Jettison-MS Nucleobase Detection Without Digestion or Adduct Bias

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Solution Overview

Problem

Current methods for detecting modified nucleobases in nucleic acids, such as DNA and RNA, face challenges including nucleobase loss during Matrix-Assisted Laser Desorption/Ionization Mass-Spectrometry (MALDI-MS), limited sensitivity, and the inability to detect both polar and nonpolar DNA adducts in a single procedure, which hinders accurate analysis of DNA and RNA modifications.

Innovation Solution

The Jettison-MS method employs a combination of a high-energy-transfer matrix, Brønsted acidic proton sources, and controlled laser fluence to directly analyze nucleic acid samples by MALDI-MS, allowing for the ultrasensitive detection of both modified and canonical nucleobases without enzymatic digestion or extensive sample preparation, enabling rapid and simultaneous detection of diverse modifications.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If MALDI-MS is used to analyze nucleic acid species, then rapid analysis is achieved, but nucleobase loss occurs due to labile N-glycosidic bonds

Engineering Contradiction:

Improveanalysis speedVSAvoidnucleobase loss

Core Design Contradiction:

ProductivityVSLoss of substance

Solution Approach 1:

The patent changes the chemical parameters of the matrix by incorporating Brønsted acidic proton sources, which modify the ionization mechanism to reduce nucleobase loss while maintaining rapid analysis capabilities

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The Brønsted acidic proton source acts as an intermediary that facilitates proton transfer during ionization, protecting the N-glycosidic bond from cleavage while enabling efficient ion formation for detection

Inventive Principle:

Principle #24Intermediary (Mediator)

2Measurement precision

If liquid chromatography electrospray MS is used for modified nucleobase analysis, then ultrasensitive detection is achieved, but two or more days of work are required for digestion and analysis

Engineering Contradiction:

Improvedetection sensitivityVSAvoidsample preparation time

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent extracts the enzymatic digestion step from the analysis workflow, using direct MALDI-MS ionization to achieve ultrasensitive detection without the time-consuming digestion and chromatography steps

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent replaces the mechanical/enzymatic digestion process with a direct laser-based ionization process, substituting a time-intensive multi-step procedure with a rapid single-step analysis

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

3Productivity

If conventional MALDI-MS is used for DNA adduct detection, then rapid analysis is achieved, but both polar and nonpolar adducts cannot be detected in a single procedure

Engineering Contradiction:

Improveanalysis throughputVSAvoiddetection range

Core Design Contradiction:

ProductivityVSAdaptability or versatility

Solution Approach 1:

The patent creates a universal matrix system with Brønsted acidic proton sources that can detect both polar and nonpolar DNA adducts through a single ionization mechanism, enabling multi-functional detection capability

Inventive Principle:

Principle #6Universality (Multi-functionality)

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

This approach significantly reduces sample preparation time, achieves high throughput, and detects both polar and nonpolar DNA adducts in a single procedure, providing ultrasensitive and accurate analysis of nucleic acid modifications, including DNA adducts and RNA modifications, with improved sensitivity and specificity compared to existing techniques.

Implementation Method 1

subjecting the sample to at least one laser pulse, wherein the laser fluence is about 70% to about 95% of the matrix storm level

Methodology Applied

Scientific EffectPhotoionisation: Photoionisation

Implementation Method 2

subjecting the sample to at least one laser pulse, wherein the laser fluence is about 70% to about 95% of the matrix storm level

Methodology Applied

Scientific EffectLaser ablation: Laser Ablation

Implementation Method 3

a matrix, wherein the matrix comprises at least one Brønsted acidic proton source

Methodology Applied

Scientific EffectLaser heating: Heating

Implementation Method 4

a matrix, wherein the matrix comprises at least one Brønsted acidic proton source

Methodology Applied

Scientific EffectThermal energy transfer: Conduction (thermal)

Data Source

PatentUS11866779B2Jettison-MS for nucleic acid species

Publication Date: 2024.01.09 NORTHEASTERN UNIV (US)

AI summary

MALDI-MS operated slightly under matrix storm conditions with a high-energy-transfer, acidic matrix, or these conditions with a high sample to matrix ratio, can with ultrasensitivity detect a nucleobase, modified or canonical, of a nucleic acid species as a jettisoned, protonated molecule.