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Published on: March 26, 2011
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Hot alkaline lysis gDNA extraction from formalin-fixed archival tissues
Erin E Hahn1, Marina Alexander1, Jiri Stiller2
1National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia.
Plos One
|January 2, 2024
Summary
Formalin-fixed specimens can now yield valuable genomic data. This new protocol enables DNA extraction from archival tissues, unlocking insights into evolutionary history and adaptation.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Formalin fixation historically hinders genomic analysis of archival specimens.
- Millions of historical samples are potential molecular assets with new methods.
Purpose of the Study:
- To present a protocol for assessing and extracting DNA from archival specimens for sequencing.
- To enable broader genomic and phylogenetic analyses of historical collections.
Main Methods:
- Non-destructive assessment of specimen degradation and preservation media.
- Hot alkaline lysis (0.1M NaOH, 1% SDS, pH 13) for tissue lysis and de-crosslinking.
- Phenol:chloroform extraction coupled with SPRI bead cleanup for DNA recovery.
Main Results:
- Yields 1-2 μg DNA per 50 mg tissue from well-preserved samples.
- Produces DNA fragments of 50-150 bp, suitable for mitochondrial and partial nuclear genome reconstruction.
- Achieves up to 25X nuclear genome coverage and enables read mapping.
Conclusions:
- The protocol makes archival specimens viable for genomic studies.
- Facilitates deeper understanding of evolutionary trends and environmental adaptation.
- Opens avenues for large-scale genetic and phylogenetic analyses of historical samples.
