RE: [DIYbio] DIY nanodrop alternative?

[Sebastian Cocioba]

I'm in the process of making a very affordable dedicated OD600 module soon. I can send you a prototype to demo free of charge. Its all open source. The final kit will be 25 bucks and initial trials are proving quite good. Its fixed at 600nm but will have lots of nice features and the ability to swap modules for other wavelengths or multiple cuvettes. If all goes well I may kick start it to make one for DNA. Ill keep you posted if you'd wish.

Sent from my Windows Phone

---

From: Koeng
Sent: 7/14/2013 12:52 AM
To: diy...@googlegroups.com
Subject: [DIYbio] DIY nanodrop alternative?

Hey!

I have been looking around for a spectrometer for my lab, and wanted to know if anyone has any recommendations on one. All I need is it to have OD600 and most of all, I want it to be able to sense how much DNA I have in a sample. I am not very experienced with spectrometers, so any suggestions?

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[Dakota Hamill]

An OD600 would be great for bacterial concentrations, and doing MIC (minimum inhibitory concentration) testing.  A cheap spec that could do that consistently would be fantastic and one I would buy in a heartbeat.  Luckily I'm able to use one at school for the time being but, that won't be forever.

For DNA concentration you'd need UV 260nm, which seems to increase the cost exponentially, as UV LED's or light sources seem to be $200-$300+.  There are other ways to get UV 260 but I still don't know of any extremely cheap way, not that I've done much research in the area.  There have been many long threads on DIYspecs on here so the archives would probably give some more info.

UV260nm gives you DNA quantification and the ratio of that to UV280 gives a basic look at "purity".  280nm is for protein contamination due to tryptophan

We had some old ghetto spec 20's my freshman year,  http://www.ebay.com/bhp/spectronic-20

and "Spec 20's" seem to be a common teaching tool in undergrad/highschool labs.  They cost more than I thought they would on ebay but I bet you could best offer at $50 on them and snag one.  Just make sure to scour the description and make sure it isn't broken and for parts only.  

I feel your pain in the DNA quantification area.  Sometimes someone lets us use the nanodrop to test DNA conc before sequencing, but honestly we've just been estimating by running a gel and comparing intensity to the ladder of known concentration.

Unfortunately if you want a UV/Vis spec it probably won't be cheaper than $1,000 off used lab equipment websites (and that's for the old ones, who knows if they work)  http://www.ebay.com/sch/i.html?_odkw=UV%2FVis+spec&_osacat=0&_from=R40&_trksid=p2045573.m570.l1313.TR0.TRC0.XUV%2FVis+spectromet.TRS0&_nkw=UV%2FVis+spectrometer&_sacat=0  

not to mention they probably weigh 50-100 lbs.

Reach out to local university professors, even if it's just "hey I have a few samples I was wondering if I could test the concentration of".  If they see you're putting in hard work and not even going to that university (or any university) they might say, "Hey this kid is a hard worker, he should come work for me!"  Or, "here is an old piece of equipment we havn't used in ages, take it".

From what I've observed 99% of people WANT to help other people, it's just a matter of asking for help.  

Personally I love the look of the small, compact Ocean Optic machines that hook up via a USB cable.  They seem really portable and easy to use, but also cost thousands of dollars.

http://www.oceanoptics.com/Products/spectrometers.asp

For any of the engineers out there, how does ocean optics manage to get a UV/Vis inside something the size of a book, while most UV/Vis specs I see are the size of a hood of a car?  Lamps and mirrors vs....whatever is driving the one in the ocean optics?

[Avery louie]

For cheap dna quantification, you could check out the spectronic 20 DU.  Sometimes spec 20s are sold and people dont know they are DUs, so they are cheap.

Or get a genequant.

