Tm-Increasing Nucleotides in Stem Loop Oligonucleotides
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Solution Overview
Problem
Existing nucleic acid inhibitor molecules face challenges in balancing stability and potency, with chemically modified nucleotides enhancing stability but potentially reducing gene target knockdown potency and duration.
Innovation Solution
Double-stranded nucleic acid inhibitor molecules with a stem loop structure containing Tm-increasing nucleotides in the stem duplex, particularly bicyclic nucleotides, enhance stability and duration of activity while maintaining potency, even when the stem duplex is shortened.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Stability of the object's composition
If chemically modified nucleotides are introduced to stabilize against nucleases and improve pharmacokinetic properties, then stability is improved, but gene target knockdown potency and duration may be reduced
Solution Approach 1:
The patent applies local quality by introducing Tm-increasing nucleotides specifically at selected positions within the sense strand (particularly at positions 1-8 from the 5' end) rather than uniformly modifying the entire oligonucleotide. This localized modification strategy enhances thermal stability and nuclease resistance at critical regions while preserving the overall structure and function necessary for potent gene knockdown.
Solution Approach 2:
The patent employs parameter changes by systematically varying the type, position, and number of Tm-increasing nucleotides to optimize the balance between stability and potency. By adjusting these parameters, the invention achieves enhanced thermal stability and pharmacokinetic properties while maintaining or improving gene target knockdown efficacy through careful selection of modification patterns.
2Productivity
If the sense strand is shortened to improve dosing efficiency, then dosing efficiency is improved, but stability may be reduced
Solution Approach 1:
The patent applies parameter changes by incorporating Tm-increasing nucleotides to compensate for the reduced length of the sense strand. These modifications increase the melting temperature and enhance thermal stability, allowing the use of shorter sense strands (e.g., 19-27 nucleotides) that improve dosing efficiency while maintaining adequate stability through the stabilizing effect of the modified nucleotides.
Solution Approach 2:
The patent uses composite materials by combining standard nucleotides with Tm-increasing modified nucleotides within the same oligonucleotide sequence. This composite structure allows the molecule to benefit from both the functional properties of natural nucleotides and the enhanced stability properties of modified nucleotides, achieving a balance between length reduction for dosing efficiency and stability maintenance.
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 incorporation of Tm-increasing nucleotides into the stem loop structure of nucleic acid inhibitor molecules improves their stability and duration of activity in vivo without reducing potency, allowing for shorter sense strands and more efficient dosing.
Implementation Method 1
the stem portion of the stem loop structure contains at least one Tm-increasing nucleotide
Data Source
AI summary
Provided herein are double-stranded nucleic acid inhibitor molecules having a sense strand with a stem loop structure and an antisense strand, where the stem portion of the stem loop structure contains one or more Tm-increasing nucleotides. Also provided are methods and compositions for reducing target gene expression and methods and compositions for treating a disease of interest.