Nucleic Acid Binding Protein Assays for Personalized Diagnostics
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for measuring the binding affinity of nucleic acid binding proteins for their recognition sites are limited in their ability to account for individual-specific mutations, are not cost-effective, and fail to provide personalized diagnostic and treatment options, particularly for rare or unknown mutations that affect binding affinities.
Innovation Solution
The development of assays that utilize capture oligonucleotides specific to an individual's genetic material, allowing for the measurement of binding affinities of both nucleic acid sequences and proteins tailored to that individual, incorporating techniques like Molecular Inversion Probes (MIP) to enrich and select recognition sites accurately, enabling the assessment of binding affinities in the presence of mutations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If chromatin immunoprecipitation with microarrays is used to measure binding affinity, then binding affinity can be measured, but the method requires specific antibodies for each binding protein which increases complexity and cost
Solution Approach 1:
The patent extracts the antibody dependency from the measurement system by using in vitro transcribed and translated binding proteins directly, eliminating the need for antibodies while maintaining measurement capability
Solution Approach 2:
The patent introduces an in vitro transcription-translation system as an intermediary to produce binding proteins from nucleic acid sequences, replacing the antibody-mediated detection approach
2Measurement precision
If chromatin immunoprecipitation techniques are used, then binding affinity can be measured, but the in vivo fixing step complicates the process and limits analysis of specific binding proteins
Solution Approach 1:
The patent inverts the traditional approach by moving from in vivo fixation to in vitro binding analysis, reversing the sequence of operations to simplify the process
Solution Approach 2:
The patent segments the binding affinity measurement into separate in vitro steps: nucleic acid preparation, in vitro transcription-translation of binding proteins, and binding analysis, eliminating the need for complex in vivo fixation
3Measurement precision
If conventional assays are used to measure binding affinity, then general binding can be measured, but individual-specific mutations cannot be accounted for
Solution Approach 1:
The patent applies local quality by tailoring the nucleic acid sequences and binding proteins to each individual's specific genetic makeup, allowing measurement of binding affinities that account for personal mutations
Solution Approach 2:
The patent introduces dynamics by making the assay adaptable to individual-specific sequences through in vitro transcription-translation, enabling the system to respond to and accommodate genetic variations
4Adaptability or versatility
If methods accounting for individual mutations are developed, then personalized diagnosis can be achieved, but the cost and complexity increase
Solution Approach 1:
The patent applies self-service by using the individual's own nucleic acid sequences to generate binding proteins through in vitro transcription-translation, eliminating the need for external antibodies or complex reagents
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
These assays provide personalized and cost-effective measurements of binding affinities, allowing for precise diagnosis and treatment by accounting for individual-specific mutations, improving the understanding of genetic contributions to medical conditions.
Implementation Method 1
a capture oligonucleotide attached to a substrate, wherein the capture oligonucleotide includes a portion that is complementary to a target nucleic acid sequence
Data Source
AI summary
Methods, compositions and kits are disclosed for assays to determine the binding affinity of DNA-binding proteins or RNA-binding proteins for their corresponding recognition site(s). In particular, assays are disclosed for measuring binding affinities when either the binding protein, or the recognition sequence of the recognition site, or cofactor proteins, contain one or more mutations. The disclosed assays can thus be utilized to measure the effect on transcription factor binding caused by mutations within the recognition site, or mutations within the binding domain of the protein, and to provide binding affinity information that can be correlated with altered gene regulation and expression. The disclosed assays can be personalized to a specific person or organism, with the measured binding affinities based upon an individual's specific binding proteins and recognition sites. Furthermore, embodiments are capable of measuring binding affinities between multiple binding proteins and multiple recognition sites through an entirely in vitro process.