--A

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[Dakota Hamill]

Do you have a link for the spec 20 DU?  It goes down to UV ranges? Never heard of one before I might have to check the ones at school now

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[Avery louie]

My bad, its a 21 du. D for digital, u for uv.  The thingon the right is the uv source.  Uses a deturium bulb.  Someone who knows more than me can comment if thay goes deep enough

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[Avery louie]

Oops, here is the link.
http://item.mobileweb.ebay.com/viewitem?index=0&sbk=1&nav=SEARCH&itemId=380660547443

[Koeng]

Genequant looks good! I am looking into buying one right now for simple calculation :)

[Sebastian Cocioba]

Qubit 2.0. Its a godsend and I used it religiously. Its from Life, cheap for a super accurate DNA quantifier.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/d1cc0506-9275-4a67-87f3-1e2862903b76%40googlegroups.com.

[Koeng]

But the only one on ebay is 1,300!

[Sebastian Cocioba]

Genequant is 7k...5k for the lesser model.

Sent from my Windows Phone

---

From: Koeng
Sent: 7/14/2013 8:49 PM
To: diy...@googlegroups.com
Subject: Re: [DIYbio] DIY nanodrop alternative?

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/91b2a166-5343-441e-93c6-b1bc1aea6de6%40googlegroups.com.

[Koeng]

But on ebay they have ones like this

http://www.ebay.com/itm/Pharmacia-GeneQuant-RNA-DNA-Calculator-80-2103-98-/160966559863?pt=LH_DefaultDomain_0&hash=item257a5ac877

or this (tested)

http://www.ebay.com/itm/TESTED-Pharmacia-Biotech-GeneQuant-RNA-DNA-Calculator-Quantify-D6-MH-294-/161054900036?pt=LH_DefaultDomain_0&hash=item257f9ebf44

[Avery louie]

I have an old genequant that was sub-200.  No need for a new one, it works fine.  It has a twin if anyone is interested, but I haven't tested it yet.  Ping me off-list if you are interested.

--A

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[Anselm Levskaya]

From someone who has quantified bajillions of DNA samples over the last decade - absorbance characterization of DNA concentration is super prone to all kinds of errors, and if you're not measuring the whole spec curve (to verify the shape) you won't know when you're completely off.

So if you really care about the numbers, I highly recommend using fluorometric methods for quantifying DNA using intercalating fluorophores.  The Qubit mentioned above is what I use professionally, and there are now dyes that are pretty specific for ssDNA as well as dsDNA, however it costs a kilobuck or so.

For DIY the most accurate and cheap way to quantify things is to mix in small amounts of ethidium bromide (or another intercalating dye) and to compare fluorescence against a calibrated dilution series by eye!  This is the old school way of doing it, but only works for fairly concentrated samples.

I imagine that a DIY fluorometer could be rigged up using blue LEDs and a small sensitive photodiode that would work with one of the longer-lambda dyes like gel red or sybr gold...  you just need a good optical longpass filter.

-A

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[Dakota Hamill]

The Qbit looks pretty cool.  Now that you linked it, I noticed it on the bench of another person in an abutting lab so I might have to ask him about it.  It definitely isn't cheap, but it also isn't the $5k-$15k a genquant or nanodrop look like they would cost.  $2k for a Qbit and 500 assays seems somewhat attainable if you don't have too many monthly bills.

Did you buy yours new Sebastian?

[Sebastian Cocioba]

It was the only peice of equipment I had to splurge on and buy new. Knowing how much DNA, RNA, Protein I have is paramount to almost everything in molecular biology. Too much has gone down the road of unpredictability because we use OD readings as absolute without a standard curve or using the OD 260/280 ratios for quantification. Its just not good enough for reliable results. Each spec is different so the readings on one can swing wildly on the other. I made the decision to use a system that does not care about salt noise and is, as advertised, 10k times more accurate than a nanodrop. Sure you are tied to the reagents but upon some investigation I found out that the dsDNA stain is a blue light induced safe stain. Im going to run some tests to see if you can use gelGreen or GelRed as the stain and TE buffer, which I think the nanodrop is using, as the assay reagents. The hardest part is making a DNA standard from scratch. Anyone savy enough may be able to hack the Qubit 2.0's firmware and make some raw data outputs and other tweaks. Bottom line is: IT IS WORTH ITS WEIGHT IN GOLD. That 2k hole burned a hole in my bank account for some time but it was well worth it. 

