Polyphenolic Compound Detection Solution for Nucleic Acid Protection

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Solution Overview

Problem

Fluorescent signal intensity loss during nucleic acid detection processes, such as sequencing by synthesis, due to light-induced degradation of nucleic acids, which limits the ability to sequence long nucleotide sequences and increases error rates in nucleic acid detection platforms.

Innovation Solution

Incorporating a polyphenolic compound, such as gallic acid, into the detection solution to inhibit light-induced degradation of nucleic acids during irradiation, thereby reducing oxidative damage and maintaining fluorescence signal integrity across multiple cycles.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If intense electromagnetic radiation is used for fluorescence detection, then detection sensitivity is improved, but nucleic acid degradation increases

Engineering Contradiction:

Improvedetection sensitivityVSAvoidnucleic acid degradation

Core Design Contradiction:

Measurement precisionVSObject-affected harmful factors

Solution Approach 1:

A polyphenolic compound is introduced as an intermediary substance in the detection solution that absorbs harmful high-energy radiation and reactive oxygen species generated during fluorescence detection, thereby protecting nucleic acids from degradation while allowing sensitive detection to proceed

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The polyphenolic compound converts harmful effects (reactive oxygen species and high-energy radiation that would otherwise damage nucleic acids) into beneficial protection by using these same mechanisms to quench harmful reactions and maintain nucleic acid integrity during repeated detection cycles

Inventive Principle:

Principle #22Blessing in disguise (Convert harm into benefit)

2Productivity

If multiple irradiation cycles are performed for iterative detection, then sequencing capability is improved, but fluorescence signal intensity is lost

Engineering Contradiction:

Improvesequencing capabilityVSAvoidfluorescence signal intensity

Core Design Contradiction:

ProductivityVSLoss of energy

Solution Approach 1:

The polyphenolic compound is added beforehand to the detection solution to cushion against cumulative damage from multiple irradiation cycles, preventing signal intensity loss and maintaining detection quality throughout extended sequencing runs

Inventive Principle:

Principle #11Beforehand cushioning (Prior cushioning)

3Length of moving object

If repeated irradiation steps are used for long sequence detection, then sequencing length is extended, but error rate increases

Engineering Contradiction:

Improvesequencing lengthVSAvoiderror rate

Core Design Contradiction:

Length of moving objectVSReliability

Solution Approach 1:

The polyphenolic compound acts as a protective intermediary that reduces photodamage and maintains nucleic acid integrity throughout repeated irradiation cycles, thereby extending reliable sequencing length while minimizing error accumulation

Inventive Principle:

Principle #24Intermediary (Mediator)

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 use of polyphenolic compounds in the detection solution significantly reduces light-induced degradation, leading to lower error rates and extended sequencing capabilities, enabling the accurate detection of long nucleotide sequences and maintaining fluorescence signal strength over multiple cycles.

Implementation Method 1

Under conditions in which intense EM radiation is being absorbed by the fluorophore, such as in laser-induced fluorescence (LIF), it is possible for a molecule to absorb two photons

Methodology Applied

Scientific EffectAbsorption (EM radiation): Absorption (EM radiation)

Implementation Method 2

Fluorescence emission normally occurs with the emission of light of a longer wavelength (lower energy), than the original irradiating source

Methodology Applied

Scientific EffectFluorescence: Fluorescence

Implementation Method 3

reactive singlet oxygen can be generated by fluorescence quenching of an excited state fluorophore by triplet oxygen

Methodology Applied

Scientific EffectFluorescence quenching:

Implementation Method 4

exposure of whole cells to ultraviolet (UV) radiation can cause DNA damage via the direct photochemical [2+2] photocycloaddition reaction of thymine or cytosine to provide cyclobutane pyrimidine dimers

Methodology Applied

Scientific EffectPhotocycloaddition reaction:

Implementation Method 5

In the UV A region through a portion of the visible region, spanning from about 315 nm to about 500 nm, a complex mixture of indirect mechanisms can also cause DNA damage through photosensitization of other cellular components

Methodology Applied

Scientific EffectPhotosensitization:

Data Source

PatentUS10106851B2Method for nucleotide detection

Publication Date: 2018.10.23 ILLUMINA INC

AI summary

A method of inhibiting light-induced degradation of nucleic acids includes irradiating a portion of the nucleic acids in the presence of a detection solution comprising a polyphenolic compound. A method of detecting a nucleic acid having a fluorescent tag includes irradiating at least a portion of the nucleic acid with light of a suitable wavelength to induce a fluorescence emission and detecting the fluorescence emission. Optionally, the polyphenolic compound is gallic acid, a lower alkyl ester thereof, or mixtures thereof. A kit includes one or more nucleotides, an enzyme capable of catalyzing incorporation of the nucleotides into a nucleic acid strand and a polyphenolic compound suitable for preparing a detection solution.