Spatial Nucleic Acid Capture With Surface Barcodes and Low-Noise Coating
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing methods fail to provide spatially resolved data on nucleic acid distribution within biological samples, lacking information on the position of single cells within a tissue sample, and require inefficient assembly and sequencing techniques.
Innovation Solution
A method involving a low non-specific binding coating with hydrophilic polymers and immobilized surface capture primers is used to capture and sequence nucleic acids, preserving spatial location information through a series of reactions including reverse transcription, circularization, and rolling circle amplification to generate spatially resolved nucleic acid concatemers.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional spatial analysis methods are used to determine nucleic acid sequences and spatial barcodes, then spatial location information can be identified, but the assembly time and computational requirements increase significantly
Solution Approach 1:
The patent incorporates spatial barcode sequences directly into the nucleic acid molecules during the initial capture step on the solid support. The surface capture primers are designed with integrated spatial barcode regions, so that when nucleic acids are captured and amplified in situ, the spatial location information is already encoded in the molecule itself before sequencing begins. This eliminates the need for post-sequencing assembly and computational reconstruction of spatial information.
Solution Approach 2:
The patent combines the nucleic acid sequence information and spatial barcode information into a single integrated molecular structure. The surface capture primers contain both the sequence-specific binding region and the spatial barcode region as one unified construct. During amplification and sequencing, both types of information are obtained simultaneously from the same sequencing read, eliminating the need for separate assembly processes.
2Measurement precision
If traditional spatial analysis methods are used to determine nucleic acid sequences and spatial barcodes, then spatial location information can be identified, but computational requirements increase significantly
Solution Approach 1:
The spatial barcode information is pre-encoded into the nucleic acid molecules during the capture and amplification steps on the solid support. The molecular structure itself contains the spatial location data in the form of integrated spatial barcode sequences, eliminating the need for complex computational assembly and reconstruction algorithms to determine spatial positions.
Solution Approach 2:
The patent creates physical copies of the spatial barcode information directly within the amplified nucleic acid molecules. Each amplified molecule contains an embedded copy of the spatial barcode sequence that corresponds to its location on the solid support. This physical encoding eliminates the need for computational inference or assembly to recover spatial information.
3Ease of manufacture
If standard solid support surfaces are used for nucleic acid capture, then simplicity is maintained, but non-specific binding increases and capture efficiency decreases
Solution Approach 1:
The patent modifies the surface properties of the solid support by coating it with hydrophilic polymers such as polyethylene glycol (PEG) or polyvinyl alcohol (PVA). This changes the surface energy and wettability parameters, creating a low non-specific binding surface that still allows specific hybridization of capture primers to their target nucleic acids. The coating density and molecular weight of the polymer are optimized to balance non-specific binding reduction with specific capture efficiency.
Solution Approach 2:
The patent uses composite surface structures combining the solid support substrate with a hydrophilic polymer coating layer. This composite material structure provides both the mechanical stability of the solid support and the low non-specific binding properties of the hydrophilic polymer. The capture primers are covalently attached to the polymer-coated surface, creating a multi-layer composite structure that enhances specific binding while reducing non-specific interactions.
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 method enables efficient spatially resolved capture and sequencing of nucleic acids, providing detailed spatial information on nucleic acid distribution within biological samples with reduced computational and assembly requirements.
Implementation Method 1
a low non-specific binding coating comprising at least one hydrophilic polymer
Implementation Method 2
hybridizing individual RNA molecules to individual immobilized surface capture primers to generate a plurality of capture primer-RNA duplexes
Implementation Method 3
conducting a reverse transcription reaction on the coated support under a condition suitable for extending the 3′ end of the immobilized surface capture primers and using the hybridized RNA as a template strand
Implementation Method 4
conducting a rolling circle amplification reaction using the terminal 3′ end of the immobilized full length first strand cDNA as an initiation site and the covalently closed circular molecule as a template strand, thereby generating a plurality of immobilized nucleic acid concatemers
Data Source
AI summary
The present disclosure provides compositions, apparatuses and methods for capturing on a support nucleic acids from cellular samples, preparing library molecules on the support, amplifying the library molecules on the support to generate nucleic acid template molecules, and analyzing the immobilized nucleic acid template molecules including detecting and/or sequencing the immobilized nucleic acid template molecules. The immobilized nucleic acid template molecules correspond to the nucleic acids from the cellular samples. The immobilized nucleic acid template molecules are spatially located on the support at positions that correspond to the spatial location of the nucleic acids from the cellular sample.