Flow Cell Aptamer Clusters for Rapid Functional Selection
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Solution Overview
Problem
The selection of aptamers capable of binding to specific targets and mediating desirable functional effects is poorly understood, and existing methods are inefficient for rapid and convenient identification, limiting their therapeutic potential.
Innovation Solution
The use of flow cells with immobilized aptamer clusters and target molecules or cells, combined with detectable labels, to identify aptamers that bind or modulate cellular properties through sequencing and fluorescence detection, allowing for the identification of functional aptamers in an Illumina sequencing instrument.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional aptamer selection methods are used, then aptamers can be selected from random pools, but the process is time-consuming and inefficient for rapid identification
Solution Approach 1:
The patent segments the aptamer library into individual clusters immobilized at specific locations on a flow cell surface. Each cluster contains aptamers with known sequences, allowing parallel screening of multiple clusters simultaneously. This segmentation enables rapid identification of functional aptamers by associating binding events with specific cluster locations, dramatically increasing throughput compared to traditional sequential selection methods.
Solution Approach 2:
The patent uses sequencing technology to create digital copies of aptamer sequence information associated with each spatial location on the flow cell. By combining physical immobilization with digital sequencing data, the system can rapidly identify which sequences correspond to functional clusters without time-consuming iterative wet-lab selection cycles.
2Measurement precision
If aptamers are screened in solution, then binding can be detected, but it is difficult to associate binding activity with specific aptamer sequences
Solution Approach 1:
The patent performs preliminary immobilization of aptamer clusters at known spatial locations on the flow cell before conducting binding assays. This preliminary spatial organization ensures that when binding occurs, the sequence information is already associated with a specific location, eliminating the need for subsequent separation and identification steps. The sequence-function relationship is preserved from the outset.
Solution Approach 2:
The patent replaces traditional mechanical separation and identification methods with optical detection and sequencing technologies. Fluorescent labels and sequencing instruments automatically detect and record which immobilized clusters bind target molecules, providing precise sequence-function associations without manual intervention or loss of sequence information.
3Adaptability or versatility
If large aptamer libraries are screened, then functional diversity can be assessed, but the complexity of the screening system increases
Solution Approach 1:
The patent creates a universal flow cell platform that can screen diverse aptamer libraries using the same immobilization and detection methodology. The system accommodates different library types, target molecules, and detection modalities through a single integrated platform, reducing the need for multiple specialized systems while maintaining the ability to assess functional diversity across large libraries.
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 the rapid and efficient identification of aptamers that bind to or modulate target cells or molecules, facilitating the development of aptamer therapeutics by associating aptamer sequences with their functional effects on a surface, thereby enhancing the understanding and application of aptamer structures and functions.
Implementation Method 1
aptamers are short, single-stranded nucleic acid oligomers that can bind to a specific target molecule
Implementation Method 2
detectable indicator of cellular function (e.g., a fluorescent indicator of apoptosis, cell proliferation, gene or protein expression)
Data Source
AI summary
The present disclosure describes compositions and methods for rapid selection of both binding and functional oligonucleotides (DNA, RNA, or any natural or synthetic analog of these). In certain embodiments, provided herein are flow cells (e.g., flow cells for an Illumina sequencing instrument or a Polonator sequencing instrument) comprising within its flow chamber a plurality of immobilized aptamer clusters (e.g., from an aptamer library described herein) and, optionally, one or more target cells (e.g., cancer cells, immune cells, etc.) and/or a detectable indicator of cellular function (e.g., a fluorescent indicator of apoptosis, cell proliferation, gene or protein expression, etc.). In certain embodiments, provided herein are methods of using such an aptamer cluster-containing flow cell to identify functional aptamers from an aptamer library (e.g., in a sequencing instrument, such as an Illumina sequencing instrument).