ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes

Area of Science:

• Biotechnology
• Molecular Biology
• Genomics

Background:

• Accurate and high-throughput protein sequencing is crucial for understanding biological functions and disease mechanisms.
• Current methods face limitations in throughput, accuracy, or cost, necessitating novel approaches.

Purpose of the Study:

• To demonstrate early progress in developing a high-throughput, single-molecule protein sequencing technology.
• To establish a method for identifying terminal amino acids of peptides using barcoded DNA aptamers.

Main Methods:

• Utilizing barcoded DNA aptamers (binders) to recognize terminal amino acids of peptides (targets) tethered on a next-generation sequencing chip.
• Employing DNA binders to deposit unique, amino acid-identifying barcodes on the chip.
• Conducting sequential binding cycles to assemble a chain of DNA barcodes for peptide sequence identification.

Main Results:

• Demonstrated successful target identification using both DNA-DNA and Peptide-Protein binding pairs.
• Showcased the assembly and sequencing of DNA barcodes over six consecutive binding cycles for DNA-DNA interactions.
• Computational simulations predict significant human proteome coverage with a small set of semi-selective DNA binders.

Conclusions:

• Early progress shows promise for a high-throughput, single-molecule protein sequencing technology.
• A binder discovery pipeline is introduced, potentially merging with the chip assay to create the ProtSeq technology.
• This technology aims to revolutionize protein sequencing by enabling rapid and accurate analysis of peptide sequences.