Gel Electrophoresis: How It Works and How to Build a Gel Box For Cheap

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Gel electrophoresis is one of the most ubiquitous techniques in molecular biology for 2 reasons; it's easy, and extremely versatile. We've used it several time over the past couple months to test various part of our ongoing spider silk project, so in this video we explore it in detail. First we build a gel box for only a couple dollars and then go through the process of making the gel, loading it up, running it and then explore how to analyze the results. We focus on DNA and agarose based gels and will come back to protein and acrylamide gels in a future episode.
This video is meant to be the foundation on which we build so that in future episodes we can use gels as part of more complex techniques.
If this is the first time you're seeing one of these biology videos you may be wondering what's going on. Well this playlist contains all of the work we've done over the last couple months and will continue to be added to as we make more progress. • Spider Beer
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Опубликовано:

30 июн 2024

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Комментарии : 115

@thethoughtemporium 5 лет назад

Lots of people have commented about ethidium bromide not actually being toxic. OK then. It'll take a while, but I'll plan a mutation test and see which of the stains is actually the most mutagenic. Don't expect the video soon though. Will take a while to source everything and I'm busy with other projects. But I'll try and get to it when I can

@ghhg-je8wv 5 лет назад

lol, so I know my homie's housemate is this cute biochem major, so when she came over I had this on right as you were getting into the part about ethidium bromide. oh yeah...got dat cred, tho I got to admit the hardcore parts of electrophoresis still had me shook! keep up the awesomeness!

@Kalanchoe1 5 лет назад

man, that's cool!

@maxmuenchow 2 года назад

This still on the agenda? I think this kinda video would be veryy interesting. Cheers mate

@CaptiveReefSystems 3 года назад

As a private sector, and disabled (and therefore independent) neurobiologist and psychopharmacologist, and somebody that started an organization solely devoted to independently and privately investigate and vet discoveries in this (and related) field(s), my team and I absolutely f*cking LOVE this channel! 😎👍 As can be expected, my team and I operate on an almost nonexistent budget (and often donated materials). Our only objective is to fund our own research and to offer free educational workshops to schools, colleges, and universities (at least as often as possible) to spread the scientific pursuit of curiosity to the next generation in whatever humble way we can... based upon equipment and supply donations. Hopefully, we will soon be able to share information with the many other independent researchers out there, including this channel! Right now, we are attempting to either acquire and/or build several new analytical instruments (primarily spectrometric and spectrographic instruments) to allow us to better analyze (primarily small-molecule) psychoactive compounds - such as SSRIs, endogenous phenetylamines, and isolated plant alkaloids, etc. May I ask, what is the white/orange instrument pictured at 4:00 is..? A colleague sent me a schematic recently for a similar instrument. Is this a spectrometer, microplate reader, etc..? Something about it looks very familiar, but I just can't place it... Any information that anybody can provide would be most appreciated!

@thethoughtemporium 3 года назад

It's called a bentolab, though this one was a prototype. It's a PCR, centrifuge and gel box all in one.

@LKAChannel 5 лет назад

As a physicist this is something I'm not really familiar with at all and I'm not sure I understand much of it, but it's a great way of broadening my horizon

@Sodabowski 5 лет назад

As another physicist (with enough chemistry to be a teacher of both) I second that. I have always been intrigued by these biochem streaky chromatographic-ish separations and always wondered why and how. Super interesting, right?

@goodboiadvsp3297 5 лет назад

*Invents a working tardis* Thought Emporium: "It's just a box"

@Ratchet4647 5 лет назад

I literally learned about and how to use Gel Electrophoresis for DNA this morning. So interesting. It was so tense and nerve wracking though.

@gamereditor59ner22 5 лет назад

I remember doing this in my 3rd and 4th year of my university, though bacterial transformation is my favorite. Thank you for providing instructions!!

