Precast Gels?
Paul Anderson
Invitrogen has this E-gel precast gel, with SYBR Safe dye already in
it. The starter kit has six gels and goes for $145. Not the cheapest
thing, but I'm not exactly running a lot of gels, either.
That does lead to an interesting question for those in the group
already doing DIY bio. How often do you run gels? How many do you
use in a given period of time?
--
Paul Anderson
VE3HOP
wacky...@gmail.com
http://www.andersonloco.com
QRP ARCI #13228, GQRP #12447
Scott Kerr
For ~$350 you can get enough agar and buffer to run ~100 of gels.
I am not into home DIYbio yet but I would think that you would crank through gels pretty quickly if you really got into any serious project.
However, I do know that you can reuse gels, after you take your picture or whatever, you keep running it until you run your sample well out of the range of your next gel. This obviously breaks down if you have really long DNA fragments but you get the idea.
Josh Perfetto
preparation of which is much more involved than agarose), and even that was
a marginal decision. For agarose gels it is just too easy, casting the gel
will only take you 5-10 mins of actually doing something once you get used
to it, and only another 20 or so mins for the gel to solidify.
Keep in mind that the pre-cast gels do expire, and unless you want to stock
up on lots of different pre-cast gels, you won't be able to adjust the gel
pore size to accommodate different DNA lengths, nor alter the lane
width/number of lanes. The only way I could see paying $145 for 6 agarose
gels would be if you've got lot loads of money and haven't a minute to
spare. Even if you've got some money, there will be plenty of other things
to spend it on besides gels.
As for frequency, it really depends on what you are doing. I could easily
use 6 gels in a week.
-Josh
peter
and more ready to deal with "small guy" orders check www.bostonbioproducts.com.
I know the guy, very reliable and always sends some free goodies ...
TE, TAE, TBE, EDTA etc. I think one can request free samples as well.
- Peter
On Feb 23, 12:54 am, Scott Kerr <uwsk...@gmail.com> wrote:
> If you are looking to spend that much money you should just by pure
> buffer<http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catP...>
> For ~$350 you can get enough agar and buffer to run ~100 of gels.
>
> I am not into home DIYbio yet but I would think that you would crank through
> gels pretty quickly if you really got into any serious project.
>
> However, I do know that you can reuse gels, after you take your picture or
> whatever, you keep running it until you run your sample well out of the
> range of your next gel. This obviously breaks down if you have really long
> DNA fragments but you get the idea.
>
>
>
>
> > I was wondering what the group's thoughts on pre-cast gels were.
> > Invitrogen has this E-gel precast gel, with SYBR Safe dye already in
> > it. The starter kit has six gels and goes for $145. Not the cheapest
> > thing, but I'm not exactly running a lot of gels, either.
>
> > That does lead to an interesting question for those in the group
> > already doing DIY bio. How often do you run gels? How many do you
> > use in a given period of time?
>
> > --
> > Paul Anderson
> > VE3HOP
Dan
You get a set of glass plates about the size of a playing card. You
make a crossbar that can go over the plate and clamp the well comb to
it so that the comb is ~0.5mm above the plate. Carefully pour the
molten agarose on to the plate until you have covered it. Surface
tension will hold the gel in place until it sets. It takes a bit of
practice to learn how to pour without ending up with agarose all over
the bench but it's fairly simple once you get the hang of it.
The minigels are only a few ml in total volume so you can get a
ridiculous number of gels per gram of agarose. They' aren't good for
preperative gels but are more than good enough for sizing DNA bands.
In an old lab, we would make minigels by the dozens and keep them on
Tupperware containers in the fridge to save time on gels.
Cory Tobin
> already doing DIY bio. How often do you run gels? How many do you
> use in a given period of time?
This last week I ran 10 gels, if I remember correctly. But the week
before I only ran 2. Although, I'm probably not considered a true DIY
biologist as I'm in a university lab.
> However, I do know that you can reuse gels, after you take your
> picture or whatever, you keep running it until you run your sample well
> out of the range of your next gel. This obviously breaks down if you have
> really long DNA fragments but you get the idea.
Good suggestion. Another way to reuse gels is simply to remelt the
gel. Although, as the old DNA is still in the gel, I would only reuse
a gel for analytical purposes. If I had to cut out a band I would
start with fresh agarose and TBE. So actually, those 10 gels I quoted
earlier were probably only ~3 gels that I reused multiple times.
Also, my opinion on the E-gels (although, I have never actually used
one) is that they are incredibly overpriced. If you buy agarose,
SYBR-Safe, and salts for your buffer separately and in bulk it should
only cost around 1-2 bucks per gel.
Cost breakdown for a 100mL gel...
Agarose from Lab Depot (
http://www.labdepotinc.com/Product_Details~id~463~pid~13541.aspx )
$700/kg. 1g in a 100mL sized, 1% agarose gel = $0.7/gel
A pouch of TBE powder from Lab Depot (
http://www.labdepotinc.com/Product_Details~id~463~pid~13544.aspx )
runs at $22.71 and makes enough 1/2x TBE for 200 100mL gels. =
$0.11/gel
* Although, you will need more TBE for your running buffer. I reuse
my running buffer for about a month.
** Extra savings if you buy the TBE ingredients separately.
Invitrogen sells 400uL of SYBR-Safe for $47. 5uL per gel. = $0.50/gel
( http://tinyurl.com/abb2o2 )
*Extra savings for using Ethodium bromide.
