RNA extraction from self-assembling peptide hydrogels to allow qPCR analysis of encapsulated cells

Kyle Burgess, Victoria Louise Workman, Mohamed Elsawy, Aline Miller, Delvac Oceandy, Alberto Saiani

Research output: Contribution to journalArticlepeer-review


Self-assembling peptide hydrogels offer a novel 3-dimensional platform for many applications in cell culture and tissue engineering but are not compatible with current methods of RNA isolation; owing to interactions between RNA and the biomaterial. This study investigates the use of two techniques based on two different basic extraction principles: solution-based extraction and direct solid-state binding of RNA respectively, to extract RNA from cells encapsulated in four β-sheet forming self-assembling peptide hydrogels with varying net positive charge. RNA-peptide fibril interactions, rather than RNA-peptide molecular complexing, were found to interfere with the extraction process resulting in low yields. A column-based approach relying on RNA-specific binding was shown to be more suited to extracting RNA with higher purity from these peptide hydrogels owing to its reliance on strong specific RNA binding interactions which compete directly with RNA-peptide fibril interactions. In order to reduce the amount of fibrils present and improve RNA yields a broad spectrum enzyme solution—pronase—was used to partially digest the hydrogels before RNA extraction. This pre-treatment was shown to significantly increase the yield of RNA extracted, allowing downstream RT-qPCR to be performed.

Original languageEnglish
Article numbere0197517
JournalPLoS ONE
Issue number6
Publication statusPublished - 4 Jun 2018


  • self-assembling peptide hydrogels
  • RNA extraction
  • Enzymatic degradation

Research Beacons, Institutes and Platforms

  • Manchester Institute of Biotechnology
  • Manchester Institute for Collaborative Research on Ageing


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