Aptamer Production Using Artificial Base Pairs
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Solution Overview
Problem
Conventional methods for producing nucleic acid aptamers, particularly DNA aptamers, face limitations due to reduced specificity and binding activity, largely attributed to the use of modified natural bases which can lead to increased cytotoxicity and reduced selectivity, limiting their therapeutic applications.
Innovation Solution
Incorporation of non-natural nucleotides with artificial bases into nucleic acid molecules, allowing for higher target substance-binding ability, combined with a novel sequencing method to determine individual nucleotide sequences, enabling the development of nucleic acid aptamers with enhanced specificity and binding activity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If modified natural bases are introduced to enhance production efficiency, then aptamer production efficiency is improved, but selectivity and cytotoxicity are reduced
Solution Approach 1:
The patent changes the chemical parameters of nucleic acid bases by introducing artificial bases with distinct chemical structures (e.g., Ds and Pa bases with different functional groups and ring structures). This allows for enhanced production efficiency while maintaining selectivity through the unique chemical properties of each artificial base, avoiding the cytotoxicity issues associated with modified natural bases.
Solution Approach 2:
The patent creates composite nucleic acid systems by combining artificial bases (Ds and Pa) with natural bases in controlled compositions. This composite approach enables high production efficiency through the stability of artificial base pairs while maintaining selectivity through the specific recognition capabilities of the artificial base structures, thereby resolving the contradiction between productivity and reliability.
2Productivity
If modified natural bases are used to increase production efficiency, then aptamer production efficiency is improved, but cytotoxicity increases
Solution Approach 1:
The patent changes the chemical parameters by using artificial bases with stable, non-toxic structures (Ds and Pa bases). These artificial bases form stable base pairs that enable efficient production without the cytotoxic effects associated with modified natural bases, as the artificial bases are designed with inherent stability and biocompatibility.
Solution Approach 2:
The patent employs artificial bases that can be efficiently incorporated and then selectively removed or replaced, analogous to using disposable components. The artificial bases serve their purpose in enhancing production efficiency during the selection process, and their temporary presence does not result in long-term cytotoxicity, thereby resolving the contradiction between productivity and harmful factors.
3Device complexity
If only 4 natural bases are used, then nucleic acid structure simplicity is maintained, but aptamer performance and variation are limited
Solution Approach 1:
The patent creates a composite base system by integrating artificial bases (Ds and Pa) with the four natural bases. This composite system maintains the overall simplicity of the nucleic acid structure while introducing additional chemical diversity through the artificial bases, thereby enhancing aptamer performance and variation without excessive complexity.
Solution Approach 2:
The artificial bases in the patent serve multiple functions: they maintain base pairing simplicity similar to natural bases (enabling easy replication and transcription), while simultaneously providing enhanced chemical diversity for improved aptamer performance. This multi-functionality allows the system to maintain structural simplicity while achieving superior aptamer capabilities.
Data Source
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AI summary
An object of the present invention is to develop and provide a method for efficiently producing a nucleic acid aptamer, particularly, a DNA aptamer, having higher specificity and binding activity against a target substance than those of nucleic acid aptamers obtained by conventional methods. The present invention provides a transcribable or replicable nucleic acid aptamer comprising a natural nucleotide and a non-natural nucleotide having an artificial base-pairable artificial base. The present invention also provides a method for sequencing a non-natural nucleotide-containing single-stranded nucleic acid molecule selected from a single-stranded nucleic acid library.