Organocatalytic removal of formaldehyde adducts from RNA and DNA bases

Nature Chemistry volume 7, pages752–758(2015)Cite this article

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  • A Corrigendum to this article was published on 20 November 2015

Abstract

Formaldehyde is universally used to fix tissue specimens, where it forms hemiaminal and aminal adducts with biomolecules, hindering the ability to retrieve molecular information. Common methods for removing these adducts involve extended heating, which can cause extensive degradation of nucleic acids, particularly RNA. Here, we show that water-soluble bifunctional catalysts (anthranilates and phosphanilates) speed the reversal of formaldehyde adducts of mononucleotides over standard buffers. Studies with formaldehyde-treated RNA oligonucleotides show that the catalysts enhance adduct removal, restoring unmodified RNA at 37 °C even when extensively modified, while avoiding the high temperatures that promote RNA degradation. Experiments with formalin-fixed, paraffin-embedded cell samples show that the catalysis is compatible with common RNA extraction protocols, with detectable RNA yields increased by 1.5–2.4-fold using a catalyst under optimized conditions and by 7–25-fold compared with a commercial kit. Such catalytic strategies show promise for general use in reversing formaldehyde adducts in clinical specimens.

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Figure 1: Formaldehyde adducts and catalysts investigated in this study.
Figure 2: Relative rates of formaldehyde adduct reversal.
Figure 3: Relative yields of adduct reversal from nucleotides after 1 h with catalyst 3 and with analogues with functional groups omitted (structures shown).
Figure 4: Assessing formaldehyde adducts on an RNA strand by mass spectrometry.
Figure 5: Improvement in reversal of RNA formaldehyde adducts after low-temperature incubation in the presence of catalyst 3.
Figure 6: Enhancement in recovery of RNAs from FFPE cell specimens using catalyst 3 (20 mM) as compared with different incubation and isolation conditions.

Change history

  • 27 October 2015

    In the original version of this Article a contributing author, Florian Scherer, was mistakenly omitted. Florian Scherer is in the Divisions of Oncology and of Hematology, Stanford School of Medicine, Stanford, California 94305, USA. This mistake has been corrected in all online versions of the Article.

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Acknowledgements

The authors acknowledge support from the US National Institutes of Health (GM068122 and GM110050, to E.T.K.) and the Lymphoma Research Foundation (LRF#245480, to A.A.A.). E.M.H. acknowledges funding from a National Science Foundation (NSF) graduate fellowship (DGE-1147470) and L.B. and C.R. acknowledge support from the Swiss National Science Foundation. D.S.H. has received funding from the Stanford ChEM-H Institute and T.E. acknowledges support from the Deutscher Akademischer Austauschdienst. The authors thank D. Winant for assistance with MALDI analysis of RNAs and R. Krishnan and F. Scherer for assistance with the cell samples and RNA isolation.

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Affiliations

  1. Department of Chemistry, Stanford University, Stanford, 94305, California, USA
    • Saswata Karmakar
    • , Emily M. Harcourt
    • , David S. Hewings
    • , Thomas Ehrenschwender
    • , Luzi J. Barandun
    • , Caroline Roost
    •  & Eric T. Kool
  2. Divisions of Oncology and of Hematology, Stanford School of Medicine, Stanford, 94305, California, USA
    • Florian Scherer
    • , Alexander F. Lovejoy
    • , David M. Kurtz
    •  & Ash A. Alizadeh
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Contributions

E.T.K. designed the project and A.A.A., A.F.L. and D.M.K. designed the cell studies. S.K., E.M.H. and D.S.H. carried out the experiments, with early exploratory studies carried out by T.E. Catalyst 3 was synthesized by S.K. and L.J.B. and RNA was prepared by C.R. The manuscript was written by E.T.K. with input from E.M.H., S.K., A.A.A. and D.S.H.

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Correspondence to Eric T. Kool.

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The authors declare no competing financial interests.

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Karmakar, S., Harcourt, E., Hewings, D. et al. Organocatalytic removal of formaldehyde adducts from RNA and DNA bases. Nature Chem 7, 752–758 (2015). https://doi.org/10.1038/nchem.2307

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