What DNA separation techniques other than electrophoresis?

[Nathan McCorkle]

Does anyone know of ways other than electrophoresis of DNA to
separate? The problems with long run times and exhaustion of buffer
seem like they could be alleviated... but how? Maybe something like
flow cytometry, but in a much smaller capillary? Maybe the DNA could
be ligated to something like sialyl-lewis-X, and the capillary coated
in CD62P (protein that binds SLX) to slow down the DNA during its
flow... then detection could proceed with UV spectroscopy (the
capillary would need to be very thin to allow differentiation of
single/few molecules)

What other ideas do people have?

--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Mackenzie Cowell]

Arbitrary sequences?

What size range?

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[Mackenzie Cowell]

"Sorting by diffusion: An asymmetric obstacle course for continuous molecular separation"

http://www.pnas.org/content/96/24/13762.abstract

A separation technique employing a microfabricated sieve has been demonstrated by observing the motion of DNA molecules of different size. The sieve consists of a two-dimensional lattice of obstacles whose asymmetric disposition rectifies the Brownian motion of molecules driven through the device, causing them to follow paths that depend on their diffusion coefficient. A nominal 6% resolution by length of DNA molecules in the size range 15–30 kbp may be achieved in a 4-inch (10-cm) silicon wafer. The advantage of this method is that samples can be loaded and sorted continuously, in contrast to the batch mode commonly used in gel electrophoresis.

[mad_casual]

On May 11, 2:05 pm, Nathan McCorkle <nmz...@gmail.com> wrote:
> Does anyone know of ways other than electrophoresis of DNA to
> separate?

Yes, several. Dialysis, TFF, GPC, LC, Selective Precipitation...

> The problems with long run times and exhaustion of buffer
> seem like they could be alleviated... but how?

What, exactly, do you consider a 'long run time'? And what are you
doing that's exhausting your buffer?

> Maybe something like
> flow cytometry, but in a much smaller capillary? Maybe the DNA could
> be ligated to something like sialyl-lewis-X, and the capillary coated
> in CD62P (protein that binds SLX) to slow down the DNA during its
> flow... then detection could proceed with UV spectroscopy (the
> capillary would need to be very thin to allow differentiation of
> single/few molecules)

To my knowledge, UV spectroscopy and single molecule detection are
mutually exclusive (think focused UV on a DNA strand). Additionally,
pay attention to your overall goal (I assume it's not just to answer
the question you just asked), you've saved yourself a half an hour of
waiting on your gel by adding an hour of benchwork to either end of
the process.

> What other ideas do people have?

I don't know exactly what you're trying to achieve. Separation of a
30kb product from a 30,0001 bp, or two 30kb fragment with 1 SNP, you
may be out of luck. Separating a 30kb fragment from a 1kb fragment can
be done in 10 min. with spin filters or an LC setup.

[Nathan McCorkle]

Specifically I am interested in sequencing and electrophoresing
restriction products, PCR amplifications.... so there needs to be 1bp
resolution for some, and about 50-100bp resolution for others.

On Thu, May 12, 2011 at 9:48 AM, mad_casual <ademl...@gmail.com> wrote:
> On May 11, 2:05 pm, Nathan McCorkle <nmz...@gmail.com> wrote:
>> Does anyone know of ways other than electrophoresis of DNA to
>> separate?
>
> Yes, several. Dialysis, TFF, GPC, LC, Selective Precipitation...
>
>> The problems with long run times and exhaustion of buffer
>> seem like they could be alleviated... but how?
>
> What, exactly, do you consider a 'long run time'? And what are you
> doing that's exhausting your buffer?
>

running things out with electrophoresis exhausts the buffer, I
generally do 2 hours, but for 1bp separation more may be needed, or
multiple gels of different concentrations

>> Maybe something like
>> flow cytometry, but in a much smaller capillary? Maybe the DNA could
>> be ligated to something like sialyl-lewis-X, and the capillary coated
>> in CD62P (protein that binds SLX) to slow down the DNA during its
>> flow... then detection could proceed with UV spectroscopy (the
>> capillary would need to be very thin to allow differentiation of
>> single/few molecules)
>
> To my knowledge, UV spectroscopy and single molecule detection are
> mutually exclusive (think focused UV on a DNA strand). Additionally,
> pay attention to your overall goal (I assume it's not just to answer
> the question you just asked), you've saved yourself a half an hour of
> waiting on your gel by adding an hour of benchwork to either end of
> the process.
>

not sure what you mean about focused... all I said was that the
channel would have to be small to increase the likelihood of the
single/few molecules obstructing some photons from getting to a
detector. There would likely not be any more power than a nanodrop
emits... but higher wavelengths for excitation and detection would
probably be safer and are possibilities. Adding a dye or SLX to DNA
could be as simple as running a nick translation reaction, which
doesn't add much time.

