Engineered Surfaces for Multiplexed DNA and RNA Modification Profiling
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Solution Overview
Problem
Current methods for profiling epitranscriptomic and epigenetic modifications in nucleic acids lack sensitivity, specificity, and are not amenable to multiplexed detection, leading to inconsistent and low-resolution identification of modifications, which hinders understanding of their role in health and disease.
Innovation Solution
Compositions and methods utilizing engineered surfaces with binding domains and adapters that specifically recognize non-canonical features of nucleic acids, enabling high-throughput, sensitive, and accurate profiling of multiple modifications by transferring nucleic acid barcodes for sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If chemical derivatization methods and molecular recognition using antibodies are used for profiling DNA and RNA modifications, then profiling capability is provided, but sensitivity is low and nucleic acid degradation/fragmentation occurs
Solution Approach 1:
The patent introduces engineered surface-bound binding domains as intermediary molecules that capture nucleic acid modifications without requiring chemical derivatization. These binding domains are immobilized on surfaces and serve as mediators between the modification targets and detection systems, enabling direct recognition and enrichment while preserving nucleic acid integrity.
Solution Approach 2:
The patent replaces chemical derivatization methods with engineered protein-DNA/RNA recognition systems. Instead of using chemical reactions to tag modifications, the invention uses specifically engineered binding domains that naturally recognize and bind to modified nucleic acids, substituting chemical mechanisms with biological recognition mechanisms.
2Measurement precision
If existing sequencing methods are used for detecting epitranscriptomic modifications, then detection capability is provided, but sensitivity is low and location resolution is poor
Solution Approach 1:
The patent segments the detection process into distinct functional modules: surface-immobilized binding domains for capture, adapter molecules for bridging, and barcode sequences for identification. This segmentation allows each component to be optimized for its specific function, achieving both high sensitivity and precise location resolution simultaneously.
Solution Approach 2:
The patent adds the dimension of spatial organization by immobilizing binding domains on surfaces, creating a two-dimensional array of capture sites. This surface-based approach enables parallel processing of multiple nucleic acid molecules while maintaining individual molecule integrity, thereby improving both sensitivity and location resolution.
3Adaptability or versatility
If conventional methods are used for analyzing DNA and RNA modifications, then analysis capability is provided, but multiplexed detection is not amenable
Solution Approach 1:
The patent creates universal surface-bound binding domains that can be designed to recognize different nucleic acid modifications through engineered specificity. The same platform architecture can be applied to detect various modifications by simply changing the binding domain sequence, enabling multiplexed detection without increasing overall method complexity.
Solution Approach 2:
The patent uses parameter changes in the binding domain sequences to achieve different specificities for various modifications. By modifying amino acid sequences while maintaining the overall structural framework, the system can detect multiple types of modifications using the same experimental platform, simplifying multiplexed analysis.
4Productivity
If chemical derivatization and antibody-based methods are used, then modification profiling is enabled, but high-throughput capability is limited
Solution Approach 1:
The patent transitions from solution-phase chemistry to surface-based analysis, utilizing two-dimensional surface arrays to enable parallel processing of numerous nucleic acid molecules simultaneously. This surface immobilization approach dramatically increases throughput while maintaining identification accuracy through the specificity of engineered binding domains.
Solution Approach 2:
The patent merges multiple functions into a single surface-immobilized binding domain construct: capture of modified nucleic acids, enrichment of targets, and preparation for sequencing. This consolidation eliminates multiple separate steps required by conventional methods, thereby increasing throughput without compromising precision.
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
Enable simultaneous, high-resolution identification and localization of DNA and RNA modifications, allowing for the determination of their nature, location, and abundance, thereby facilitating the discovery of key regulatory mechanisms in biology and disease.
Implementation Method 1
molecular recognition (typically using antibodies, both for enrichment and detection)
Data Source
AI summary
Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and/or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA/RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for identification and/or localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA/RNA modifications in parallel.