Mass Spectrometry Profiling of Modified Nucleic Acids
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Solution Overview
Problem
Current methods lack high-throughput approaches for detecting and tracking levels of DNA and RNA post-transcriptional modifications, which hampers the elucidation of their biological functions due to the inability to identify and profile patterns of modified nucleic acid structures associated with specific medical conditions.
Innovation Solution
The use of high-throughput methods involving direct infusion electrospray ionization mass spectrometry (ESI-MS), multistep tandem mass spectrometry (MSn), consecutive reaction monitoring (CRM), ion mobility spectrometry mass spectrometry (IMS-MS), and high-resolution MS for genome-wide profiling of DNA and RNA nucleotides/nucleosides, enabling the identification of specific profiles of variant nucleic acid structures associated with medical conditions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If targeted analytical approaches (bisulfite chemistry, restriction enzymes) are used to identify specific nucleic acid modifications, then detection accuracy for individual modifications is improved, but high-throughput capability and ability to profile multiple modifications simultaneously deteriorates
Solution Approach 1:
The patent employs mass spectrometry as a universal analytical platform that can detect and quantify multiple types of nucleic acid modifications (methylation, hydroxymethylation, formylation, etc.) simultaneously through a single high-throughput workflow, eliminating the need for separate targeted approaches for each modification type while maintaining detection accuracy
Solution Approach 2:
The patent utilizes mass-to-charge ratio (m/z) as a distinguishing parameter to differentiate between various modified nucleic acid structures. By measuring precise mass differences caused by different chemical modifications, the system achieves both high detection accuracy and high-throughput capability across multiple modification types in parallel
2Ease of operation
If conventional analytical methods are used for nucleic acid modification detection, then method simplicity is maintained, but diagnostic accuracy and ability to identify disease-associated modification patterns deteriorates
Solution Approach 1:
The patent replaces complex multi-step chemical workflows (bisulfite conversion, restriction enzyme digestion) with a streamlined mass spectrometry-based approach that directly measures mass-to-charge ratios of nucleic acid modifications, simplifying the operational process while dramatically improving diagnostic accuracy through precise mass-based identification of disease-associated modification patterns
Solution Approach 2:
The patent creates comprehensive modification profiles by measuring and recording the mass spectral signatures of multiple nucleic acid modifications simultaneously, generating detailed diagnostic fingerprints that capture complex disease-associated patterns without requiring separate analytical steps for each modification
3Quantity of substance
If genome-wide profiling of all nucleic acid modifications is attempted, then comprehensive coverage is improved, but analytical complexity and data interpretation difficulty worsens
Solution Approach 1:
The patent segments the complex problem of genome-wide modification profiling into manageable components by measuring individual nucleoside modifications (m1A, m6A, m5C, etc.) as distinct mass spectral features. Each modification type is identified and quantified separately based on its unique mass-to-charge ratio, allowing comprehensive coverage while maintaining analytical tractability through systematic categorization
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
These methods provide accurate and comprehensive profiles of modified nucleic acid structures, enhancing diagnostic accuracy by linking patterns of chemical modifications to specific cellular states, thereby improving the identification of medical conditions such as cancer and infections.
Implementation Method 1
direct infusion electrospray ionization mass spectrometry (ESI-MS)
Implementation Method 2
mass spectrometer by determining molecular masses
Implementation Method 3
ion mobility spectrometry mass spectrometry (IMS-MS)
Data Source
AI summary
The present invention relates to high-throughput methods comprising direct infusion electrospray ionization mass spectrometry (ESI-MS), multistep tandem mass spectrometry (MSn), consecutive reaction monitoring (CRM), ion mobility spectrometry mass spectrometry (IMS-MS), high-resolution MS, and IMS-MS, for genome-wide (whole cell or tissue) profiling of DNA and RNA nucleotides/nucleosides having a wide variety of variant structural modifications. In particular, these methods are contemplated for providing a specific profile of variant DNA and/or RNA chemically modified nucleic acids (i.e. structures) associated with specific medical conditions. Medical conditions may include, but are not limited to: cancer; including prostate, lung, uterus, larynx, ovary, breast, kidney, and many other types of cancers; specific stages of cancer; bacterial infections; viral infections; genetic and metabolic disorders; and any condition involving changes in DNA and/or RNA structural modifications.