Targeted Biomolecule Shrinking via Polymer Conjugates
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Solution Overview
Problem
Current methods for in situ analysis of biological samples using crosslinking often result in off-target disruption of molecules and structures, leading to poor resolution and detection of biomolecules due to global shrinking or expansion of the sample.
Innovation Solution
The use of a polymer that forms a polymer conjugate with target biomolecules, allowing for targeted shrinking or expansion without affecting adjacent molecules or the entire sample, using functional groups that react via click reactions to form covalent bonds, enabling precise control over the size and accessibility of biomolecules.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If crosslinking is used to shrink or expand a biological sample, then resolution of individual biomolecules is improved, but off-target disruption of molecules and structures occurs
Solution Approach 1:
The patent applies local quality by using polymers with specific functional groups that selectively react only with complementary functional groups on target biomolecules, creating localized modification at specific sites rather than global crosslinking. This selective reaction ensures that only intended target molecules are shrunk or expanded while surrounding structures remain unaffected, resolving the contradiction between improving resolution and avoiding off-target disruption.
Solution Approach 2:
The patent employs polymer intermediaries that contain specific functional groups serving as mediators between the crosslinking agent and target biomolecules. These polymer intermediaries with complementary functional groups enable controlled, specific crosslinking reactions at target sites while preventing non-specific interactions with surrounding molecules, thus achieving high resolution without off-target effects.
2Measurement precision
If the entire sample is compacted to increase resolution, then detection of individual molecules is improved, but adjacent structures are also disrupted
Solution Approach 1:
The patent implements local quality by designing polymers with specific functional groups that recognize and bind only to complementary functional groups on target molecules. This specificity ensures that compaction occurs locally at individual target molecule sites rather than globally across the entire sample, maintaining the integrity of adjacent structures while achieving high detection resolution for individual molecules.
3Measurement precision
If global crosslinking is applied to shrink biomolecules, then signal resolution is enhanced, but the complexity of the process increases due to non-specific interactions
Solution Approach 1:
The patent uses polymer intermediaries with specific functional groups as mediators to achieve specific crosslinking reactions. These intermediaries simplify the process by providing selective recognition and binding, eliminating the need for complex purification steps to remove non-specific interactions. The specific functional group complementarity ensures that only target molecules are modified, reducing process complexity while maintaining high signal resolution.
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 resolution and detection of individual biomolecules by compacting or expanding them selectively, improving signal intensity and accessibility without disrupting the surrounding sample, thereby facilitating better analysis of densely packed regions.
Implementation Method 1
reacting the one or more functional groups A with the one or more functional groups B, thereby coupling the polymer to the probe or product thereof to form a polymer conjugate
Implementation Method 2
initiating polymer-polymer cross-linking to form a polymer network between the polymers of the polymer conjugate
Data Source
AI summary
The present disclosure in some aspects relates to methods and compositions for processing a biological sample, including methods and compositions for targeted shrinking and expansion of biomolecules in a biological sample for in situ analysis. In some aspects, a polymer is conjugated with a probe or product thereof (e.g., rolling circle amplification products) in the biological sample, and the polymer conjugate may be shrunk or expanded. In some aspects, a size-controllable polymer network is used to shrink or expand the biomolecules in the biological sample. Targeted shrinking can create more space for analyzing more biomolecules at the same time inside a confined space within the sample and expand the space between adjacent probes or products thereof at locations in the sample.