Modular Nucleotide Compositions Using Non-Covalent Linkages

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Solution Overview

Problem

Existing nucleotide compositions lack flexibility and modularity for functionalization, making it difficult to adapt them for various applications such as genetic analysis, pharmaceutical research, and medical diagnostics, as they often require complex synthesis processes and are limited by covalent linkages that are not easily interchangeable.

Innovation Solution

The development of modular nucleotide compositions that utilize non-covalent linkages, specifically affinity binding pairs, to attach functional groups to nucleoside polyphosphates, allowing for easy interchange and configuration of functional components without complex synthesis, enabling a cassette approach for tailoring nucleotides for specific applications.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If covalent linkages are used to attach functional groups to nucleotides, then the functionalization is stable, but the flexibility and ease of interchangeability of functional components is reduced

Engineering Contradiction:

Improvestability of functional group attachmentVSAvoidflexibility of functionalization

Core Design Contradiction:

ReliabilityVSAdaptability or versatility

Solution Approach 1:

The patent introduces an intermediary mechanism (affinity binding pairs such as biotin-streptavidin, antibody-antigen, or complementary oligonucleotide sequences) that mediates the attachment between functional groups and nucleotide analogs. This intermediary approach allows stable yet reversible binding, enabling both reliable functionalization and easy interchangeability of functional components without requiring covalent bond formation.

Inventive Principle:

Principle #24Intermediary (Mediator)

2Manufacturing precision

If complex synthesis processes are used to functionalize nucleotides, then the functional groups can be precisely attached, but the time and complexity of the manufacturing process increases

Engineering Contradiction:

Improveprecision of functional group attachmentVSAvoidsimplicity of synthesis process

Core Design Contradiction:

Manufacturing precisionVSEase of manufacture

Solution Approach 1:

The patent segments the functionalization process into two independent components: (1) nucleotide analogs with built-in affinity binding moieties, and (2) separate functional groups with complementary binding partners. This segmentation allows each component to be prepared independently with high precision, then combined through simple affinity binding, eliminating the need for complex stepwise synthesis procedures while maintaining attachment precision.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The affinity binding moieties are pre-installed on the nucleotide analogs during nucleotide synthesis, and the complementary binding partners are pre-installed on the functional groups. This preliminary action ensures that when the components are mixed, the functional groups are automatically and precisely attached to the correct nucleotide analogs without requiring complex real-time synthesis or positioning procedures.

Inventive Principle:

Principle #10Preliminary action

3Adaptability or versatility

If modular nucleotide compositions with non-covalent linkages are used, then the adaptability and ease of functional interchange is improved, but the stability of the linkage may be reduced

Engineering Contradiction:

Improveease of functional interchangeVSAvoidstability of non-covalent linkage

Core Design Contradiction:

Adaptability or versatilityVSReliability

Solution Approach 1:

The patent employs composite affinity binding systems that combine multiple interaction forces (hydrogen bonding, hydrophobic interactions, electrostatic attractions, and van der Waals forces) to create non-covalent linkages with stability comparable to or exceeding covalent bonds in certain conditions. Examples include biotin-streptavidin (Kd ~10^-15 M), antibody-antigen, and complementary oligonucleotide sequences, which provide both the adaptability of non-covalent bonding and the stability required for practical applications.

Inventive Principle:

Principle #40Composite materials

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 rapid and flexible functionalization of nucleotides, allowing for a wide range of applications by easily swapping nucleotide and functional components, improving detection sensitivity and specificity, and enabling the use of diverse functional groups like fluorescent labels and pharmaceutical compounds.

Implementation Method 1

The non-covalent linkage preferably comprises one or more of an affinity linkage, biotin, avidin (or biotin-binding subunit thereof), streptavidin (or biotin-binding subunit thereof), neutravidin (or biotin-binding subunit thereof), an antibody or fraction thereof, a polynucleotide, a nucleic acid binding protein

Methodology Applied

Scientific EffectAffinity binding: Adsorption

Data Source

PatentUS10745750B2Modular nucleotide compositions and uses therefor

Publication Date: 2020.08.18 PACIFIC BIOSCIENCES OF CALIFORNIA INC

AI summary

Nucleic acid compositions, methods of making and using such compositions that comprise modular functional groups that can be configured to provide desired functionality to different nucleotide types through a swappable and preferably non-covalent linkage component. Such compositions are useful in a variety of applications including nucleic acid analyses.