DNA sequencing using nanopores and kinetic proofreading
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MINI REVIEW DNA sequencing using nanopores and kinetic proofreading Xinsheng Sean Ling* Department of Physics, Brown University, Providence, RI 02912, USA * Correspondence: [email protected] Received December 5, 2019; Revised January 16, 2020; Accepted January 29, 2020 We discuss the feasibility of using a nanopore sandwich device to implement the principle of kinetic proofreading to discriminate incorrect hybridizing oligonucleotides on a target DNA or RNA. We propose a method of sequencing DNA or RNA using this approach. The design parameters for such a DNA sequencer are estimated from the HopfieldNinio theory of kinetic proofreading and Schrödinger’s first-passage-time distribution function.
Keywords: DNA sequencing; nanopore sequencing; biosensing using kinetics Author summary: A novel device concept is proposed for DNA sequencing without employing polymerases that were essential in Sanger and other DNA sequencing methods. The idea is to combine the nanoscale sensitivity of solid-state nanopores and the kinetics of oligonucleotides. The device consists of two nanopores in close proximity such that correct hybridization probes stay on the DNA during the passage, while the incorrect ones will be melted off during the transit. The proposed device contains two essential functions of a DNA polymerase, suppression of Brownian motion and discrimination based on the kinetics of the correct and incorrect Watson-Crick pairs.
INTRODUCTION DNA sequencing, namely the determination of the sequential arrangement of the four basic nucleotides on a DNA molecule, involves at least two fundamental challenges. The first challenge is to determine the identity of the nucleic acids, i.e., adenine (A), guanine (G), thymine (T), and cytosine (C). The second is to accurately determine the relative positions between the nucleotides. The challenges are immense due to the minute differences in their chemical composition and physical scales. There are two hydrogen bonds between A-T pairing, and three between G-C pairs. The nearest neighbor nucleic acids are spaced at 0.34 nm in the double helix compact form [1], at 0.7 nm when it is single stranded [2,3]. To date, the most accurate method of sequencing a DNA molecule was developed by Sanger and coworkers, known as the Sanger method [4,5], or the method of 3′ dideoxy chain termination. In the Sanger method, before the start of a DNA replication polymerase chain reaction (PCR), dideoxyribonucleoside triphosphates
(ddNTPs) with proper coding (using dye or other labels) are mixed with the four deoxyribonucleoside triphosphates (dNTPs). When a ddNTP is incorporated by the DNA polymerase into the growing strand of DNA, the reaction is terminated due to the lack of an OH group at the 3′ position of the ddNTP which is required for forming a phosphodiester (covalent) bond with the next dNTP [4]. These terminated strands of DNA are melted off from the template strand and separated by electric field in a gel and then compared with the ddNTP coding [5]. The order by which the termination occurs pr
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