RNA-PNA Oligonucleotide Probes for DNA Detection

Resolve Bottlenecks,
Find Innovative SolutionsGenerate Solutions

Solution Overview

Problem

DNA probes fail to provide specific, template-dependent signals in the presence of proteins capable of binding to single-stranded DNA, often producing false signals even without a template.

Innovation Solution

Incorporating at least 20% RNA nucleotides, modified RNA nucleotides, or PNA nucleotides into oligonucleotide probes labeled with a fluorophore and quencher, which resist disruption of the fluorescent signal by proteins binding to single-stranded DNA.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If DNA probes are used for detection, then detection capability is provided, but false signals occur in the presence of proteins capable of binding to single-stranded DNA

Engineering Contradiction:

Improvedetection reliabilityVSAvoidinterference by single-stranded DNA binding proteins

Core Design Contradiction:

ReliabilityVSObject-affected harmful factors

Solution Approach 1:

The patent changes the chemical composition parameter of the oligonucleotide probe by incorporating at least 20% RNA nucleotides, modified RNA nucleotides, and/or PNA nucleotides. This compositional change makes the probe resistant to disruption by single-stranded DNA binding proteins while maintaining target binding capability, thereby resolving the contradiction between detection reliability and protein interference

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The patent creates a composite oligonucleotide probe structure combining different nucleic acid types (DNA, RNA, modified RNA, and/or PNA) in a single molecule. This composite structure leverages the unique properties of each component - particularly the resistance of RNA and PNA to protein binding - to overcome the limitations of pure DNA probes in the presence of interfering proteins

Inventive Principle:

Principle #40Composite materials

2Measurement precision

If DNA probes are used, then template-dependent detection is attempted, but specific signal detection fails when proteins bind to single-stranded DNA

Engineering Contradiction:

Improvetemplate-dependent signal detectionVSAvoidsignal specificity

Core Design Contradiction:

Measurement precisionVSReliability

Solution Approach 1:

By changing the nucleotide composition parameter to include at least 20% RNA, modified RNA, and/or PNA nucleotides, the probe maintains its ability to bind specifically to the target template while becoming resistant to non-specific binding by proteins. This enables reliable template-dependent detection even in the presence of interfering proteins

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

Enables reliable template-dependent detection of DNA amplification even in the presence of proteins that interfere with DNA probes, ensuring specific detection of target nucleic acid sequences.

Implementation Method 1

an oligonucleotide probe comprising a fluorophore, a quencher and a region complementary to the target nucleic acid sequence

Methodology Applied

Scientific EffectFluorescence: Fluorescence

Implementation Method 2

Such probes exhibit a change in quenching activity on binding to a target nucleic acid, allowing for quantitative detection of target

Methodology Applied

Scientific EffectQuenching: Fluorescence

Implementation Method 3

the incorporation of RNA nucleotides, modified RNA nucleotides and/or Peptide Nucleic acid (PNA) nucleotides into the sequence of an oligonucleotide probe labeled with a fluorophore and a quencher provided resistance to disruption of fluorescent signal by proteins capable of binding to single-stranded DNA

Methodology Applied

Scientific EffectResistive binding:

Data Source

PatentUS11008625B2Detection of nucleic acids by strand invasion based amplification

Publication Date: 2021.05.18 AIDIAN OY

AI summary

A method for detecting a target nucleic acid sequence in a sample in the presence of at least protein capable of binding to single-stranded DNA is provided, comprising contacting said sample with at least one oligonucleotide probe comprising a fluorophore, a quencher and a region complementary to said target nucleic acid sequence. The sequence of the oligonucleotide probe comprises at least 20% RNA nucleotides, modified RNA nucleotides and/or PNA nucleotides.