L-nucleic acid aptamer screening via mirror-image selection
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Solution Overview
Problem
Current methods for selecting L-nucleic acid aptamers are limited by the need for chemically synthesizing mirror-image target molecules, which is problematic for large proteins with complex post-translational modifications and low folding efficiencies.
Innovation Solution
A direct 'mirror-image selection' scheme is developed, where L-nucleic acid aptamers are screened by contacting them with the target molecule, amplifying bound aptamers, and isolating them using electrophoresis-based methods, bypassing the need for mirror-image target synthesis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If the selection-reflection method is used to select L-nucleic acid aptamers, then the aptamers can bind to target molecules, but the method requires chemically synthesizing mirror-image target molecules which is problematic for large proteins with complex post-translational modifications and low folding efficiencies
Solution Approach 1:
Instead of synthesizing mirror-image target molecules and selecting D-aptamers then converting to L-aptamers (selection-reflection), the patent inverts the approach by directly synthesizing L-nucleic acid libraries and selecting L-aptamers against native target molecules. This eliminates the need for mirror-image target synthesis while achieving the same binding affinity results.
Solution Approach 2:
The patent extracts and eliminates the problematic step of mirror-image target molecule synthesis from the selection process. By directly using native target molecules in the selection process, the method removes the bottleneck that limited applications to only small molecules and short peptides.
2Ease of manufacture
If natural unmodified aptamers are used, then they can be easily produced, but they are vulnerable to degradation by nucleases ubiquitous in vitro and in vivo
Solution Approach 1:
The patent uses L-nucleic acids which are chirally inverted from natural D-nucleic acids. This creates a composite material that maintains the structural and binding properties of natural aptamers while being resistant to nuclease degradation, as nucleases evolved to recognize and degrade only natural D-nucleic acids.
3Reliability
If chemical modification and xeno nucleic acid designs are used to enhance aptamer stability, then nuclease degradation is reduced, but specialized nucleotides are required for discovery and production
Solution Approach 1:
The patent changes the chiral parameter of nucleic acids from natural D-form to L-form. This single parameter change fundamentally alters the stereochemistry to achieve nuclease resistance while maintaining all other natural nucleotide components, eliminating the need for specialized modified nucleotides or complex xeno nucleic acid systems.
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
This approach enables the discovery of high-affinity L-DNA aptamers targeting large proteins, achieving biostability and practical applications in diagnostics and therapeutics, while resisting nuclease degradation.
Implementation Method 1
contacting the plurality of L-nucleic acid aptamers with the target molecule under conditions that selectively capture target-bound L-nucleic acid aptamers
Implementation Method 2
isolating amplified double stranded L-nucleic acid oligonucleotides using an electrophoresis based method
Data Source
AI summary
A method for screening L-nucleic acid aptamers for binding to a target molecule is disclosed. The method comprises:(a) contacting the plurality of L-nucleic acid aptamers with the target molecule under conditions that selectively capture target-bound L-nucleic acid aptamers from the plurality of L-nucleic acid aptamers;(b) amplifying L-nucleic acid aptamers of the target-bound L-nucleic acid aptamers to generate amplified, double-stranded L-nucleic acid oligonucleotides; and(c) isolating amplified double stranded L-nucleic acid oligonucleotides using an electrophoresis based method, thereby screening the plurality of L-nucleic acid aptamers.