Region-Specific Amplification Templates Using Photoremovable Cage Molecules
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Solution Overview
Problem
Current transcriptomics methods cannot efficiently generate region-specific amplification templates for multiple regions of interest in a biological sample with high spatial resolution, leading to the inability to assign analysis results to their respective original regions.
Innovation Solution
A method involving the use of oligonucleotide constructs with photoremovable cage molecules and differing light parameters for scanning, allowing for the generation of region-specific amplification templates by forming uncaged constructs and subsequent strands, enabling precise assignment to specific regions of interest.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If multiple oligonucleotide constructs with different photoremovable cage molecules are added to the biological sample, then region-specific amplification templates can be generated for multiple regions of interest, but the device complexity and process complexity increase
Solution Approach 1:
The patent divides the biological sample into multiple regions of interest, each associated with distinct oligonucleotide constructs containing different photoremovable cage molecules. Each cage molecule responds to specific light parameters (wavelength, intensity, duration), enabling independent control and uncaging in each region. This segmentation allows simultaneous or sequential analysis of multiple regions while maintaining spatial resolution and template assignment.
2Measurement precision
If photoremovable cage molecules are used to enable region-specific uncaging, then spatial resolution is improved, but the process time and complexity increase
Solution Approach 1:
The patent employs periodic or pulsed light scanning to sequentially uncage different photoremovable cage molecules in different regions of interest. By using pulsed light exposure with specific parameters (wavelength, intensity, duration) for each cage type, the system achieves high spatial resolution while optimizing the time required for each uncaging event. The periodic action allows systematic progression through multiple regions without requiring continuous light exposure.
3Measurement precision
If focused light beams with differing parameters are used to scan different regions, then region-specific template assignment is improved, but the energy consumption and potential damage to biological structures increase
Solution Approach 1:
The patent applies local quality by using focused light beams with parameters (wavelength, intensity, duration) specifically optimized for each photoremovable cage molecule type in each region of interest. This localized optimization ensures that only the intended cage molecules are uncaged in their specific regions, improving template assignment accuracy. The focused nature of the light beams minimizes exposure to surrounding biological structures, reducing potential damage while maintaining precise spatial control.
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 capture and analysis of genetic content from multiple regions with high spatial resolution, allowing for the comparison of amplification templates between regions, such as cancerous and healthy cells, while minimizing damage to biological structures.
Implementation Method 1
scanning at least a first region of interest of the biological sample with a first focused light beam and a second region of interest of the biological sample with a second focused light beam to form uncaged first oligonucleotide constructs in the first region of interest and uncaged second oligonucleotide constructs in the second region of interest
Data Source
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AI summary
A method for generating region-specific amplification templates (102, 204) of a biological sample (400) is provided, comprising the following steps: adding at least a first plurality of oligonucleotide constructs (100, 200) comprising a first cage molecule (112) and a second plurality of oligonucleotide constructs (100, 200) comprising a second cage molecule (112) to the biological sample (400); synthesising a complementary first strand (118) from a template (116) bound to target binding regions (110) of the oligonucleotide constructs (100, 200); scanning at least a first region of interest (406, 408) of the biological sample (400) with a first focused light beam and a second region of interest (406, 408) of the biological sample (400) with a second focused light beam to form uncaged first oligonucleotide constructs (120) in the first region of interest (406, 408) and uncaged second oligonucleotide constructs (120) in the second region of interest (406, 408); and synthesising a complementary second strand (122) to form amplification templates (102, 204). In a further aspect a system for performing the method is provided.