Strawberry DNA Isolation

To officially christen the blog I've decided I'd do a DNA isolation. As I don't have access to any of the reagents we use in the lab I decided to find an at-home procedure online. I found this youtube video (below) and followed their procedure.



Overall it worked really well. I made two modifications:

1. I used a fork to pull out the strawberries chunks before I poured the cell mixture into the coffee filter. This prevented the coffee filter from getting clogged and made it easer to hold the filter with one hand.

2. I put the rubbing alcohol in the freezer before adding it to the cell mixture.

So how does this procedure differ from DNA isolation in a lab? And what is actually happening?

The Lysis

Below I compare the chemicals used in at Home DNA isolations to a Lab DNA isolation and their purpose.

Purpose Home Lab
Dissolves Cell Membrane Soap Triton X-100

Binds to DNA Table Salt NaCl2

Polar Buffer Water Tris-Cl

Denatures Proteins SDS

Removes Mg2 (PCR prep) EDTA

In a laboratory the next step would be adding phenol:clorophorm which destroys enzymes that digest DNA (DNAase).

After adding the phenol:chloroform the DNA is then spun in a centrifuge. This like the coffee filter separates all the cell chunks and debris from the DNA. It essentially creates two layers the bottom contains all the cell junk and the top contains your DNA. The top layer is then put into another tube and alcohol usually ethanol is added to precipitate the DNA.

The Precipitation

The video didn't explain well what is happening here, so I will. DNA is a negatively charged polar molecule. In liquids NaCL2 separates into Na+ and Cl- via a process called ionization. The negative charge on the DNA attracts the Na+ when this happens the DNA clumps. Now ethanol is relatively non-polar meaning it doesn't carry a charge. When added to the solution it forces the DNA to the surface. The same principle causes the oil to separate from vinegar when making Italian dressing.

Try this at home with your kids.

Cheers!

The Beginning and My Graduation Gift

In the beginning..... For the first time in 4 years I can call myself a free man, just graduated from University of Maryland. Well I'm free at least untill I start a job next year.

I've always had a few ideas on different research I wanted to conduct and until now I've been waiting till I get my own lab space. Well that was until a few weeks ago when I found myself was reading an article on biohacking and the biopunk movement. After spending the last few years using expensive reagents and equipment, I was surprised to learn what some biopunks were achieving at home. Combine my new found inspiration with a kid who loves genetics and has a insatiable curiosity that lead him to take many things apart only to reassemble them I instantly wanted to join.

My new found interest had me ordering the book Biopunk: Kitchen-Counter Scientists Hack the Software of Life, thankfully it came after finals. After reading a few chapters I became acquainted with some names in the movement specifically Meredith L. Patterson. She's an at home scientist who blogs about her effort to engineer a bacteria that would sense if melamine had been added to milk. After reading her post for biohacking I learned about some other players in the biopunk world Josh Perfetto and Tito Jankowski who have created an open source PCR machine that is portable and relatively cheaper than models currently on the market. After reading this was possible, I wanted to do the same.

After a few hours of reading their site I realized that none of the files were online yet! So I did a quick google search stumbling upon Cathal Garvey and James Peyer two another biohackers who are building PCR machines. Cathal started to build his own PCR machine but stopped after hearing about Josh and Tito's OpenPCR. James's PCR machine seems to have a neat design but other than the pics I can't find anymore information (aka schematics). He does have a video where he talks about the design. So where does this leave me?

Buying a PCR maching off ebay to start with.


The PowerBlock System. The company, Ericomp went under in 2000, probably not a good sign. There is however a repair available kinda pricey but I'll keep it in mind. I'll probably find myself bombarding them with questions but it's all a learning experience right? The PCR machine cost me $55 with shipping, I sent the seller an offer originally it was listed at $100. Although the seller said it turned on they have not actually done extensive testing. I'm thinking that it probably does not work that well (it was kinda cheap) but that's ok. I plan to use it for parts or just remove the non working components and use it as a learning experience.

My design like Josh, Tito and Cathal will include an arduino board which will allow me to program and hook the machine up to my computer. So honestly there won't be much of the machine left when I'm done redesigning it. I definitely can't wait till it comes in the mail until then.

Cheers!