Biotin-Streptavidin Cleavage Composition for Flow Cell Hybridization

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Solution Overview

Problem

Existing methods for cleaving biotin-streptavidin bonds on solid supports in biological arrays often interfere with the chemistry of the flow cell surface, leading to undesirable effects on hybridization of biotinylated DNA library fragments.

Innovation Solution

A cleavage composition comprising formamide and a salt buffer is used to break biotin-streptavidin interactions at temperatures below 70°C, allowing efficient release of biotinylated DNA library fragments without affecting the flow cell surface chemistry.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If strong cleavage methods (e.g., high temperature, harsh chemicals) are used to break biotin-streptavidin bonds, then bond cleavage efficiency is improved, but the flow cell surface chemistry is damaged

Engineering Contradiction:

Improvebond cleavage efficiencyVSAvoidflow cell surface damage

Core Design Contradiction:

ReliabilityVSObject-affected harmful factors

Solution Approach 1:

The invention changes the chemical parameters of the cleavage composition by incorporating formamide (10-50% v/v) and specific salt buffers (sodium chloride and sodium citrate) to achieve effective biotin-streptavidin bond cleavage at temperatures below 70°C, avoiding the need for harsh conditions that would damage the flow cell surface

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The invention uses formamide as an intermediary agent that facilitates bond cleavage through specific chemical interactions without directly damaging the flow cell surface. The salt buffer components (sodium chloride and sodium citrate) act as mediators to optimize the cleavage conditions while preserving surface integrity

Inventive Principle:

Principle #24Intermediary (Mediator)

2Speed

If high temperature incubation is used to cleave biotin-streptavidin bonds, then cleavage speed is improved, but hybridization of DNA fragments is affected

Engineering Contradiction:

Improvecleavage speedVSAvoidhybridization quality

Core Design Contradiction:

SpeedVSReliability

Solution Approach 1:

The invention changes the temperature parameter to operate below 70°C (e.g., 60-70°C or lower) while compensating with optimized chemical composition (formamide and salt buffer) to maintain rapid cleavage kinetics, thereby preserving DNA fragment hybridization capability to the flow cell surface

Inventive Principle:

Principle #35Parameter changes

3Reliability

If prolonged incubation is used to ensure complete bond cleavage, then cleavage completeness is improved, but process time increases

Engineering Contradiction:

Improvecleavage completenessVSAvoidincubation time

Core Design Contradiction:

ReliabilityVSLoss of time

Solution Approach 1:

The invention optimizes the chemical parameters of the cleavage composition (formamide concentration, salt buffer composition and concentration) to accelerate the cleavage reaction kinetics, achieving complete bond cleavage within a shortened incubation period while maintaining reliability

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 cleavage composition effectively breaks biotin-streptavidin bonds quickly, ensuring immediate hybridization of released DNA fragments while preserving the integrity of the flow cell surface, reducing incubation times and minimizing interference with other reagents.

Implementation Method 1

The affinity of avidin or streptavidin for biotin is one of the strongest non-covalent biological interactions

Methodology Applied

Scientific EffectBiotin-streptavidin interaction:

Implementation Method 2

A cleavage composition comprising formamide and a salt buffer is used to break biotin-streptavidin interactions at temperatures below 70°C

Methodology Applied

Scientific EffectFormamide denaturation:

Implementation Method 3

ensuring immediate hybridization of released DNA fragments

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentEP3969611B1Biotin-streptavidin cleavage composition and library fragment cleavage

Publication Date: 2025.12.10 ILLUMINA INC

Figure 1A~1B
Figure 2A~2B
Figure 2C

AI summary

An example of a biotin-streptavidin cleavage composition includes a formamide reagent and a salt buffer. The formamide reagent is present in the biotin-streptavidin cleavage composition in an amount ranging from about 10% to about 50%, based on a total volume of the biotin-streptavidin cleavage composition. The salt buffer makes up the balance of the biotin-streptavidin cleavage composition. In some examples, the biotin-streptavidin cleavage composition is used to cleave library fragments from a solid support. In other examples, other mechanisms are used to cleave library fragments from a solid support.