Signal-Activatable RNA Constructs for Controlled Molecular Delivery
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Solution Overview
Problem
Current methods for controlled delivery of biomolecules to specific environments, such as cells or tissues, face challenges in achieving precise and controllable release, especially in medical and biological applications.
Innovation Solution
Signal-activatable constructs, including pseudoknot structures, are developed to enable controlled release of targeting domains by switching between inactive and active conformations upon binding to signal molecules, utilizing duplex RNA and sensor domains to minimize processing by enzymes like Dicer and Argonaute, allowing for targeted molecular delivery.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If conventional methods are used for delivery of biomolecules, then delivery can be achieved, but controlled release to specific environments remains challenging
Solution Approach 1:
The patent embeds multiple functional domains within a single RNA construct: a targeting domain (siRNA) is nested within a sensor domain structure that includes pseudoknot elements. The sensor domain acts as a container that houses the targeting domain and only releases it upon signal activation, achieving controlled delivery while maintaining a compact, integrated structure rather than separate complex components
Solution Approach 2:
The RNA construct transitions between static inactive conformations and dynamic active conformations upon signal binding. The pseudoknot structure undergoes conformational changes that switch the construct between a protected state (where the targeting domain is sequestered) and an active state (where the targeting domain is released for cellular processing), enabling controlled release precision through dynamic structural transformation
2Reliability
If the targeting domain is always accessible, then it can be processed by enzymes, but this prevents controlled release and signal-activated functionality
Solution Approach 1:
The construct is designed in advance with the targeting domain pre-positioned within the protected conformation of the sensor domain. The structure is pre-configured so that under normal conditions, the targeting domain is shielded from enzymatic processing, but upon signal activation, the conformational change automatically exposes the targeting domain to enzymes like Dicer and Argonaute, ensuring reliable signal-activated control
Solution Approach 2:
The sensor domain acts as an intermediary between the signal molecule and the targeting domain. It mediates the interaction by first binding the signal molecule, then undergoing conformational change to release the targeting domain. This intermediary structure enables controlled protection and release, preventing premature enzyme processing while maintaining readiness for signal-activated processing
3Productivity
If a compact integrated structure is used, then delivery efficiency improves, but the structure must be small enough to be delivered to cells
Solution Approach 1:
The targeting domain (typically 19-27 bp siRNA) is nested within the sensor domain structure, which itself contains the pseudoknot elements and signal-binding regions. This nested arrangement allows the construct to maintain functional integrity and delivery efficiency while minimizing the overall molecular size, as the targeting domain occupies space within the sensor domain rather than adding linear length
Solution Approach 2:
Multiple functional elements are merged into a single RNA molecule: the sensor domain, pseudoknot structures, signal-binding regions, and targeting domain are all combined in one construct. This merging achieves compact integration that improves delivery efficiency by reducing the number of separate molecular entities that need to be transported into cells, while the functional domains remain distinct and operable
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
These constructs facilitate cell-type specific molecular delivery, integrating signal detection and targeting in a single compact form, enhancing efficiency and enabling precise control over the release of therapeutic cargo within biological environments.
Implementation Method 1
the sensor strand further comprises at least one toehold segment presented for binding to a signal molecule
Implementation Method 2
the targeting domain is in a configuration minimizing processing by Dicer and/or an Argonaute enzyme
Data Source
AI summary
Provided herein are signal activatable molecular constructs for delivery of molecules and related components, compositions, methods, and systems, having a 17 to 30 bp targeting domain duplex RNA, at least one protection strand having a protection segment and linker segment and a sensor strand having a displacement segment and a toehold segment, in which in an inactive conformation the protection segment and the displacement segment form a sensor domain duplex polynucleotide covalently attached to the targeting domain and presenting the toehold segment for binding to a signal molecule. In an active conformation the sensor strand is bound to the signal molecule and is detached from the at least one protection strand and from the targeting domain; and the targeting domain attaches the at least one protection strand in a configuration allowing processing by Dicer and/or an Argonaute enzyme.