Orthogonal Nucleic Acid Oligomer Design for Assay Specificity

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Solution Overview

Problem

Designing nucleic acid affinity pairs for multi-analyte tests poses challenges due to non-specific cross-interactions, especially with longer oligomers, which can lead to assay specificity issues and increased hybridization stability, making it difficult to prevent undesired hybridizations in applications like microarrays and nano-fabrications.

Innovation Solution

The development of a software program that generates orthogonal nucleic acid oligomer sequences, such as pRNA and pDNA, using a semi-random algorithm to ensure stability and avoid cross-reactivity, allowing for user-controlled variables to dictate the properties of the affinity pairs, including length and stringency of non-cross-interaction, and incorporating chimeric oligomers for improved binding characteristics.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Stability of the object's composition

If longer oligomers are used to increase binding stability, then hybridization stability is improved, but non-specific cross-interactions increase leading to decreased assay specificity

Engineering Contradiction:

Improvehybridization stabilityVSAvoidassay specificity

Core Design Contradiction:

Stability of the object's compositionVSReliability

Solution Approach 1:

The patent uses a software program that systematically varies oligomer sequence parameters to identify combinations that achieve high binding stability while minimizing cross-interactions. The program evaluates multiple sequence parameters including GC content, melting temperature, and sequence composition to optimize the balance between stability and specificity

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The patent employs computational modeling and in silico evaluation to create virtual representations of oligomer behavior before physical synthesis. The software program simulates hybridization stability and cross-interaction potential, allowing selection of optimal sequences without extensive experimental trial and error

Inventive Principle:

Principle #26Copying

2Adaptability or versatility

If more oligomer affinity pairs are designed for multi-analyte tests, then test coverage is improved, but cross-interaction between non-specific pairs increases

Engineering Contradiction:

Improvemulti-analyte test capabilityVSAvoidcross-interaction between pairs

Core Design Contradiction:

Adaptability or versatilityVSObject-generated harmful factors

Solution Approach 1:

The patent designs a universal software program that can generate affinity pairs for multiple different analytes using the same methodology. The program evaluates sequences against a comprehensive database of potential cross-interactions, ensuring that pairs designed for different analytes maintain orthogonality and do not cross-react

Inventive Principle:

Principle #6Universality (Multi-functionality)

Solution Approach 2:

The software program acts as an intermediary that mediates between the requirement for multiple affinity pairs and the need to avoid cross-interactions. It systematically evaluates potential pairs against each other, identifying and eliminating sequences that would cause non-specific binding before physical implementation

Inventive Principle:

Principle #24Intermediary (Mediator)

3Reliability

If short oligomers are used to avoid cross-interactions, then assay specificity is improved, but binding stability decreases

Engineering Contradiction:

Improveassay specificityVSAvoidbinding stability

Core Design Contradiction:

ReliabilityVSStability of the object's composition

Solution Approach 1:

The patent systematically varies sequence parameters including GC content, melting temperature, and sequence composition to identify optimal short oligomer sequences that maximize binding stability while maintaining low cross-interaction potential. The software evaluates multiple parameter combinations to find the best balance

Inventive Principle:

Principle #35Parameter changes

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

The approach effectively produces oligomer affinity pairs that minimize non-specific cross-interactions, enhancing the specificity of diagnostic assays and allowing for efficient site-specific immobilization of proteins and peptides on solid surfaces, thereby improving the accuracy of multi-analyte tests and lateral flow assays.

Implementation Method 1

one half of the pair is bound to the protein and the corresponding complementary oligomer is bound to the membrane

Methodology Applied

Scientific EffectHybridization:

Implementation Method 2

Pyranosyl nucleic acid (pRNA), and 3-deoxypyranosyl nucleic acid (pDNA) are polymers that preferentially pair with complementary pRNA or pDNA versus natural RNA and DNA sequences

Methodology Applied

Scientific EffectComplementary base pairing:

Data Source

PatentUS10127349B2Method of producing oligomer affinity pairs

Publication Date: 2018.11.13 ELITECHGROUP MDX LLC

AI summary

The invention provides methods to identify pRNA- and pDNA oligomer affinity pairs. Affinity pairs comprised of nucleic acid oligomers which demonstrate no cross-reactivity (“orthogonal”) are designed using software and empirically verified by thermodynamic study and lateral flow testing. The design software uses a semi-random algorithm to build such sequences of nucleic acid oligomers based on user-input parameters for affinity strength and orthogonal stringency. These pairs can be applied for use in multi-analyte solid support and lateral flow diagnostic tests.