Duplex Oligonucleotides Mismatched Sense Strands
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Solution Overview
Problem
Chemical modifications added to the sense strand of duplex oligonucleotides, such as 2′-O-methyl modifications, can enhance stability but also have negative effects on their functionality, particularly by acting as miRNA inhibitors, limiting the function of miRNA mimics.
Innovation Solution
Incorporating specific mismatches at distinct positions within the duplex oligonucleotide, such as between nucleotides 1, 7, and 14, minimizes these negative effects by preventing the sense strand from inhibiting the action of the antisense strand, thus maintaining or enhancing the functionality of the miRNA mimics.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Stability of the object's composition
If chemical modifications such as 2′-O-methyl groups are added to the sense strand to enhance stability, then nuclease resistance is improved, but the sense strand begins to act as a miRNA inhibitor, reducing the functionality of the duplex oligonucleotide
Solution Approach 1:
The patent removes the problematic sense strand from the duplex structure by introducing mismatches that prevent it from functioning, while preserving the stable modified sense strand's resistance to nucleases. The mismatches effectively extract the harmful inhibitory function while retaining the beneficial stability.
Solution Approach 2:
The patent converts the harmful effect of the modified sense strand acting as a miRNA inhibitor into a beneficial design feature. By strategically placing mismatches, the sense strand's modified nucleotides provide nuclease resistance while the mismatches prevent inhibitory activity, turning a potential harm into a controlled feature.
2Duration of action of stationary object
If chemical modifications are added to enhance stability and binding affinity, then the oligonucleotide becomes more resistant to degradation, but the overall functionality is reduced due to sense strand inhibition
Solution Approach 1:
The patent applies local quality by modifying only specific nucleotides in the sense strand (40-90% modification) rather than the entire strand, and by placing mismatches at specific positions. This localized approach maintains stability where modifications are present while preserving functionality in regions where mismatches prevent inhibitory activity.
Solution Approach 2:
The patent changes the structural parameters of the duplex by introducing mismatches at specific positions (nucleotide 1, 7, or 14 of the antisense strand). This parameter change disrupts the sense strand's ability to inhibit miRNA function while maintaining the stabilizing effect of the chemical modifications on the overall structure.
3Reliability
If the sense strand is highly stable due to chemical modifications, then it resists degradation, but it competes with the antisense strand for RISC loading, reducing gene silencing activity
Solution Approach 1:
The patent applies preliminary anti-action by introducing mismatches in advance that specifically prevent the stable modified sense strand from loading into RISC and inhibiting miRNA function. The mismatches are positioned to block sense strand activity before it can interfere with the antisense strand's gene silencing function.
Data Source
AI summary
Disclosed are methods of enhancing functionality of duplex oligonucleotides and compositions made by the methods. The duplex oligonucleotides include siRNAs, miRNA mimics, and piRNA mimics which contain modified nucleotides and mismatches between the two strands of the molecule at specific nucleotide positions.