Hi everyone,
My name is Ruan Oliveira, and I am currently pursuing a Master’s degree in Engineering Physics. I am exploring the expansion of open-source microscopy platforms for advanced optical and biochemical sensing applications.
I am highly impressed by the modularity of the OpenFlexure project, and I would love to open a discussion here to see if anyone has prior experience imaging Quantum Dots (QDs) on the platform, or if there are community members interested in collaborating on a proof-of-concept for low-cost DNA sequencing.
The Core Concept: QDs & Pyrophosphate Detection
The exploratory idea is to evaluate whether the OpenFlexure microscope can be utilized to monitor the amplification or sequencing of small DNA fragments. To complement the standard OpenFlexure setup, alternative and auxiliary tools—such as smartphone-based imaging or modest CMOS camera modules—could also be integrated into the system for enhanced flexibility.
The strategy relies on a known biochemical mechanism: during nucleotide incorporation by DNA polymerase, pyrophosphate (PPi) is released. This PPi chelates and sequesters specific metal ions (which act as fluorescence quenchers on the QDs), thereby restoring or significantly enhancing the Quantum Dot fluorescence.
By slowing down or diluting the system, we want to investigate if we can isolate individual molecules/probes and optically detect these fluorescence shifts using this open-source setup.
Reference Papers
To ground this discussion, here are the core concepts and applications regarding smartphone/modular QD imaging and the PPi-mediated fluorescence enhancement:
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Smartphone-based QD sensing:
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Pyrophosphate-mediated QD fluorescence enhancement:
Where We Can Collaborate
Quantum Dots are promising due to their high brightness compared to traditional biological fluorophores, which makes them an excellent fit for the modest sensors typically used in open-source setups. However, looking at the current fluorescence documentation and hardware modules, there are a few bottlenecks and engineering challenges we could address together:
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Overcoming Filter Switching Limitations: The current fluorescence setups for OpenFlexure can make swapping between different dichroic filters manually intensive. Since this proposed biochemistry targets specific QD wavelengths, we could either:
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Design the assay to run on a single, static dichroic filter setup to bypass this issue, OR
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Collaborate with hardware developers to design a modular, easily adaptable filter switcher for the standard microscope geometry.
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Optics Module Optimization: The goal would be to build upon the standard high-resolution microscope (given its robust inverted geometry and support) and optimize a customized epifluorescence optics module tailored for QD excitation/emission profiles.
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Microfluidics Integration: Designing or adapting low-cost microfluidic modules to couple with the OpenFlexure stage to manage the dynamic flow of DNA polymerase, nucleotides, and quenching ions.
If you have experience tracking Quantum Dots, or if you are a hardware designer, microfluidics enthusiast, or biochemist intrigued by the prospect of open-source molecular diagnostics, I would love to hear your thoughts and brainstorm potential implementations!
Looking forward to a great discussion,
Best regards,
Ruan Oliveira