Oligonucleotide 5' End Modification for AGO2 Affinity
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Solution Overview
Problem
Current oligonucleotides lack a specific method to improve affinity for Argonaute 2 (AGO2) and enhance knockdown activity, which is essential for effective RNA interference.
Innovation Solution
An oligonucleotide with a nucleotide residue or nucleoside residue represented by a specific formula at the 5' end, featuring modifications such as 8-Br-dA, which binds to adjacent residues through an oxygen atom, improving affinity for AGO2 and enhancing knockdown activity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If natural nucleotides are used in oligonucleotides, then the structure is simple and easy to manufacture, but the affinity for AGO2 and knockdown activity are insufficient
Solution Approach 1:
The patent applies parameter changes by modifying the chemical structure of nucleotides at specific positions (5' end and adjacent position) of the oligonucleotide. This involves changing physical and chemical parameters such as adding bromine atoms, modifying sugar moieties, or altering base structures to enhance affinity for AGO2 while maintaining manufacturability through systematic structural modifications
Solution Approach 2:
The patent employs composite materials by creating oligonucleotides with hybrid structures that combine natural nucleotide components with modified unnatural nucleotide components. This composite approach allows the oligonucleotide to maintain recognizability by biological systems while incorporating enhanced binding properties through the modified nucleotides at critical positions
2Productivity
If natural nucleotides are used in oligonucleotides, then the synthesis process is simple, but the knockdown activity against target mRNA is insufficient
Solution Approach 1:
The patent applies local quality by introducing modified nucleotides specifically at local critical positions (5' end and adjacent position) rather than throughout the entire oligonucleotide structure. This localized modification strategy enhances knockdown activity at the binding interface with AGO2 while keeping the rest of the structure simple and easy to synthesize
Solution Approach 2:
The patent changes chemical parameters of nucleotides at specific positions to enhance knockdown activity. This includes modifying properties such as electronegativity, steric bulk, or hydrogen bonding capacity of nucleotides at the 5' end and adjacent position to improve interaction with AGO2 and thereby enhance overall knockdown efficacy
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 modified oligonucleotide demonstrates increased affinity for AGO2 and enhanced knockdown activity, as shown by increased inhibition of target mRNA expression compared to natural nucleotides.
Implementation Method 1
a nucleotide residue or a nucleoside residue represented by formula (I) at the 5' end thereof, wherein the nucleotide residue or the nucleoside residue binds to an adjacent nucleotide residue through the oxygen atom at position 3
Implementation Method 2
the nucleotide residue or the nucleoside residue binds to an adjacent nucleotide residue through the oxygen atom at position 3... the oligonucleotide has a length of 10 to 80 bases... improves affinity for AG02
Data Source
Figure 1
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Figure 3~4
AI summary
The present invention provides an oligonucleotide having improved affinity for AG02, and the like. The oligonucleotide has a nucleotide residue or a nucleoside residue represented by formula (I) {wherein X1 is an oxygen atom or the like, R1 is formula (IIA) (wherein R5A is halogen or the like, and R6A is a hydrogen atom or the like) or formula (IVA) (wherein Y3A is a nitrogen atom or the like, and Y4A is CH or the like), or the like, R2 is a hydrogen atom, hydroxy, halogen, or optionally substituted lower alkoxy, and R3 is a hydrogen atom or the like} at the 5' end thereof, and the nucleotide residue or the nucleoside residue binds to an adjacent nucleotide residue through the oxygen atom at position 3.