@wrightcj01 5 лет назад

Got a Thermo Fisher gel electrophoresis ad lol

@unusualfabrication9937 5 лет назад

hey, at least it's not a google ad and it actually relates

@JesopherJones 5 лет назад

Got the Same add but it’s quite funny

@JesopherJones 5 лет назад

@darealpoopster 5 лет назад

wrightcj01 Same

@edgeeffect 5 лет назад

You do tend to get "a higher class" of ads on Thought Emporium videos.

@madisondrum9179 3 года назад

Information presentation is the biggest factor for me when learning because I technically know all this stuff, but because of the way you presented it as if its no big deal, I feel more confident in it.

@KX36 5 лет назад

Love that you made your own equipment again! If you do eventually expand this with blotting, I'd like to see something about isoelectric focussing too.

@thethoughtemporium 5 лет назад

Got 3-4 more diy equipment builds coming up. Already finished one, starting on the next two soon. I've been looking at 2d gels and isoelectric focusing is the first step. Been wanting to try it

@franciscobohm1699 5 лет назад

Love your videos they're really informative!!

@irri3191 5 лет назад

So much data in pitch perfect speed.ty 😊

@zralokk 5 лет назад

I'd say it's a bit too fast here and there. Great video though.

@jimmiununger2767 5 лет назад

For me who will probably watch this video several times. The speed is just right. The volt/mm is more than enough value in the learning vs time spent watching for me. And there is slower videos with less parts on other channels. (Mostly the companies who sell the stuff)

@franglish9265 5 лет назад

Good idea to make your own gel dock! Also, southern blots are cool!

@Munden 5 лет назад

Gel boxes and what they're good for demystified - Thought Emporium, keep up the amazing work!

@bjarnes.4423 5 лет назад

Keep up the good work!

@Sazoji 5 лет назад

you can use 50%-60% glycerol instead of a colored loading dye if your DNA content is low. some dyes can leave a shadow and when the exposure times are high the shadow can ruin the picture.

@Protospacer 5 лет назад

My lab also uses ethidium bromide to stain gels. According to the PI, it's not cell permeable and therefore not a major carcinogen.

@markayala7752 5 лет назад

nice as always

@franglish9265 5 лет назад

Those ladders look sick yo!

@someperson9 Год назад

I recently used this in my Bio class, and it was pretty interesting

@Veptis 5 лет назад

This was wonderful. We had this topic in our biology class just very recently and I requested our teacher to do a demonstration. To her knowledge our school owns a kit that does not work, I will ask for it on Monday and see what's wrong as this seems like a very simple concept. In our textbook we had the example of cutting up DNA using enzymes that cut at specific base sequences into shorter strangs. And uses gel to confirm the results. What kind of simple demonstration do you suggest that shows results easily? We don't had access to a PCR machine.

@thethoughtemporium 5 лет назад

I mean the very simplest demo is to load a mixture of dyes. But for DNA you'll need some more reagents. A plasmid with known cut sites and the corresponding restriction enzymes works, which is what you were taught about.

@alyburr6645 3 года назад

Thanks for this, I finally understand it!

@ashimahmed2193 3 года назад

Are you perhaps some way related to bill burr?

@alyburr6645 3 года назад

@@ashimahmed2193 no, this isn't even my real name, I was obsessed with the musical Hamilton when I made this account, so my name here is a pun on Aaron Burr

@XOIIOXOIIO 5 лет назад

Awesome video, I have an elecrophoresis power supply sitting around, it's great to see such a detailed but concise video explaining the concept. I had a rough idea of what it was for but this is fantastic. It has quite a range of voltages up to several hundred volts, would that be to help samples separate faster, or would it be more for larger sections of gel for longer ladders/higher "resolution" for lack of a better term?

@thethoughtemporium 5 лет назад

Mostly gel size. My friend runs gels that are almost a foot long from time to time so it needs a ton of voltage.

@XOIIOXOIIO 5 лет назад

@@thethoughtemporiumCool to know. I can't recall the specifics, too lazy to dig around through my videos but I think the one I have goes up to 600v or something along that range. The output is relatively unstable, but I suppose it doesn't need to be dead solid for this sort of application. (or maybe it's defective, not sure if a 20v fluctuation is acceptable). Might be fun to try and use it for it's proper use sometime.