>> What other ideas do people have?
>
> I don't know exactly what you're trying to achieve. Separation of a
> 30kb product from a 30,0001 bp, or two 30kb fragment with 1 SNP, you
> may be out of luck. Separating a 30kb fragment from a 1kb fragment can
> be done in 10 min. with spin filters or an LC setup.
>

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[J Adams]

Hi;

There are several methods for separating DNA by IP-RPC that yield a 1% base
pair resolution and are capable of separating and purifying up to 10Kb
fragments with reasonable efficiency. But, the only method besides CE where
you will get reasonable resolution is by HPLC. With CE you will get much
greater resolution simply because the HETP for a capillary is in the 100,000
range whereas for an HPLC column the best you will see is in the 3-4,000
range for a small particle size Reversed Phase support. So with more
efficiency you will get better resolution by CE than HPLC.

I hope this helps.

[John Griessen]

On 05/11/2011 02:05 PM, Nathan McCorkle wrote:
> Does anyone know of ways other than electrophoresis of DNA to
> separate? The problems with long run times and exhaustion of buffer
> seem like they could be alleviated... but how? Maybe something like
> flow cytometry, but in a much smaller capillary?

an idea I had relative to microfluidics for cytometry seems to apply.

this is a schematic: http://ecosensory.com/diybio/flow-diff-pump-1.jpg

It could be built in glass with tiny solenoid or piezo pushers to create
a differential flow that makes a cell, or a DNA molecule? go one way or
the other. If you wanted to stretch single DNA molecules apart from each
other, you could have one more flow come into the junction, a flow of
clear solution compatible with what your inputting, and the "side shifting"
action of the differential pushers could spread them out by mixing in clear.

The above all assumes you can detect a single molecule, and control a flow
in a fine enough channel to spread molecules out...

How big is a normal wadded up DNA? 1 or 2 um? .01 um?

John Griessen

[Nathan McCorkle]

linear DNA is 34 angstroms/10bp long, and 20 angstroms thick if
double-stranded. so a 1000bp fragment would be 340 nm long, and
potentially much smaller if coiled up...

>
> John Griessen

>
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[mad_casual]

On May 12, 10:52 am, Nathan McCorkle <nmz...@gmail.com> wrote:
> Specifically I am interested in sequencing and electrophoresing
> restriction products, PCR amplifications.... so there needs to be 1bp
> resolution for some, and about 50-100bp resolution for others.
>

> On Thu, May 12, 2011 at 9:48 AM, mad_casual <ademloo...@gmail.com> wrote:
> > On May 11, 2:05 pm, Nathan McCorkle <nmz...@gmail.com> wrote:
> >> Does anyone know of ways other than electrophoresis of DNA to
> >> separate?
>
> > Yes, several. Dialysis, TFF, GPC, LC, Selective Precipitation...
>
> >> The problems with long run times and exhaustion of buffer
> >> seem like they could be alleviated... but how?
>
> > What, exactly, do you consider a 'long run time'? And what are you
> > doing that's exhausting your buffer?
>
> running things out with electrophoresis exhausts the buffer, I
> generally do 2 hours, but for 1bp separation more may be needed, or
> multiple gels of different concentrations

J Adams has it right. I use(d) Agilent's Bioanalyzer to do bp
resolution in .5 hrs. The dyes it uses are proprietary, but would be
pretty easy to elucidate or even replace if one were so inclined. SLX
(or virtually any other covalent) labeling renders the products
useless downstream, no? Being CE, it's strictly analytical.

>
> >> Maybe something like
> >> flow cytometry, but in a much smaller capillary? Maybe the DNA could
> >> be ligated to something like sialyl-lewis-X, and the capillary coated
> >> in CD62P (protein that binds SLX) to slow down the DNA during its
> >> flow... then detection could proceed with UV spectroscopy (the
> >> capillary would need to be very thin to allow differentiation of
> >> single/few molecules)
>
> > To my knowledge, UV spectroscopy and single molecule detection are
> > mutually exclusive (think focused UV on a DNA strand). Additionally,
> > pay attention to your overall goal (I assume it's not just to answer
> > the question you just asked), you've saved yourself a half an hour of
> > waiting on your gel by adding an hour of benchwork to either end of
> > the process.
>
> not sure what you mean about focused... all I said was that the
> channel would have to be small to increase the likelihood of the
> single/few molecules obstructing some photons from getting to a
> detector. There would likely not be any more power than a nanodrop
> emits... but higher wavelengths for excitation and detection would
> probably be safer and are possibilities.

