RNA Labeling via Oligonucleotide Pool Segmentation
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Solution Overview
Problem
Current RNA labeling technologies face limitations such as a limited number of distinguishable detectable moieties, time-consuming processes, equipment requirements, and high costs, which hinder efficient and cost-effective labeling of RNAs for research and industrial applications.
Innovation Solution
The method involves generating unique labels by sequentially attaching randomly selected oligonucleotides, allowing for the synthesis of a large number of unique labels using a small number of oligonucleotides, which can be easily detected and distinguished, enabling efficient labeling of RNAs in real-time and storing information about the agent, such as its origin or conditions exposed to.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If current labeling technologies are used, then RNAs can be labeled, but the number of distinguishable detectable moieties is limited
Solution Approach 1:
The labeling system is segmented into multiple components: a pool of oligonucleotides with unique sequences that can be combined in different arrangements. Each oligonucleotide acts as a modular unit that can be sequentially attached to form composite labels, enabling exponential expansion of distinguishable labels from a limited set of building blocks
Solution Approach 2:
Multiple oligonucleotide tags are nested or combined in sequential layers to form hierarchical label structures. The random sequential attachment creates nested combinations where inner oligonucleotides are followed by outer ones, generating unique multi-component labels from fewer individual components
2Productivity
If current labeling methods are used, then RNAs can be labeled, but the process requires a large amount of time
Solution Approach 1:
A pre-established pool of oligonucleotides with known unique sequences is prepared in advance. This preliminary preparation allows for rapid sequential attachment during the actual labeling process, eliminating the need to generate or select labels during labeling, thus reducing time loss
Solution Approach 2:
The system uses random sequential attachment where oligonucleotides self-assemble or self-attach to form unique labels without requiring complex external control or selection processes. This autonomous labeling mechanism accelerates the process by eliminating manual intervention steps
3Ease of manufacture
If current labeling technologies are used, then RNAs can be labeled, but specialized equipment is required
Solution Approach 1:
The invention uses simple, inexpensive oligonucleotide building blocks that can be synthesized using standard, widely available equipment. These disposable-like molecular components eliminate the need for complex, expensive specialized labeling equipment, making the system easier to manufacture and operate
Solution Approach 2:
The labeling process replaces complex mechanical or instrumental systems with biochemical processes. Instead of using sophisticated equipment to generate and assign labels, the system uses enzymatic or chemical attachment of pre-synthesized oligonucleotides, substituting mechanical complexity with simpler biochemical reactions
4Quantity of substance
If current labeling methods are used, then RNAs can be labeled, but the cost involved is high
Solution Approach 1:
A universal pool of oligonucleotide building blocks serves multiple functions: they can be combined in different sequences, attached to different RNA targets, and reused across multiple labeling experiments. This multi-functionality reduces per-label cost by maximizing the utility of each oligonucleotide component
Solution Approach 2:
The system changes the parameter of label diversity by combining a limited number of oligonucleotide types in different sequential arrangements. This combinatorial approach generates exponential label diversity from linear input costs, as the number of possible unique labels equals the factorial or exponential function of the oligonucleotide pool size
Data Source
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AI summary
The invention provides, inter alia, methods for uniquely labeling populations of agents of interest using random combinations of oligonucleotides. The oligonucleotides may comprise a unique nucleotide sequence and/or one or more non-nucleic acid detectable moieties.