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

Research output: Contribution to journalArticle

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 languageEnglish
Article numbere0225807
Number of pages13
JournalPLoS One
Volume15
Issue number1
DOIs
Publication statusPublished - 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

Fingerprint Dive into the research topics of 'Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens'. Together they form a unique fingerprint.

  • Cite this

    Totoiu, C. A., Phillips, J. M., Reese, A. T., Majumdar, S., Girguis, P. R., Raston, C. L., & Weiss, G. A. (2020). Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens. PLoS One, 15(1), [e0225807]. https://doi.org/10.1371/journal.pone.0225807