Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore

Laura Restrepo-Pérez, Gang Huang, Peggy R. Bohländer, Nathalie Worp, Rienk Eelkema, Giovanni Maglia, Chirlmin Joo, Cees Dekker

Research output: Contribution to journalArticlepeer-review

71 Scopus citations


While DNA sequencing is now amply available, fast, and inexpensive, protein sequencing remains a tremendous challenge. Nanopores may allow for developing a protein sequencer with single-molecule capabilities. As identification of 20 different amino acids currently presents an unsurmountable challenge, fingerprinting schemes are pursued, in which only a subset of amino acids is labeled and detected. This requires modification of amino acids with chemical structures that generate a distinct nanopore ionic current signal. Here, we use a model peptide and the fragaceatoxin C nanopore to characterize six potential tags for a fingerprinting approach using nanopores. We find that labeled and unlabeled proteins can be clearly distinguished and that sensitive detection is obtained for labels with a spectrum of different physicochemical properties such as mass (427-1275 Da), geometry, charge, and hydrophobicity. Additionally, information about the position of the label along the peptide chain can be obtained from individual current-blockade event features. The results represent an important advance toward the development of a single-molecule protein-fingerprinting device with nanopores.

Original languageEnglish
Pages (from-to)13668-13676
Number of pages9
JournalACS Nano
Issue number12
StatePublished - 24 Dec 2019

Bibliographical note

Publisher Copyright:
© 2019 American Chemical Society.


  • amino acid labeling
  • biological nanopores
  • nanopore
  • protein analysis
  • protein fingerprinting
  • single-molecule protein sequencing


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