Proximity Ligation for Protein Analyses - Multiplexing protein detection on DNA microarrays

This project aims to develop a highly scalable multiplexed analysis-platform for proteins. Specific proteins will be converted into unique nucleic acid sequences, molecular barcodes, by homogenous proximity ligation. The resulting pool of protein complement DNA can then be analyzed by traditional methods of molecular genetics such as qPCR and DNA microarrays for relative or absolute measurements.

The protein to DNA transformation is enabled by oligonucleotide tagged antibodies, so called proximity probes, binding pair wise to specific proteins.

Personnel

Simon Fredriksson
Michael Mindrinos
Hanlee Ji
Albert Koong
Ronald W. Davis

They thereby come in such close proximity enabling an enzymatic ligation reaction forming PCR amplicons.

Impact/Significance

  • Make barcoded DNA microarrays into a universal platform for analysis of DNA, RNA, and now also proteins
  • Enable biomarker discovery in precious biobanked sample collections
  • Increased sensitivity and multiplexing will yield greater insight in biology, more data per sample
  • Bring the features of nucleic acid analysis to the protein world

Accomplishments

  • Proof of concept published (Fredriksson et al, Nat Methods. 2007 Apr;4(4):327-9. Epub 2007 Mar 18)
  • 4 panels of 7-plex cancer biomarker assays developed and validated against a standard ELISA in pancreatic, ovarian and lung cancer samples
  • No loss in performance found upon multiplexing and stable reagent storage
  • DNA sequence and enzymatic activity optimizations completed
  • Antibody-DNA couplings performed with covalent aldehyde/hydrazine chemistry
  • Increased sensitivity,1 fM in 1 µL sample
  • 10 µL qPCR readouts in 384 well format
 
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