@rojusurbonas6583 Год назад

Madlad!!!!

@diegorusso2315 Год назад

Pls more video... I love you

@Eric_Pham 5 лет назад

I learned this in biology

@Djoodibooti 5 лет назад

**watches one thought emporium video** I'M SO POWERFUL, MY MIND UGHHH IT EVEN AMAZES ME SOMETIMES.

@tainicon4639 5 лет назад

I still use EtBr... it’s pretty common. And there is actually no evidence of any mutagenic behavior. And I mean 0 evidence. People just guessed it would be because it intercalates dna. And why did you mix the amplified dna and loading dye on a piece if para-film? It’s so much easier to just add it to your master-mix. But anyways cool series! It’s great to get people into molecular bio!!!

@bok.. 5 лет назад

I'd still be more concerned about the vast amount of metabolites that are unknown. Even then this requires relatively high amounts of exposure for an average sized human .

@tainicon4639 5 лет назад

Bok well, obviously don’t drink it haha. But it isn’t any more dangerous than any of the other dyes

@bok.. 5 лет назад

Yea of course. Even then a few uL won't do much lol.

@rivendrive 5 лет назад

EtBr is used as an antiparasitic in cattle in comparatively high doses and there are still no known metabolites recognized to be harmful.

@MCtomgie 5 лет назад

How should you dispose of it if many people think its safer than what it is said to be?

@chimekkoo-old Год назад

Could you provide a link where you bought the agarose?

@tf3confirmedbuthv54 5 лет назад

i have that exact same power supply!

@chuckvanderbildt 5 лет назад

Ethidium bromide is not something you want to use to flavour your coffee, naturally, but it is not the boogeyman people make it out to be. For the application of staining gels, with a modicum of sensible procedures, it is perfectly safe to work with. Please don't take my word for it though, and look into the literature yourself. But If you were to ask me, I think the people seemingly sounding off the loudest are those with supposedly 'safer' alternatives on offer.

@Sodabowski 5 лет назад

As is often the case! Thanks for the info.

@MCtomgie 5 лет назад

I have been reading on it, for a home lab would it still be considered safe? I was also wondering how you would dispose of it in a home lab if it is safe?

@notamouse5630 5 лет назад

You can even make your own power supply with some basic electronics skills. Get the cheapest ATX power supply on amazon and add a boost converter and a DC voltage panel readout meter to the 12v rail with a variable PWM switch input. Use an Arduino to take a potentiometer input and generate the fast variable PWM output for the boost circuit at 40khz or higher and a PID control loop to stabilize it. That will be much more than enough power for what you have built and could run many gels in parallel if designed to use 80 percent of the output power of the ATX PSU. You can even keep the Arduino hooked up to the computer and use serial terminal at max speed for the interface to keep the cost below $50-$80 and the engineering time short. ~one electrical engineer

@thethoughtemporium 5 лет назад

Or you buy a DC to DC up-converter for 10 dollars which is what I'll be using.

@notamouse5630 5 лет назад

@@thethoughtemporium Yes, that is exactly what I am talking about making, and with mine, you have more adjustment and power. Its also a good educational experience in basic electronics and control systems. Using a program called LTSpice, you can do easy and efficient circuit modelling. Though this takes self education to get into and many don't have the time, it pays for any BMEs watching to have knowledge of how the electronics they use work. Control systems is also a useful field of study with applications to artificial repair of biological systems by means of establishing a control loop. Take diabetes for example. The long term health effects of type 1 diabetes can be completely eliminated through creation of an artificial pancreas. The amount of glucose in the blood can be monitored and controlled in real time for a more stable blood glucose level. Low and High sugar levels will happen only as they do to a normal human. Lyunapov stability of blood sugar by means of manual injection is a poor standard of care and involves excessive need to innovate in the design of more and more expensive insulin products rather than a suitable system for dispensing them for a superior outcome. The Math and Science: www.ncbi.nlm.nih.gov/pmc/articles/PMC4455398/ www.physiology.org/doi/full/10.1152/jappl.1998.85.3.935 en.wikipedia.org/wiki/State-space_representation The Engineered Outcome: www.bloomberg.com/news/features/2018-08-08/the-250-biohack-that-s-revolutionizing-life-with-diabetes

