Analyte Immobilization via Nucleic Acid Chimeras on Solid Supports
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for preparing analytes for analysis and sequencing lack efficiency in generating nucleic-acid analyte conjugate formats compatible with protein analysis, particularly in immobilizing analytes on solid supports to withstand chemical and enzymatic reactions during protein analysis assays.
Innovation Solution
A method involving attaching an analyte to a bait nucleic acid to form a nucleic acid-analyte chimera, which is then hybridized and covalently coupled to a capture nucleic acid attached to a solid support, ensuring the analyte remains immobilized and available for analysis with a spacing of about 50 nm or greater between adjacent chimeras.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If analytes are immobilized on solid supports using conventional methods, then the analytes can be retained for analysis, but the analytes may detach or degrade during chemical and enzymatic reactions
Solution Approach 1:
The patent introduces a nucleic acid-based intermediary system consisting of bait nucleic acids attached to analytes and capture nucleic acids on the solid support. This intermediary nucleic acid system provides stable, specific binding through hybridization, allowing analytes to remain firmly attached during chemical and enzymatic reactions without direct strong chemical attachment that might cause degradation
Solution Approach 2:
The patent creates a composite structure where analytes are conjugated to nucleic acids (forming nucleic acid-analyte chimeras), which then bind to capture nucleic acids on the solid support. This composite approach combines the specificity and stability of nucleic acid hybridization with the immobilization capability of solid supports, enhancing both attachment strength and reliability
2Productivity
If multiple analytes are immobilized in high density on solid supports, then analysis throughput increases, but adjacent analytes may interfere with each other's reactions
Solution Approach 1:
The patent applies local quality by spacing adjacent nucleic acid-analyte chimeras approximately 50 nm apart on the solid support. This specific local spacing ensures that each analyte has sufficient reaction space and prevents interference between adjacent analytes, while still maintaining high overall density for good throughput
Solution Approach 2:
The patent transitions from two-dimensional planar immobilization to three-dimensional spatial arrangement by specifying vertical spacing (approximately 50 nm) between adjacent chimeras. This dimensional approach allows high density immobilization while maintaining reaction accuracy through controlled spatial separation
3Strength
If strong chemical attachment methods are used to immobilize analytes, then attachment strength increases, but the analyte structure may be damaged or altered
Solution Approach 1:
The nucleic acid components act as intermediaries that provide stable attachment through hybridization rather than strong chemical bonding. This intermediary approach maintains analyte structural integrity while achieving sufficient attachment strength for withstanding reaction conditions
Solution Approach 2:
The patent replaces strong chemical/mechanical attachment methods with nucleic acid hybridization-based attachment. This substitution uses specific base-pairing interactions instead of harsh chemical bonding, preserving analyte structure while providing stable immobilization
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 enables efficient preparation and analysis of analytes, allowing for multiple cycles of chemical and enzymatic reactions while maintaining the integrity of both the analyte and nucleic acid components, enhancing compatibility with protein sequencing and analysis.
Implementation Method 1
bringing the nucleic acid-analyte chimera into proximity with a solid support by hybridizing the bait nucleic acid in the nucleic acid-analyte chimera to a capture nucleic acid attached to the solid support
Data Source
AI summary
Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids. In some embodiments, the analyte is coupled to a solid support. Also provided are kits containing components for performing the provided methods for preparing the analytes. In some embodiments, the methods are for preparing an analyte for sequencing.