Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

Christian A. Totoiu; Jessica M. Phillips; Aspen T. Reese; Sudipta Majumdar; Peter R. Girguis; Colin L. Raston; Gregory A. Weiss

doi:10.1371/journal.pone.0225807

Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

Christian A. Totoiu, Jessica M. Phillips, Aspen T. Reese, Sudipta Majumdar, Peter R. Girguis, Colin L. Raston, Gregory A. Weiss

College of Science and Engineering

Research output: Contribution to journal › Article › peer-review

8 Citations (Scopus)

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Abstract

DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species.

Original language	English
Article number	e0225807
Number of pages	13
Journal	PLoS One
Volume	15
Issue number	1
DOIs	https://doi.org/10.1371/journal.pone.0225807
Publication status	Published - 1 Jan 2020

Bibliographical note

Copyright: © 2020 Totoiu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Keywords

formalin-preserved
formalin-fixed
specimens
Vortex
fluidics-mediated
DNA
vortex fluidic device
VFD

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Published versionFinal published version, 1.18 MBLicence: CC BY

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abstract = "DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species.",

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AU - Girguis, Peter R.

AU - Raston, Colin L.

AU - Weiss, Gregory A.

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Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

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