On Sun, Jul 14, 2013 at 10:31 PM, Dakota Hamill <dko...@gmail.com> wrote:

The Qbit looks pretty cool.  Now that you linked it, I noticed it on the bench of another person in an abutting lab so I might have to ask him about it.  It definitely isn't cheap, but it also isn't the $5k-$15k a genquant or nanodrop look like they would cost.  $2k for a Qbit and 500 assays seems somewhat attainable if you don't have too many monthly bills.

Did you buy yours new Sebastian?

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[Aaron Vollrath]

i use the first iteration of the qubit and it works fine.  not that much fun setting up 50 samples to assay though as it makes for a long(er) day.

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[Dakota Hamill]

Just asked the girl that works next to me to show me the Qbit in action.  Was pretty insanely awesome.  Touch screen like a smartphone, she put in a blank, control, and sample and all were run in 10 seconds with a DNA concentration given at the end.  

That machine is badass....

[Koeng]

Damn.... I want that machine now :/ although I would probably just use the NanoDrop at the lab I work at so I don't know if I should get it or not :\ It looks worth it....

[Hugo Correia]

So what's the status on this? Kickstart ready?

[Cathal Garvey]

Don't go Kickstarter; they've already demonstrated a dislike of
Science. Go with any of the other crowdfunders or selfstarter.

I will be happy to snap one of these up; I still have no working spec
and could use one.

On Mon, 14 Oct 2013 05:37:29 -0700 (PDT)
Hugo Correia <har...@gmail.com> wrote:

> So what's the status on this? Kickstart ready?
>
> On Sunday, 14 July 2013 07:45:36 UTC+2, Sebastian wrote:
> >
> > I'm in the process of making a very affordable dedicated OD600
> > module soon. I can send you a prototype to demo free of charge. Its
> > all open source. The final kit will be 25 bucks and initial trials
> > are proving quite good. Its fixed at 600nm but will have lots of
> > nice features and the ability to swap modules for other wavelengths
> > or multiple cuvettes. If all goes well I may kick start it to make
> > one for DNA. Ill keep you posted if you'd wish.
> >
> > Sent from my Windows Phone

> > ------------------------------
> > From: Koeng <javascript:>

> > Sent: 7/14/2013 12:52 AM

> > To: diy...@googlegroups.com <javascript:>

> > Subject: [DIYbio] DIY nanodrop alternative?
> >
> > Hey!
> >
> > I have been looking around for a spectrometer for my lab, and
> > wanted to know if anyone has any recommendations on one. All I need
> > is it to have OD600 and most of all, I want it to be able to sense
> > how much DNA I have in a sample. I am not very experienced with
> > spectrometers, so any suggestions?
> >
> > --
> > -- You received this message because you are subscribed to the
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> > For more options, visit this group at
> > https://groups.google.com/d/forum/diybio?hl=en
> > Learn more at www.diybio.org
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> > <javascript:> .

[Sebastian Cocioba]

I posted off list by accident. Here was my response to hugo's question:

So far so good. Still working on the integrated microcontroller PCB and
arduino shield alternative. I've been using my prototype for the last
few weeks making competent cells and such and it works quite well. The
only issue is that due to the arduino's crappy clock and edge detection
I lose some edges if you make a reading at the wrong time so I'm not
comfortable charging anything until I get this important issue fixed.
It does not hinder the performance, rather you may have to blank a few
times to get a 100% transmittance reading. I'd like to add a custom
circuit for edge detection so the only thing the arduino needs to do is
output to the LCD and down the USB as serial IO. Will start working on
that issue with more intensity now that I know someone is interested.
There are others on the list working on a similar device so they may
chime in too.


Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D From: Cathal Garvey
Sent: 10/14/2013 9:28 AM

To: diy...@googlegroups.com
Subject: Re: [DIYbio] DIY nanodrop alternative?

