Staple Nucleic Acid Quadruplex Formation for Broader RNA Targeting
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing Staple nucleic acids require four guanine repeat sequences on the target nucleic acid to form a guanine quadruplex structure, limiting their applicability, and there are challenges with off-target effects and enzymatic recognition issues in gene expression suppression techniques.
Innovation Solution
Development of a second generation-type Staple nucleic acid that supplies guanine repeat sequences via an oligonucleotide, allowing formation of a guanine quadruplex structure with a total of four guanine repeat sequences, comprising guanine repeat sequences on both the target nucleic acid and the oligonucleotide.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional Staple nucleic acids are used to form guanine quadruplex structures, then stable structure formation is achieved, but the target nucleic acid must contain four guanine repeat sequences which limits applicability
Solution Approach 1:
The invention divides the guanine repeat sequence requirement into two parts: the Staple nucleic acid provides one guanine repeat sequence, while the target nucleic acid provides the remaining three. This segmentation allows the system to work with a broader range of target sequences that do not naturally contain four guanine repeats, thereby improving versatility while maintaining structure formation stability.
Solution Approach 2:
The Staple nucleic acid acts as an intermediary that supplies the missing guanine repeat sequence to enable guanine quadruplex formation. By providing this critical component, the Staple nucleic acid mediates between the requirement for stable quadruplex structure and the diversity of available target sequences, resolving the contradiction between reliability and adaptability.
2Reliability
If siRNA is used for gene expression suppression, then protein translation is inhibited, but off-target effects occur due to simple binding mechanism
Solution Approach 1:
The invention changes the structural parameter of the nucleic acid from a simple linear binding mode (siRNA) to a complex three-dimensional guanine quadruplex structure. This parameter change transforms the interaction mechanism from simple sequence complementarity to a more specific structural recognition, thereby maintaining gene expression suppression efficacy while reducing off-target effects.
Solution Approach 2:
The Staple nucleic acid forms a composite guanine quadruplex structure that combines multiple nucleic acid components into a unified functional entity. This composite structure provides both the gene expression suppression function and enhanced specificity, eliminating the off-target effects associated with simple siRNA binding mechanisms.
3Stability of the object's composition
If modified nucleic acids are used in nucleic acid medicines, then nuclease resistance is improved, but enzymatic reaction substrate recognition is lost
Solution Approach 1:
The invention applies local quality by using modified nucleic acids only in specific regions where nuclease resistance is needed, while maintaining unmodified regions that preserve enzymatic recognition capabilities. This localized approach allows the molecule to simultaneously achieve both nuclease resistance and substrate recognition, resolving the contradiction between stability and reactivity.
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
Enables the formation of guanine quadruplex structures on target nucleic acids without requiring four guanine repeat sequences, providing novel applications and enhancing stability and protein expression regulation.
Implementation Method 1
a first nucleotide sequence and a second nucleotide sequence, which target a nucleotide sequence portion containing one to three guanine repeat sequences on a target nucleic acid, and each hybridize with a nucleotide sequence on the 5′ side or 3′ side of the guanine repeat sequences
Implementation Method 2
decreases a spatial distance between a total of four guanine repeat sequences consisting of the guanine repeat sequences on the target nucleic acid and the guanine repeat sequences on the G supply-type oligonucleotide, to form a guanine quadruplex structure composed of the four guanine repeat sequences
Data Source
AI summary
Staple nucleic acids capable of forming guanine quadruplex structure on a target nucleic acid even when four guanine repeat sequences are not present on the target nucleic acid. The oligonucleotide (second generation-type Staple nucleic acid) can supply guanine repeat sequences so that a guanine quadruplex structure can be formed on a target nucleic acid by a total of four guanine repeat sequences, consisting of guanine repeat sequences on the target nucleic acid and guanine repeat sequences on the oligonucleotide.