@thethoughtemporium 5 лет назад

@@notamouse5630 OR, you could not because its a massive waste of time. What you're describing is called "learning electrical engineering". If I wanted to study control systems, I would do that. I just want my gel box to work. If I have to take a week to design and test my circuit, order all the parts, wait for it to all arrive, and then build and test a thing, I've monumentally wasted my time if my goal is to just do biology. But the premade thing, wait 2 days for it to arrive, adjust it to your gel box, then connect it up and never think about it again. I only build my own tools when I need to, and if I need control systems, I use them and at that point extra effort is worth it. But a gel box needs nothing more than an upconverter and a light switch.

@uzmashah9618 3 года назад

Could you please let me know how to remove the loading dye from gel

@cryptonein 5 лет назад

So, really curious, while these are fantastic videos, can you please give us a rundown of your ultimate - or any hypothetical - use cases for this?

@thethoughtemporium 5 лет назад

Making a tank of spider silk, spinning it into fabric, and using it to build super lightweight airplanes without needing furnaces to make carbon fiber, or smelters to prepare aluminum. Producing drugs in vats. Bioremediation. ETC ETC ETC. Biology is the most versatile technology on earth and allows you to manipulate matter in ways nanoscientists and chemists can only dream of. PCR specifically can be used to tell if you've got mutations that will wreck your life like huntingtons disease, or any of 10000 other uses. Its ubiquitous for a reason. Also this same basic principle is how a massive variety of techniques work.

@cryptonein 5 лет назад

@@thethoughtemporium thank you, those are some excellent points and illustrations. I think hearing and reading that kind of information when viewing these great videos gives proper CONTEXT for inspiration and getting your own ideas. Thanks!

@realcygnus 5 лет назад

cool as all hell

@temukaify 4 года назад

What about copper-clad graphite?

@user-ug4ow1qq2h 4 года назад

Damn, we still use EtBr in our lab/ (._. ) Though we're all informed about its toxicity and take all precautions that we can think of.

@piprod01 4 года назад

The gel electrophoresis box is just a box!? :O Next you'll tell me that the PCR machine is just a glorified kettle!

@SmashedHatProject 5 лет назад

Every video convinces me more that you would be a great backwards-time-traveler

@thethoughtemporium 5 лет назад

I have put an fair amount of thought into that particular fantasy XD I don't think you're wrong

@SmashedHatProject 5 лет назад

@@thethoughtemporium my number 1 item to take back would be a roll of aluminum foil...so much value and use in the past

@Erikawby 5 лет назад

Rip caveman eyeballs. Time to genetically modify my eyes.

@ashimahmed2193 3 года назад

Let's make our eyes like the witcher or shiringans and rinnegans from Naruto

@franglish9265 5 лет назад

...We're kinda also covered in lots of microbes like S. aureus and sometimes eggs for multicellular parasites... What organism produces DNAase?

@zralokk 5 лет назад

S. aureus that you mentioned can produce DNase.

@Nagytika 5 лет назад

you do not want to cover yourself with DNase

@franglish9265 5 лет назад

@@Nagytika yes.... I know that man...

@Nagytika 5 лет назад

+Anthony M my bad, i jumped to a concluson too fast. sorry man.

@Ccccaatfish 5 лет назад

Do you ever plan on publishing independently?

@weirdshamanwizzard3156 5 лет назад

You have 1 hater, you're famous now

@israelramos7441 5 лет назад

👍👍👍

@Winther83 5 лет назад

Have a quick question, Can you use agar agar powder for this? or is it better with pure Agarose? mainly asking due to the price difference.

