Detection of proteins based on amino acid sequences by multiple aptamers against tripeptides

Wenze Niu, Nan Jiang, Yinghe Hu

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

A number of different ligands have been tested in the course of the development of protein array technology. The most extensively studied example of protein ligands has been based on antibody-antigen interaction. Other examples include protein-protein, protein-nucleic acid, and protein-small molecule interactions. All these ligands can recognize and specifically bind to protein epitopes. In this study, we have developed a novel technology using DNA-based aptamers to detect proteins based on their amino acid sequences. Mouse cathepsin D was used for the proof of principle experiment. Four tripeptides, Leu-Ala-Ser, Asp-Gly-Ile, Gly-Glu-Leu, and Lys-Ala-Ile, were selected based on the published amino acid sequence of mouse cathepsin D. DNA aptamers against the tripeptides were isolated using the systematic evolution of ligands of exponential enrichment method. We have demonstrated that the aptamers specifically interacted with mouse cathepsin D using the structure-switch method. We further performed a proximity-dependent ligation assay to demonstrate that multiple aptamers could specifically detect the protein from cell extracts. In principle, one library containing 8000 aptamers should be enough to detect almost all proteins in the whole proteome in all organisms. This technology could be applied to generate a new generation of protein arrays.

Original languageEnglish (US)
Pages (from-to)126-135
Number of pages10
JournalAnalytical Biochemistry
Volume362
Issue number1
DOIs
StatePublished - Mar 1 2007

Fingerprint

Amino Acid Sequence
Amino Acids
Proteins
Nucleotide Aptamers
Protein Array Analysis
Ligands
Technology
SELEX Aptamer Technique
Proteome
Cell Extracts
Nucleic Acids
Libraries
Ligation
Epitopes
Assays
Antigens
Switches
Antibodies
Molecules
DNA

Keywords

  • Aptamer
  • Protein ligand
  • Proximity-dependent ligation assay
  • SELEX
  • Tripeptide

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

Detection of proteins based on amino acid sequences by multiple aptamers against tripeptides. / Niu, Wenze; Jiang, Nan; Hu, Yinghe.

In: Analytical Biochemistry, Vol. 362, No. 1, 01.03.2007, p. 126-135.

Research output: Contribution to journalArticle

Niu, Wenze ; Jiang, Nan ; Hu, Yinghe. / Detection of proteins based on amino acid sequences by multiple aptamers against tripeptides. In: Analytical Biochemistry. 2007 ; Vol. 362, No. 1. pp. 126-135.
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