Cellular Nucleic Acid Imaging With Error-Correcting Probe Codes
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Solution Overview
Problem
Single-molecule fluorescent in situ hybridization (smFISH) methods face limitations in throughput due to the lack of distinguishable probes and high costs associated with producing large amounts of labeled probes, limiting the ability to efficiently detect multiple genes simultaneously.
Innovation Solution
The use of nucleic acid probes with error-correcting codes and combinatorial labeling techniques, including primary and secondary probes, allows for high-resolution imaging and determination of nucleic acids within cells, enabling the identification of a large number of targets using a small number of labels.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional smFISH methods are used to detect mRNA molecules, then detection precision is achieved, but throughput remains low due to lack of distinguishable probes
Solution Approach 1:
The probe is divided into multiple segments: a target-binding portion and multiple read sequences. Each read sequence can be independently varied to create distinguishable probes, enabling high-throughput detection of multiple genes simultaneously while maintaining precise target binding
Solution Approach 2:
Different regions of the probe have specialized functions: the target-binding portion provides specificity for mRNA detection, while the read sequences provide distinguishability for identifying different genes. This local differentiation allows the probe to simultaneously achieve both detection precision and high throughput
2Measurement precision
If large amounts of labeled probes are produced to improve detection efficiency, then detection precision increases, but cost increases significantly
Solution Approach 1:
The read sequences serve multiple functions: they enable probe distinguishability for different genes, provide bases for combinatorial labeling strategies, and facilitate error-correcting code implementation. This multi-functionality reduces the need for producing large amounts of uniquely labeled probes for each gene
Solution Approach 2:
Instead of changing the chemical label for each gene, the invention changes the nucleotide sequence parameters of the read regions. This allows combinatorial labeling where a small set of read sequences can be combined in different patterns to label many different genes, reducing the total amount of labeled probe material needed
3Productivity
If combinatorial labeling with error-correcting codes is implemented to increase throughput, then number of detectable genes increases, but probe design complexity increases
Solution Approach 1:
The invention uses combinatorial copying of read sequences to encode gene identities. Instead of designing unique probes for each gene, standard read sequences are copied and combined in different patterns according to error-correcting codes, simplifying the overall system while increasing the number of detectable genes
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 enhances the throughput of nucleic acid detection by reducing misidentification and increasing the number of genes that can be detected simultaneously, achieving resolutions better than visible light wavelengths.
Implementation Method 1
The plurality of read sequences are distributed on the plurality of nucleic acid probes so as to define an error-correcting code
Data Source
AI summary
The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.