Engineered Nucleotide Labels for Cleaner SBS Signal Detection

Solution Overview

Problem

Existing nucleic acid sequencing methods, particularly sequencing by synthesis (SBS), face challenges with residual tags and linkers from nucleotide modifications causing background noise and short read lengths due to incomplete tag cleavage, which affect sequencing accuracy and efficiency.

Innovation Solution

Engineered nucleotide molecules with a protecting group and identifier moiety are developed, where the protecting group inhibits additional nucleotide coupling and the identifier moiety is linked to a polyphosphate chain, allowing complete removal upon incorporation, ensuring clear signal attribution and minimizing interference.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If nucleotide modifications with tags and linkers are used in sequencing by synthesis, then sequencing capability is enabled, but background noise increases and read lengths decrease due to residual tags and linkers

Engineering Contradiction:

Improvesequencing accuracyVSAvoidbackground noise

Core Design Contradiction:

Measurement precisionVSObject-generated harmful factors

Solution Approach 1:

The patent extracts and removes the identifier moiety from the nucleotide structure after sequencing detection is complete. By designing the identifier to be removable (through hydrolysis or other cleavage mechanisms), the system eliminates the source of background noise while maintaining the sequencing capability during the active sequencing phase.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The nucleotide is segmented into distinct functional components: the sequencing-active portion (nucleotide with base and sugar) and the detectable identifier portion (moiety attached via linker). This segmentation allows the identifier to perform its detection function independently without interfering with the nucleotide's incorporation and sequencing functions, and enables selective removal of just the identifier after use.

Inventive Principle:

Principle #1Segmentation

2Productivity

If nucleotide modifications with tags and linkers are used in sequencing by synthesis, then sequencing capability is enabled, but read lengths decrease due to incomplete tag cleavage

Engineering Contradiction:

Improvesequencing efficiencyVSAvoidread lengths

Core Design Contradiction:

ProductivityVSLength of moving object

Solution Approach 1:

The patent extracts and removes the identifier moiety from the nucleotide structure after sequencing detection is complete. By designing the identifier to be removable (through hydrolysis or other cleavage mechanisms), the system eliminates the source of background noise while maintaining the sequencing capability during the active sequencing phase.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent changes the chemical state of the linker or identifier moiety through controlled hydrolysis or cleavage reactions. By adjusting pH, temperature, or enzymatic conditions, the system transforms the stable identifier-linker-nucleotide complex into separable components, completely removing the identifier and preventing any residual interference in subsequent sequencing cycles.

Inventive Principle:

Principle #35Parameter changes

3Loss of information

If identifier moiety is attached to nucleotide for detection, then signal detection is enabled, but signal attribution becomes ambiguous due to residual tags

Engineering Contradiction:

Improvesignal attribution clarityVSAvoidinterference from residual tags

Core Design Contradiction:

Loss of informationVSObject-generated harmful factors

Solution Approach 1:

The patent extracts and removes the identifier moiety from the nucleotide structure after sequencing detection is complete. By designing the identifier to be removable (through hydrolysis or other cleavage mechanisms), the system eliminates the source of background noise while maintaining the sequencing capability during the active sequencing phase.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The identifier moiety is designed to be discarded after its detection function is fulfilled. The removable design allows the identifier to be discarded through hydrolysis or cleavage, preventing it from causing background noise in subsequent cycles. This discarding mechanism ensures clean signal attribution for each sequencing cycle.

Inventive Principle:

Principle #34Discarding and recovering

Data Source

PatentUS20250382323A1Compositions, methods, and systems for detecting nucleotides

Publication Date: 2025.12.18 AXBIO INC

AI summary

An aspect of the present disclosure provides an engineered nucleotide molecule. The engineered nucleotide molecule can comprise a pentose sugar. The engineered nucleotide molecule can comprise a base coupled to the pentose sugar, wherein the base is selected from the group consisting of adenine, guanine, cytosine, thymine, uracil, and an analogue thereof. The engineered nucleotide molecule can comprise a polyphosphate chain coupled to the pentose sugar. The engineered nucleotide molecule can comprise a protecting group coupled to the pentose sugar, wherein the protecting group is configured to inhibit coupling of an additional nucleotide to the engineered nucleotide molecule. The engineered nucleotide molecule can comprise an identifier moiety coupled to the pentose sugar via the polyphosphate chain, wherein the identifier moiety is specific for the engineered nucleotide molecule.