juergen Hajibabaei, Mehrdad Blackburn, David C Hanken, James Cantin, Elizabeth Posfai, Janos Evans, Thomas C., Jr. |
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 |
BioMed Central |
publishDate |
2008 |
url |
http://nrs.harvard.edu/urn-3:HUL.InstRepos:4458173 https://doi.org/10.1186/1742-9994-5-18 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
doi:10.1186/1742-9994-5-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579423/pdf/ Frontiers in Zoology Zimmermann, Juergen, Mehrdad Hajibabaei, David C. Blackburn, James Hanken, Elizabeth Cantin, Janos Posfai, and Thomas C. Evans Jr. 2008. DNA damage in preserved specimens and tissue samples: a molecular assessment. Frontiers in Zoology 5:18. 1742-9994 http://nrs.harvard.edu/urn-3:HUL.InstRepos:4458173 |
op_doi |
https://doi.org/10.1186/1742-9994-5-18 |
container_title |
Frontiers in Zoology |
container_volume |
5 |
container_issue |
1 |
_version_ |
1766265868734431232 |