@FedericoAOlivieri 5 лет назад

You can use agar powder, but the result won't be as good.

@Winther83 5 лет назад

@@FedericoAOlivieri Ahh as i suspected, well might be good to invest in the proper materials then and use agar agar for less sensitive applications. thank you for the answer. :)

@matthiasBdot 5 лет назад

please peel off that plastic foil from the mini one for me

@somanyfnbananas2774 5 лет назад

"Just make sure the whole room is dark and it makes seeing things a lot easier" Well...

@SixTough 5 лет назад

So you don't need to step up the voltage from 30V?

@thethoughtemporium 5 лет назад

No you reaaaaally should. Our results at 30v sucked. Use the proper voltage for the length of gel. The minione runs at 42v and the gel is 42mm. That one is close enough that you could get away with 30V. But a 60mm gel needs more voltage.

@SixTough 5 лет назад

@@thethoughtemporium Thank you. I wanted to build one and this has been the main question

@vega1287 5 лет назад

if dna is negatically chatrged couldnt a strong enoghth electro static field seperate the negatically charged dna

@FedericoAOlivieri 5 лет назад

All DNA is negatively charged. That's why the electric field makes it move.

@vega1287 5 лет назад

@@FedericoAOlivieri dont you mean current

@CreeperOnYourHouse 5 лет назад

is your lactose intolerance still cured?

@FreeSkillsStyle 4 года назад

2:35 not gonna pay 300$ for a box but has this machine that cost so much more

@bogdanbogdanovich140 4 года назад

What are your thoughts on the man who genetically modified babies

@tiburciodelfinoacostaymanj5217 3 года назад

And what about electroporation devices? hehe

@Nagytika 5 лет назад

i miss biotech lab.

@Hailfire08 4 года назад

I wonder what unsophisticated barbarian disliked this.

@unvergebeneid 5 лет назад

Is this sped up or am I just being slow right now?

@zralokk 5 лет назад

I feel the same, haha. I think it's a bit too fast in certain places.

@Sodabowski 5 лет назад

Maybe you should reduce your shrooms consumption? ;p dude sure is fast-paced!

@jimmiununger2767 5 лет назад

Luckily you can pause, relisten if you mean the entire video. Or if you mean specific areas, he might already have expanded it in other videos or will in future ones.

@unvergebeneid 5 лет назад

@@jimmiununger2767 It's less that it's too fast to follow, it just _sounds_ sped up somehow. As if all the sounds are cut short a bit.

@eminemlandsteiner168 5 лет назад

What happened with your fluorescent microscope? Have you succeeded?

@thethoughtemporium 5 лет назад

Got busy and further attempts didn't really work. Will keep tinkering with it

@eminemlandsteiner168 5 лет назад

@@thethoughtemporium Try to use a flourscent substance instead of water in your sample. The easiest one to get is Chlorophyll. It's pretty easy to isolate it from any green plant. All what you need is ethanol to lower the concentration of Chlorophyll. Chlorophyll is green and it "shifts" the UV light to the red color range. Hope you succeed ❤️

@eminemlandsteiner168 5 лет назад

@@thethoughtemporium by the way, you didn't fail. Actually, you have built a real flourscent microscope, but it is an old one. the old flourscent microscopes were just like what you have built. Open the page of the "University of Toronto" on Wikipedia. You will see down under the section of "research" a real photo of stem cell which was captured back in the 80s. It's just the same as what you have done

@aidynwyatt5415 5 лет назад

Hopefully you don't get duped again and get water😂

@jadirneto2130 5 лет назад

How easy is to create a super virus with the equipment you have right now?

@thethoughtemporium 5 лет назад

Not. That's the myth of biology. Chances of you successfully making the thing are way lower than getting yourself killed in the process. That's a biosafety level 4 kind of thing which I'm sooooo not set up for. My lab is for working with bacteria and yeast that are non pathogenic.