[Patrik D'haeseleer]

This still only for 600 nm, right? I keep thinking there should be a cheap hack to do a simple 260/280 nm spec for RNA/DNA quantitation and purity testing. Much more demand for that than for a general UV/Vis spectrophotometer. Maybe just a diffraction grating and two UV sensors at fixed angles?

Patrik

[John Griessen]

On 10/15/2013 02:00 AM, Patrik D'haeseleer wrote:
> This still only for 600 nm, right? I keep thinking there should be a cheap hack to do a
> simple 260/280 nm spec for RNA/DNA quantitation and purity testing.
>
> Much more demand for that than for a general UV/Vis spectrophotometer.
> Maybe just a diffraction grating and two UV sensors at fixed angles?

I'm looking for things to develop as kits always, and my current project ends soon.
Where does the demand you see come from? How does one quantify that demand?
Please tell me more about the testing goals in RNA/DNA quantitation and purity testing.

[Sebastian Cocioba]

You could go the Qubit route and use a blue excitable intercalating dye like Midori Green and a blue LED. The expensive or hard to find part would be the sensor to detect the green within the blue. Filtering the light post excitation would help...something like an orange filter to block out the blue and let the green shine through. The sensor would need to be around the emission spectra which is very tight to the excitation freq, which is why most blue light boxes use an orange filter. The resolution would be low but comparable to older GeneQuant devices.

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

---

From: Patrik D'haeseleer
Sent: 10/15/2013 3:00 AM

To: diy...@googlegroups.com
Subject: Re: [DIYbio] DIY nanodrop alternative?

This still only for 600 nm, right? I keep thinking there should be a cheap hack to do a simple 260/280 nm spec for RNA/DNA quantitation and purity testing. Much more demand for that than for a general UV/Vis spectrophotometer. Maybe just a diffraction grating and two UV sensors at fixed angles?

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[Sebastian Cocioba]

My next spec would be a project like that...using a set of standards like the Qubit (0 and 5ug) to calibrate the device and a really good ADC.

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

---

From: Sebastian Cocioba
Sent: 10/15/2013 11:36 AM
To: diy...@googlegroups.com
Subject: RE: [DIYbio] DIY nanodrop alternative?

[Josh Melnick]

any news on this project?

[Marc Dusseiller]

hoi zäme,

we have built various designs, as low-cost as possible, try to keep it belo 5$ manufacturing cost.

http://www.hackteria.org/projects/turbidity-meter/

and also this one by gaudilabs:

http://www.hackteria.org/wiki/DIY_NanoDrop

at the moment there is another discussion on the GOSH forum, we are getting supported by hamamatsu to get some free micro-spectrometer modules:

https://forum.openhardware.science/c/communities/single-pixel-camera-dev-group

ciao ciao,

marc

On Sunday, July 14, 2013 at 7:45:36 AM UTC+2, Sebastian wrote:

I'm in the process of making a very affordable dedicated OD600 module soon. I can send you a prototype to demo free of charge. Its all open source. The final kit will be 25 bucks and initial trials are proving quite good. Its fixed at 600nm but will have lots of nice features and the ability to swap modules for other wavelengths or multiple cuvettes. If all goes well I may kick start it to make one for DNA. Ill keep you posted if you'd wish.

Sent from my Windows Phone

---

From: Koeng

Sent: 7/14/2013 12:52 AM
To: diy...@googlegroups.com

Subject: [DIYbio] DIY nanodrop alternative?

Hey!

I have been looking around for a spectrometer for my lab, and wanted to know if anyone has any recommendations on one. All I need is it to have OD600 and most of all, I want it to be able to sense how much DNA I have in a sample. I am not very experienced with spectrometers, so any suggestions?

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[Abizar Lakdawalla]

Nice designs in the links. Just going back to the original question - quantitation of DNA by absorbance will  require 260 nm light source. And if you are doing a UV-visible spectral range you will need a deuterium halogen light source or equivalent. UVC LEDs are expensive. UVC bulbs are about US$10 but large. Anyone know of a miniature UVC light source that is not too expensive?

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