Microscope-free imaging with DNA barcoded probes
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Solution Overview
Problem
Current microscopy techniques face challenges in simultaneously imaging relevant molecules of complex molecular systems at single molecule resolution, particularly with high-throughput and multiplexing analyses, and are often destructive, preventing repeat sampling to elucidate molecular networks.
Innovation Solution
The development of microscope-free imaging (MFI) methods using nucleic acid barcoded probes that form hairpin structures, allowing for high spatial resolution, multiplexing capabilities, and high-throughput analyses without the need for microscopes, enabling in situ access to molecular targets in their native states.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If microscope techniques are used to image molecular targets, then spatial resolution can be achieved, but the analysis throughput is limited and multiplexing capabilities are reduced
Solution Approach 1:
The patent uses DNA barcodes as information carriers that can be copied and amplified through PCR. Each molecular target is labeled with a unique DNA barcode, allowing millions of targets to be imaged simultaneously through high-throughput sequencing, thereby achieving both high spatial resolution and high analysis throughput without the limitations of traditional microscopy
Solution Approach 2:
The patent replaces the mechanical/optical imaging system (microscope) with a chemical/biological information encoding system (DNA barcodes). Instead of using optical lenses to resolve individual molecules, the system uses DNA sequence information to identify and locate molecular targets, enabling massively parallel analysis that overcomes the throughput limitations of microscopy
2Loss of information
If destructive techniques such as co-immuno-precipitation are used to resolve molecular interactions, then interaction data can be obtained, but repeat sampling is prevented
Solution Approach 1:
The patent creates DNA records that copy the spatial and interaction information of molecular targets without destroying the original molecules. The DNA barcodes are amplified through PCR to generate sufficient copies for sequencing, allowing the original sample to remain intact for repeated sampling and dynamic analysis of molecular networks
Solution Approach 2:
The patent introduces DNA barcodes as intermediary information carriers that mediate between molecular targets and detection systems. These barcodes encode interaction data without requiring physical manipulation or destruction of the target molecules, enabling non-destructive imaging and repeat sampling
3Measurement precision
If traditional imaging approaches are used, then molecular targets can be visualized, but access to molecular targets in their native states is limited
Solution Approach 1:
The patent replaces invasive imaging techniques with a molecular tagging approach using DNA barcodes that can be attached to targets in their native cellular environment. This allows visualization and analysis of molecular targets in situ without requiring extraction, fixation, or other processing that would alter their native state
Solution Approach 2:
The patent develops a universal DNA barcode system that can be applied to diverse molecular targets (proteins, nucleic acids, metabolites) while maintaining their native states. The same basic methodology can be adapted to different target types and biological contexts, providing versatile in situ access to molecular networks
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
MFI provides ultra-high resolution imaging of molecular structures and dynamics, enabling precise computational production of images and analysis of molecular interactions, connectivity, and state distribution within individual networks without damaging sample processing.
Implementation Method 1
a second nucleic acid strand comprising a second palindromic sequence that is complementary to and binds to the first palindromic sequence
Implementation Method 2
a synthetic non-DNA linker that terminates polymerization is located between the double-stranded palindromic region and the loop region
Data Source
AI summary
Provided herein, in some aspects, are methods of imaging molecules without a microscope or other specialized equipment, referred to herein as “microscope-free imaging (MFI).” Herein, “molecular instruments” (e.g., DNA-based and protein-based molecules) are used, instead of microscopes, in a “bottom-up” approach for inspecting molecular targets.