Preprint Short Note Version 2 Preserved in Portico This version is not peer-reviewed

On Sequencing a Protein with Nanopores, tRNAs, and RNAs with Matching Terminal Codons

Version 1 : Received: 22 November 2019 / Approved: 26 November 2019 / Online: 26 November 2019 (11:52:57 CET)
Version 2 : Received: 4 December 2019 / Approved: 4 December 2019 / Online: 4 December 2019 (12:32:26 CET)
Version 3 : Received: 13 January 2020 / Approved: 13 January 2020 / Online: 13 January 2020 (09:43:28 CET)
Version 4 : Received: 17 February 2020 / Approved: 18 February 2020 / Online: 18 February 2020 (11:50:29 CET)

How to cite: Sampath, G. On Sequencing a Protein with Nanopores, tRNAs, and RNAs with Matching Terminal Codons. Preprints 2019, 2019110318 (doi: 10.20944/preprints201911.0318.v2). Sampath, G. On Sequencing a Protein with Nanopores, tRNAs, and RNAs with Matching Terminal Codons. Preprints 2019, 2019110318 (doi: 10.20944/preprints201911.0318.v2).

Abstract

A method for sequencing a protein from a codon sequence is proposed. An unfolded protein molecule is threaded through a nano-sized pore in an electrolytic cell carboxyl end first and held with a voltage such that only the first residue is exposed in the trans chamber of the cell. A tRNA molecule in trans with matching anticodon for the residue binds itself to the latter in the presence of suitable catalysts. It is then cleaved and transferred to an extended electrolytic cell with N pores, 40 ≤ N ≤ 61, in N individual cis chambers and a single trans chamber. Each pore holds an RNA molecule ending in a unique codon that is held exposed in the trans chamber. In the presence of suitable catalysts the anticodon in the transferred tRNA binds with the codon of a matching RNA molecule. By reversing the voltages in the extended cell every RNA molecule except the one to which the transferred tRNA is bound retracts into its cis chamber, this identifies the residue unambiguously. The detected residue in the first cell is cleaved and the process repeated. Unlike in other nanopore-based methods, it suffices to detect the occurrence of a current blockade without having to measure the pore current precisely. A simplified but more time-consuming version that uses only the first cell is also described. In either case no a priori information about the protein is needed so de novo sequencing is possible. A feasibility analysis of the proposed scheme is presented.

Subject Areas

protein sequencing; nanopore; tRNA; RNA; codon; amino acid charging; optical tag

Comments (1)

Comment 1
Received: 4 December 2019
Commenter: G Sampath
Commenter's Conflict of Interests: Author
Comment: Added two paragraphs on the use of tethering + minor edits
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