Author Archives: Peter

qPCR and graphene for aptamer selection

We’ve been selecting aptamers in the lab for the last year. Having a qPCR on the bench has really helped, and so we wrote up a methods paper in ACS Combinatorial Science. The company that made our qPCR instrument has put up a blurb about it, too.

The qPCR function is great for cycle course optimization, and we have been using the melt curve analysis function of the Open qPCR (thermofluorimetry) to do a binding assay. It works pretty well. We put a dye in with the aptamer and measure the temperature at which the dye dye-DNA complex melts. The bound aptamer has a different melt temperature, so it gives a specific signal. We plot that specific signal as a function of concentration and to determine the binding constant. It’s based on the Easley lab’s method paper from 2015 with low-cost equipment.

The instrument simplifies some of the more touchy parts of the aptamer selection. Undergrads have been turning rounds pretty efficiently this year with the help of the open qPCR instrument.

We have also been using graphene oxide to try some selections. I have only heard of graphene oxide SELEX recently, but it grabs unstructured DNA to separate them from aptamers bound to target. It’s looking good. I hope to report on that soon.

 

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Thank you to Crowdfunding Supporters

Thank you to all of the kind supporters who helped raise money for undergraduate research in iron batteries here at the U of Idaho. Together we put together $5000 that will be put toward a fellowship and materials for a student to explore this and we will put together a open source plans document next year. We’re also going to document the process with a weekly video about the project, so please do stay tuned.

Crowdfunding the iron age of batteries

I’ve launched a crowdfunding campaign to try to support a student in building an iron battery. I’ve got video up that talks about where we’ve been so far this year. We have had some success in building the battery and we’re moving to a better construction method.

We would like to test different cathode salts including a better test of potassium ferricyanide. We would also like to test different solvents such as a deep eutectic solvent and ionic liquid. The big, open question is the separator. We can try some natural gels, some in-house polymers and we can see if we can find a commercial polymer that is cheap and available enough to do the job.

I think it will be a great project for an undergraduate chemist with an interest in renewable energy. If you’d like to check out or share the campaign, the link is here:

http://c-fund.us/cg0

crystals of potasium phoaphate incorporating the chemical amaranth dye

Amaranth Potassium Phosphate Crystals

Potassium phosphate crystal chemistry

This weekend I grew some potassium phosphate crystals with amaranth dye. I did this back in 2001 in Bart Kahr’s O-Chem class and remembered it recently. It’s a fun demonstration of the chemistry of crystal growth, the different chemistry of the crystal faces, and it’s pretty. I found Prof. Kahr’s paper[1] that gives a “foolproof recipe” and it did not disappoint. Even this fool could make it work.

As the crystals grow, each face of the crystal has a unique topology. The corners are growing with a different spacing of atoms than the faces, and the faces can be different from each other. Sometimes, the faces have the right spacing to allow a dye molecule to stick. In this case, there is a big difference between how well amaranth dye sticks to each face. So as the crystal rows, it only gets dyed in two quadrants.

We can learn about chemistry from crystals

Crystals are super useful to chemists. A good crystal of a chemical can be used to get x-ray diffraction data on the structure of the chemical. The most detailed structures are derived from x-ray diffraction data.

Knowing how molecules assemble into crystals is also really important to materials scientists. If you want to design a material from its atoms, you need to know how they are going to come together. I’ve been working on making an iron battery and reading up on battery chemistry. One of the interesting papers I read talked about designing a cathode material to hold sodium atoms. The chemists designed the “holes” in the structure to hold sodium atoms – and they needed to know how the other atoms would come together to make that shape.

Why chemically dyed crystals are cool

Of course, dyed crystals just look cool. Maybe that’s silly, but if you’re trying to teach organic chemistry, it’s good to have something visual and striking to hold on to. A lot of O-chem is solvents and white powder, so anything that sticks in the memory is a help.

The other reason I think that dyed crystals are so cool is that they dyes can be held still very precisely. One of prof. Kahr’s later papers used a crystal to hold a fluorescent dye in place at a specific orientation. Then they used a fluorescence microscope to look at single dye molecules[2]. I think that’s just really cool. I gather that they are more stable in the crystal than they are in solution.

I also made a time-lapse movie of the crystallization

Instructions (following [1])

  • Dissolve 17 g potassium dihydrogen phosphate (KDP) in 50 ml water with heating. Using a teflon stir bar helps.
  • Dissolve 4 mg amaranth dye in ~1ml of water and add to the mix.
  • Pour into a wide dish and allow to cool and evaporate slowly over ~4-24 hours.

Sources

1.Kahr, B. & Vasquez, L. Painting crystals. CrystEngComm 4, 514–516 (2002). http://dx.doi.org/10.1039/B204845K

2.Wustholz, K. L., Kahr, B. & Reid, P. J. Single-Molecule Orientations in Dyed Salt Crystals. J. Phys. Chem. B 109, 16357–16362 (2005).http://dx.doi.org/10.1021/jp053051x

NORM 2017 Corvallis

I’m attending The Northwest Regional Meeting of the American Chemical Society in Corvallis. I just wandered around downtown. That was nice. My hope is to see some computational chemistry, commercialization, and nanoparticles tomorrow.

What tools are getting used for simulations? I’m especially interested in coarse-grained simulations of macromolecules. I see several Density Functional Theory talks and that should be interesting. Maybe folks from that world can point me in the right direction. Is anyone using tensorflow for such things?

There’s a panel on market-driven innovations. I would love to hear if people are funding academic labs through collaborations with industry. I feel like that would be a win-win, but I don’t know where to start there, either.

There’s also a bunch of analytical chemists giving MS talks and a “smart” nanoparticle talk. That’s just the morning session. I’ll have a hard time choosing.

If you’re in Corvallis and are reading this, do please shoot me a gmail (pballen). I’ll buy the first round at Tommy’s.