Simple Fluorometer Makes Nucleic Acid Detection Cheap And Easy

Back in the bad old days, dealing with DNA and RNA in a lab setting was often fraught with peril. Detection technologies were limited to radioisotopes and hideous chemicals like ethidium bromide, a cherry-red solution that was a fast track to cancer if accidentally ingested. It took time, patience, and plenty of training to use them, and even then, mistakes were commonplace.

Luckily, things have progressed a lot since then, and fluorescence detection of nucleic acids has become much more common. The trouble is that the instruments needed to quantify these signals are priced out of the range of those who could benefit most from them. That’s why [Will Anderson] et al. came up with DIYNAFLUOR, an open-source nucleic acid fluorometer that can be built on a budget. The chemical principles behind fluorometry are simple — certain fluorescent dyes have the property of emitting much more light when they are bound to DNA or RNA than when they’re unbound, and that light can be measured easily. DIYNAFLUOR uses 3D-printed parts to hold a sample tube in an optical chamber that has a UV LED for excitation of the sample and a TLS2591 digital light sensor to read the emitted light. Optical bandpass filters clean up the excitation and emission spectra, and an Arduino runs the show.

The DIYNAFLUOR team put a lot of effort into making sure their instrument can get into as many hands as possible. First is the low BOM cost of around $40, which alone will open a lot of opportunities. They’ve also concentrated on making assembly as easy as possible, with a solder-optional design and printed parts that assemble with simple fasteners. The obvious target demographic for DIYNAFLUOR is STEM students, but the group also wants to see this used in austere settings such as field research and environmental monitoring. There’s a preprint available that shows results with commercial fluorescence nucleic acid detection kits, as well as detailing homebrew reagents that can be made in even modestly equipped labs.

Open-Source LAMP Instrument Aimed At Clinicians And Biohackers Alike

Over the last few years, we’ve all been given a valuable lesson in both the promise and limitations of advanced molecular biology methods for clinical diagnostics. Polymerase chain reaction (PCR) was held up as the “gold standard” of COVID-19 testing, but the cost, complexity, and need for advanced instrumentation and operators with specialized training made PCR difficult to scale to the levels demanded by a pandemic.

There are other diagnostic methods, of course, some of which don’t have all the baggage of PCR. RT-LAMP, or reverse transcriptase loop-mediated amplification, is one method with a lot of promise, especially when it can be done on a cheap open-source instrument like qLAMP. For about 50€, qLAMP makes amplification and detection of nucleic acids, like the RNA genome of the SARS-CoV-2 virus, a benchtop operation that can be performed by anyone. LAMP is an isothermal process; it can be done at one single temperature, meaning that no bulky thermal cycler is required. Detection is via the fluorescent dye SYTO 9, which layers into the base pairs inside the amplified DNA strands, using a 470-nm LED for excitation and a photodiode with a filter to detect the emission. Heating is provided by a PCB heater and a 3D-printed aluminum block that holds tubes for eight separate reactions. Everything lives in a 3D-printed case, including the ESP32 which takes care of all the housekeeping and data analysis duties.

With the proper test kits, which cost just a couple of bucks each, qLAMP would be useful for diagnosing a wide range of diseases, and under less-than-ideal conditions. It could also be a boon to biohackers, who could use it for their own citizen science efforts. We saw a LAMP setup at the height of the pandemic that used the Mark 1 eyeball as a detector; this one is far more quantitative.

Coronavirus Testing: CRISPR Technology Set To Streamline Viral Testing

If we could run back 2020 to its beginning and get a do-over, chances are pretty good that we’d do a lot of things differently. There’s a ton of blame to go around on COVID-19, but it’s safe to say that one of the biggest failures of this whole episode has been the lack of cheap, quick, accurate testing for SARS-CoV-2, the virus behind the current pandemic. It’s not for lack of information; after all, Chinese scientists published the sequence of the viral genome very early in the pandemic, and researchers the world over did the same for all the information they gleaned from the virus as it rampaged around the planet.

But leveraging that information into usable diagnostics has been anything but a smooth process. Initially, the only method of detecting the virus was with reverse transcriptase-polymerase chain reaction (RT-PCR) tests, a fussy process that requires trained technicians and a well-equipped lab, takes days to weeks to return results, and can only tell if the patient has a current infection. Antibody testing has the potential for a quick and easy, no-lab-required test, but can only be used to see if a patient has had an infection at some time in the past.

What’s needed as the COVID-19 crisis continues is a test with the specificity and sensitivity of PCR combined with the rapidity and simplicity of an antibody test. That’s where a new assay, based on the latest in molecular biology methods and dubbed “STOPCovid” comes in, and it could play a major role in diagnostics now and in the future.

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Gertrude Elion, DNA Hacker

Some people become scientists because they have an insatiable sense of curiosity. For others, the interest is born of tragedy—they lose a loved one to disease and are driven to find a cure. In the case of Gertrude Elion, both are true. Gertrude was a brilliant and curious student who could have done anything given her aptitude. But when she lost her grandfather to cancer, her path became clear.

As a biochemist and pharmacologist for what is now GlaxoSmithKline, Gertrude and Dr. George Hitchings created many different types of drugs by synthesizing natural nucleic compounds in order to bait pathogens and kill them. Their unorthodox, designer drug method led them to create the first successful anti-cancer drugs and won them a Nobel Prize in 1988.

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