Improving Yields in Multi-analyte Extractions by Utilizing Post-homogenized Tissue Debris

J Histochem Cytochem. 2023 May;71(5):273-288. doi: 10.1369/00221554231172823. Epub 2023 Apr 29.


In multi-analyte extractions, tissue is typically homogenized in a lysis buffer, and then DNA, RNA, and protein are purified from the supernatant. However, yields are typically lower than in dedicated, single-analyte extractions. In a two-part experiment, we assessed whether yields could be improved by revisiting the normally discarded, post-homogenized tissue debris. We initially performed additional homogenizations, each followed by a simultaneous extraction. These yielded no additional RNA, 13% additional DNA (which became progressively more degraded), and 161.7% additional protein (which changed in proteome when analyzed using SDS-PAGE). We then digested post-homogenized tissue debris from a simultaneous extraction using proteinase K and extracted DNA using silica spin columns or alcohol precipitation. An average additional DNA yield of 27.1% (silica spin columns) or 203.9% (alcohol precipitation) was obtained with/without compromising DNA integrity (assessment by long-range PCR, DNA Integrity Numbers, and size at peak fluorescence of electropherogram). Validation using a cohort of 65 tissue blocks returned an average additional DNA yield of 31.6% (silica columns) and 54.8% (alcohol precipitation). Users can therefore refreeze the homogenized remnants of tissue blocks rather than disposing of them and then perform additional DNA extractions if yields in the initial multi-analyte extractions were low.

Keywords: AllPrep; Puregene; QIAamp; biospecimen science; homogenization; optimization; simultaneous.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA*
  • Endopeptidase K
  • Humans
  • Polymerase Chain Reaction
  • Proteins*
  • RNA


  • DNA
  • Proteins
  • Endopeptidase K
  • RNA