Engineered RNA Strand Displacement for Specific Activation
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current engineered RNA technologies face issues with unwanted activation in the absence of an input signal, leading to off-target effects and limitations in gene therapy applications, particularly in targeting critical host genes or viral replication processes.
Innovation Solution
Designing engineered RNAs with a large energy gap between their lowest energy state and a recognizable secondary structure by an actuator, such as Drosha or Cas protein, ensuring activation only in the presence of an input signal, thereby minimizing off-target effects and enhancing specificity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If engineered RNA is designed to be activated by an actuator, then the RNA can perform its function, but it may be activated in the absence of the input signal causing off-target effects
Solution Approach 1:
The engineered RNA is pre-designed with a specific secondary structure that prevents actuator recognition in the absence of input signal. The RNA sequence is engineered beforehand to form a stable inactive conformation that only transitions to an active, actuator-recognizable structure when the specific input signal is present, thereby preventing premature or off-target activation.
Solution Approach 2:
The invention modifies the thermodynamic parameters of the RNA secondary structure by engineering the sequence to create a large energy gap between the inactive lowest energy state and the active secondary structure. This parameter change ensures that the RNA remains in the inactive state under normal conditions and only transitions to the active state when sufficient energy is provided by the specific input signal.
2Ease of operation
If engineered RNA forms a secondary structure recognizable by actuator at lowest energy state, then activation is easier, but unwanted activation occurs in absence of input signal
Solution Approach 1:
The RNA is pre-engineered with a sequence that naturally folds into an inactive secondary structure at its lowest energy state, which is not recognizable by the actuator. This preliminary structural design ensures that the RNA remains inactive by default and can only be activated when the specific input signal induces a conformational change to an actuator-recognizable structure.
Solution Approach 2:
The invention engineers the RNA sequence to create a large thermodynamic energy gap between the inactive lowest energy state and the active secondary structure. This parameter modification ensures that the RNA requires significant energy input (from the specific input signal) to transition from the stable inactive state to the active state, thereby preventing unwanted activation while maintaining controlled activation capability.
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 increases the specificity of engineered RNAs, allowing them to target essential genes or viral components only in the presence of an input signal, improving therapeutic efficacy while ensuring safety by reducing off-target effects.
Implementation Method 1
in the absence of an input signal, the engineered RNA forms a first secondary structure in which the engineered RNA is not capable of being recognized by an actuator
Implementation Method 2
Trans-activated functional RNA by strand displacement and uses thereof
Implementation Method 3
When the input signal is present, it induces a conformational change of the engineered RNA molecule, such that the engineered RNA forms a second secondary structure
Data Source
AI summary
The present disclosure, at least in part, relates to an engineered RNA (e.g., microRNA and sgRNA), in the absence of an input signal, that is engineered to have a large enough energy gap between the formations of a first secondary structure, which is unrecognizable by an actuator, and a second secondary structure, which is recognizable by an actuator (e.g., Drosha and Cas protein).