Modified Oligonucleotides for Slower Nanopore Base Reading
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Solution Overview
Problem
Nanopore sequencers struggle with accurately sequencing polynucleotides due to fast translocation speeds, leading to deletion errors and skipped bases, as they read multiple bases at once rather than individually, complicating deconvolution and exceeding the rate compatible with current electronics and detectors.
Innovation Solution
Modified oligonucleotides with specific modifications in the phosphate backbone, nucleobase, or sugar are introduced to impede translocation through nanopores, increasing non-covalent interactions, bulk size, charge density, and steric hinderance, thereby controlling the speed of polynucleotide passage.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If nanopore sequencing is performed with natural polynucleotides, then the sequencing process can proceed, but the translocation speed is too fast causing deletion errors and skipped bases
Solution Approach 1:
The patent modifies the physical and chemical parameters of the polynucleotide by incorporating modified nucleotides with altered sugar moieties, phosphate backbone structures, or nucleobase modifications. These parameter changes increase steric hindrance and non-covalent interactions with the nanopore, thereby reducing translocation speed to a range compatible with accurate base-by-base detection by the electronics and detector system.
2Productivity
If multiple bases pass through the nanopore quickly, then the sequencing process maintains speed, but the detection system cannot resolve individual bases
Solution Approach 1:
By changing the translocation speed parameter through modified nucleotide structures, the patent enables the detection system to resolve individual bases in time. The modified nucleotides create sufficient interaction with the nanopore to slow passage to a rate where the detector can accurately measure the electrical current changes corresponding to each base, achieving both speed and precision.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The modifications slow down the translocation of polynucleotides, improving sequencing accuracy by allowing for individual base reading, enhancing the compatibility with detection systems and reducing errors.
Implementation Method 1
increase non-covalent interactions with an interior of the nanopore
Implementation Method 2
increase the bulk size of the oligonucleotide, increase the steric hinderance of the oligonucleotide
Implementation Method 3
alter the charge density of the oligonucleotide
Implementation Method 4
which can provide a path for an ionic electrical current. For example, as the polynucleotide traverses through the nanopore, it influences the electrical current through the nanopore
Data Source
AI summary
Disclosed herein is a modified oligonucleotide, the modified oligonucleotide comprises one or more modifications in at least one of a phosphate backbone, a nucleobase, or a sugar. The one or more modifications impede translocation through a nanopore by increasing non-covalent interactions with the interior of the nanopore or the lipid bilayer that supports the nanopore, increasing the bulk size or the steric hinderance of oligonucleotide, or alter the charge density of the oligonucleotide.