Nucleic Acid Analysis Buffer Decontamination via Thermal and Enzymatic Treatment

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Solution Overview

Problem

Next-generation sequencing technologies face challenges in accurately analyzing clinical samples due to contamination from trace amounts of nucleic acids, which can lead to false positive results and negative clinical outcomes, as these contaminants resemble the target nucleic acids in terms of sequence, concentration, or fragment length.

Innovation Solution

Methods are developed to inactivate or reduce contaminant nucleic acids by heating nucleic acid analysis buffers or exposing them to non-ionizing or ionizing radiation, thereby producing decontaminated buffers that can be used in sequencing assays, ensuring the accuracy and efficiency of nucleic acid analysis.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If next generation sequencing is used to detect trace amounts of nucleic acids, then sensitivity of detection is improved, but false positive results increase due to contaminant nucleic acids

Engineering Contradiction:

Improvedetection sensitivityVSAvoidresult accuracy

Core Design Contradiction:

Measurement precisionVSReliability

Solution Approach 1:

The patent applies preliminary action by treating the buffer and labware with nuclease enzymes before sample processing to pre-eliminate contaminant nucleic acids. This preventive measure removes contaminants before they can interfere with the sequencing assay, allowing high sensitivity detection without false positives from environmental contaminants.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent extracts and removes contaminant nucleic acids from the buffer and labware using nuclease treatment. By selectively degrading and removing environmental DNA and RNA contaminants while preserving the buffer's functional properties, the system maintains detection sensitivity while eliminating the source of false positives.

Inventive Principle:

Principle #2Taking out (Extraction)

2Reliability

If nuclease treatment is applied to remove contaminant nucleic acids, then result accuracy is improved, but buffer functionality may be affected

Engineering Contradiction:

Improveresult accuracyVSAvoidbuffer functionality

Core Design Contradiction:

ReliabilityVSStability of the object's composition

Solution Approach 1:

The patent applies local quality by using nuclease treatment selectively on specific buffer components and labware surfaces where contaminant nucleic acids are most likely to persist, rather than treating the entire buffer system uniformly. This targeted approach removes contaminants from critical areas while preserving the overall buffer composition and functionality needed for sample processing.

Inventive Principle:

Principle #3Local quality

Solution Approach 2:

The patent employs parameter changes by carefully controlling nuclease treatment conditions such as enzyme concentration, treatment time, temperature, and pH to optimize contaminant removal while maintaining buffer functionality. By adjusting these parameters, the system achieves effective decontamination without compromising the buffer's ability to support subsequent sequencing reactions.

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 proposed methods significantly reduce the signal from contaminant nucleic acids, improving the accuracy and efficiency of sequencing assays by minimizing false positives and enhancing the detection of target nucleic acids in clinical samples.

Implementation Method 1

heating a nucleic acid analysis buffer, wherein the heating lasts for a length of time sufficient to inactivate at least a portion of the contaminant nucleic acids

Methodology Applied

Scientific EffectThermal denaturation: Heating

Implementation Method 2

exposing a nucleic acid analysis buffer to non-ionizing radiation or to a nuclease, wherein the exposure to the non-ionizing radiation or to the nuclease lasts for a length of time sufficient to inactivate at least a portion of the contaminant nucleic acids

Methodology Applied

Scientific EffectRadiation damage: Radiation

Implementation Method 3

Methodology Applied

Scientific EffectEnzymatic degradation: Enzyme

Data Source

PatentUS20240309427A1Reduction of signal from contaminant nucleic acids

Publication Date: 2024.09.19 KARIUS INC

AI summary

This disclosure provides methods that are useful for reducing or inactivating contaminant nucleic acids.