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science, meet art

the cepa gallery is holding an auction of some photographs. this one in particular caught my attention.

p. vanouse

here's the link for the description of the piece and other associated information.

do you know what that picture's showing? i'll give you a hint, they're building blocks.

if you guessed dna, you would be correct. in order to get the result that is shown on the photo, samples of dna need to be fluorescent stained and cut by restriction enzymes and loaded into the wells at the bottom of the photo. after that they are run through the gel submerged in solution with an electric current applied. the current forces the fragments of dna to migrate through the gel from one end to the other. the distance traveled by the fragments give us information on how long the fragment is, which helps us determine the dna sequences of the fragments and sample*. as restriction enzymes only cut at certain sequences of dna. all those letters at each sample well are the different restriction enzymes applied to the sample. in order for the art/scien-tist to come upon the design, for those lanes that are symmetrical on the left and right sides, you can see the same enzymes were used. lanes 1, 13, 14 had no enzymes applied and no sample loaded. lanes 2, 12 are the same. lanes 3, 11 are the same also. you can see where there is a difference in lanes 5 and 10 which use completely different enzymes, thus getting different cut pieces which migrate at different rates across the agarose gel. if you're interested in the process of preparing the dna, read on... otherwise you can skip the rest and do something more interesting.

the whole process takes around a full day if we are working with a sample of dna that has already been purified and only needs amplification. we copied the dna by using an enzyme called dna polymerase through a process called the polymerase chain reaction (pcr). through heating of the double stranded dna (which seperates the double helix into single strands), we can also use and activate dna polymerase to copy each strand with the opposite base pair nucleic acid. the cooling action allows bonds between the strands to form again. the result from 1 double strand of dna is 2 strands of dna that come apart from heating pre-dna polymerase, and 4 strands of dna post-dna polymerase action. we can program a thermacycler to raise and drop the temperatures of the sample multiple times until we have sufficient quantity to run them through the gel. in my lab, we usually put the sample into the thermacycler at the end of the day and let it run overnight.

so the next morning (or afternoon), we'd come in ready for another fun day. we have a sufficient amount of sample now, and this is where we stain and cut the sample. we can use a hot water bath to activate the enzymes we place in our samples and leave that going while we prepare our gel. this whole process took an hour or more as the gel is prepared from a liquid mixture and allowed to cool and set (think jello but not edible and more ew). when everything is finally set, we can apply a large current if we're really rushed (though this is not a good idea, as the dna fragment bands can run off the gel and you lose all your work), or we can even apply a very low current and let it run overnight if we decide to go out that evening. usually though, we pick something in between so that we can check in every once in awhile to make sure things are all going as planned. after all this is done, we carefully remove the quite fragile gel and take it to our geldoc scanner for school pictures. usually this best case scenario was not what was played out. since dna does not show up unless it is stained with a fluorescent compound that glowed under uv light, this was always a scary time. the geldoc scanner's uv light allows us to determine if our results were what was expected. there were many times when the uv light went on and curses were shouted after a day's worth of work was for nothing.

i do have to say though, there are days when i miss being a grad student in my lab. the biotech department was a small department, and we were a pretty tight knit group always encouraging each other despite our many attempts at getting these damn experiments to work. i miss the solitude and clarity i had when i went into the lab late at night to culture or prep cells. i miss being able to use the name of some restriction enzymes on a daily basis. my top 3 faves are HindIII, BamHI, and EcoRI. i also miss the surprises and successes that came, such as seeing that clump of dna in 70% isopropanol (yes you can actually see the dna if you successfully amplify and purify it). i will say this though, i do not miss keeping a lab notebook and writing a long document about it.

*i want to point out that we have better technologies now to sequence dna, we can just put our sample into a sequencer. it uses the fluorescence intensity to measure what each base is as it passes through a reader. the use of restriction enzymes is the old and "cheap" original but time consuming way to do it.

Comments (2)

www.facebook.com/profile.php?id=514500505 [TypeKey Profile Page]:

Ahh, restriction enzymes. I remember the Bam ones from some course in uni.

I like doing the whole extracting DNA using dishsoap and ethanol with my classes. It's a good time.

-jason- [TypeKey Profile Page]:

hmmmm dish soap and ethanol? you lyse the cells with the soap, ethanol will precipitate the dna... what goes on in between and after all that in your class? sounds like you've got an interesting lesson plan. i remember only running one electrophoresis gel with my ap bio class in high school. we took a field trip to a local college since they had all the equipment and we didn't.

i just love saying the 'Bam' in BamH1. i was wondering the other day if we could reuse restriction enzymes that have already been used in in vitro experiments if we could unbind them from the substrates and purify them? maybe run the unbound enzymes through a column to purify. that is unless they become irreversibly denatured, we should be able to reuse them right? or am i completely wrong on this?

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