Grand total for a 100mL, 1% agarose gel: $1.31
The key here is buying in bulk (ie. 1kg of agarose) and pouring the
gels yourself.
-Cory
Tom
quick, they deliver to residential addresses and did give some useful
free solutions. I sent in another order today. You can always prep and
store gels far cheaper than buying pre-cast, that is a rip off unless
you have loads of grant money and just dont care. As for the agar vs
agarose issue, the time you save using agarose right from the start,
which will allow you to go straight to analyzing DNA, will easily
outweigh the money and time you spend trying to make agar/gelatin
work. If that had worked 30-40 yrs ago for resolving DNA by size, we
would all be doing it now.
Daniel C.
> that is a rip off unless
> you have loads of grant money and just dont care.
This makes me curious - assuming you have unlimited grant money (but
are still for some reason concerned about economy), at what point
would it become cheaper to hire an undergrad to prep your gels than to
purchase them premade? Assume your only cost is the hourly rate you
pay your wage-slave and the consumable materials, no re-use of
materials, no cost to run the autoclave and other equipment, and the
molds, combs, etc. are already paid for.
I would do this myself but I don't know how long it takes to prep a
gel from scratch and how much the average wage slave (excuse me,
"Valuable Junior Team Member") gets paid these days.
-Dan
Cory Tobin
> are still for some reason concerned about economy), at what point
> would it become cheaper to hire an undergrad to prep your gels than to
> purchase them premade? Assume your only cost is the hourly rate you
> pay your wage-slave and the consumable materials, no re-use of
> materials, no cost to run the autoclave and other equipment, and the
> molds, combs, etc. are already paid for.
>
> I would do this myself but I don't know how long it takes to prep a
> gel from scratch and how much the average wage slave (excuse me,
> "Valuable Junior Team Member") gets paid these days.
The cost of consumables, assuming they are bought in bulk, is around
1.5 dollars. I can usually set up a gel in 5-10 minutes assuming the
buffer is already made and the microwave is not currently in use.
Although, I have no clue how much the undergrads get paid.
There is another factor besides money that I suspect also may be
important. Hiring someone to make gels (or do other routine tasks)
means there is one more person to manage. First they have to be
trained. Paperwork has to be done to put them on payroll. Then, if
they don't show up one day, someone else needs to be delegated to make
the gels for the week. In large labs it may be simpler logistically
to order pre-made gels. Invitrogen makes it simple so every Monday
there is a box of gels sitting in a fridge at Shipping & Receiving.
-Cory
Daniel C.
> There is another factor besides money that I suspect also may be
> important. Hiring someone to make gels (or do other routine tasks)
> means there is one more person to manage. First they have to be
> trained. Paperwork has to be done to put them on payroll. Then, if
> they don't show up one day, someone else needs to be delegated to make
> the gels for the week.
This is where I wave my magical economist's wand and utter the phrase
"all else being equal". Watch how all of the perfectly salient,
germane and reasonable points you just made disappear. Sometimes I
think I should have studied something less grounded in reality ;-)
I realize that there are considerations beyond the financial which
affect behavior and decision making. I was really just curious about
the financial cost differences between the two options, though.
Dan
Bryan Bishop
> On Mon, Feb 23, 2009 at 6:09 PM, Tom <tara...@gmail.com> wrote:
>> that is a rip off unless
>> you have loads of grant money and just dont care.
>
> This makes me curious - assuming you have unlimited grant money (but
> are still for some reason concerned about economy), at what point
> would it become cheaper to hire an undergrad to prep your gels than to
> purchase them premade? Assume your only cost is the hourly rate you
And how about making fixtures and giant mechanical mechanisms for
automatically loading up many gels to cast all at once? Then just
refridgerate them, and have your fun. This doesn't sound like
something that should be too hard, but it will require someone with
mechanical knowledge to design. Throwing one of these up at a
community lab could help operations go much more smoothly.
Daniel C.
> And how about making fixtures and giant mechanical mechanisms for
> automatically loading up many gels to cast all at once? Then just
> refridgerate them, and have your fun. This doesn't sound like
> something that should be too hard, but it will require someone with
> mechanical knowledge to design. Throwing one of these up at a
> community lab could help operations go much more smoothly.
This is just begging for a steampunk rendition.
Paul Anderson
>
>
>
> And how about making fixtures and giant mechanical mechanisms for
> automatically loading up many gels to cast all at once?
>
a heated pot, a metering pump, and a mold. Mix a vat of gel with
appropriate proporations. Heat. Place the mold under the nozzle and
dispense the required volume of gel. Make up a cart full of molds
then take them to a walk-in or other suitable fridge. With a suitable
junk supply you could rig it up in an afternoon.
--
Paul Anderson
VE3HOP
wacky...@gmail.com
Scott Kerr
If they are looking to get their foot in the door and learn research they can count research hours towards credit (at least at my undergrad university). Then it is free for the lab to have them do work. (But then they take up your time, which was the premise for hiring an undergrad to make gels in the first place I guess.)
Dan
Paleolithic, this is quite common in larger labs. I'm not certain
what the turnabout time is as all the undergrads peons I've ever known
about did lots of other menial tasks in addition to gel pouring.
Unless any DIYers are going through obscene amounts of gels, I can't
imagine the economics would work out well to hire someone to do this.
Dedicating an afternoon to pouring 50 minigels and then storing them
for use is probably the most efficient use of one's time and money,
IMO.