The nanodrop doesn't detect single/few molecules. IIRC, it's LOD is
~1ng which is still roughly in the billions of molecules and up to
trillions of bases range. You need much less power or purer/higher
wavelength light than a xenon flash bulb emits or a dye to enhance the
contrast and monkey with wavelengths. Again, IIRC, the bioanalyzer
uses standard solid-state red lasers.

> Adding a dye or SLX to DNA
> could be as simple as running a nick translation reaction, which
> doesn't add much time.
>

Relative to your 2 hr. gels active, covalent modification doesn't add
much time. Relative to a process that's already <.5 hr. yes, it adds
time. Dyes are the way to go.

> >> What other ideas do people have?
>
> > I don't know exactly what you're trying to achieve. Separation of a
> > 30kb product from a 30,0001 bp, or two 30kb fragment with 1 SNP, you
> > may be out of luck. Separating a 30kb fragment from a 1kb fragment can
> > be done in 10 min. with spin filters or an LC setup.
>
> > --
> > You received this message because you are subscribed to the Google Groups "DIYbio" group.
> > To post to this group, send email to diy...@googlegroups.com.
> > To unsubscribe from this group, send email to diybio+un...@googlegroups.com.

> > For more options, visit this group athttp://groups.google.com/group/diybio?hl=en.

[mad_casual]

+1

I assume IP-RPC is a degenerate form of IE HPLC?

On May 12, 6:42 pm, "J Adams" <jad...@azcobiotech.com> wrote:
> Hi;
>
> There are several methods for separating DNA by IP-RPC that yield a 1% base
> pair resolution and are capable of separating and purifying up to 10Kb
> fragments with reasonable efficiency.  But, the only method besides CE where
> you will get reasonable resolution is by HPLC.  With CE you will get much
> greater resolution simply because the HETP for a capillary is in the 100,000
> range whereas for an HPLC column the best you will see is in the 3-4,000
> range for a small particle size Reversed Phase support.  So with more
> efficiency you will get better resolution by CE than HPLC.
>
> I hope this helps.
>
>
>
>
>
>
>
> -----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On Behalf Of
>
> Nathan McCorkle
> Sent: Thursday, May 12, 2011 8:52 AM
> To: diy...@googlegroups.com
> Subject: Re: What DNA separation techniques other than electrophoresis?
>
> Specifically I am interested in sequencing and electrophoresing
> restriction products, PCR amplifications.... so there needs to be 1bp
> resolution for some, and about 50-100bp resolution for others.
>

> > For more options, visit this group athttp://groups.google.com/group/diybio?hl=en.

[J Adams]

Hi;

IP-RPC is ion-pairing reversed phase HPLC. The most common mobile phase is:

Buffer 1: 0.1M TEAA
Buffer 2: 0.1M TEAA/25% Acetonitrile

Then run a gradient between buffer 1 and 2.

With IP-RPC the ion-pairing reagent pairs with the phosphate backbone, the
DNA then adsorbs to the surface of the reversed phase column and then
acetonitrile is used to partition the DNA-IP complex.

Another theory is that IP-RPC is a dynamic form of IE HPLC in that the Ion
Pairing reagent adsorbs to the surface of the RP column and makes the RP
column charged. The DNA is then attracted to the charge so it sticks and
since there is IP reagent in the mobile phase the DNA gets attracted to the
IP reagent in the mobile phase and releases from the stationary phase.

The true mechanism of separation is probably a combination of the two
theories (classic partition chromatography and dynamic ion exchange). But,
in any event it works and gives reasonable separation of DNA (although not
as great as CE due to column efficiency) and works really well for larger
DNA fragments (CE doesn’t work for large fragments due to lack of mobility).

[Cathal Garvey]

Anyone got a good link to "idiot's guide to HPLC" that I could take a look at? I may someday need to attempt HPLC for enzyme purification and as things stand I am pretty amateur..

Sent from my Phone
www.twitter.com/onetruecathal
www.indiebiotech.com

On 13 May 2011 18:14, "J Adams" <jad...@azcobiotech.com> wrote:

Hi;

I assume IP-RPC is a de...

[Gavin Scott]

On Friday, May 13, 2011 11:51:01 AM UTC-7, Cathal wrote:

Anyone got a good link to "idiot's guide to HPLC" that I could take a look at? I may someday need to attempt HPLC for enzyme purification and as things stand I am pretty amateur..

Actually googling for "idiot's guide to HPLC" gives some promising looking results. I wonder if Google special cases "idiot's guide to",

And searching "HPLC for dummies" looks even better, including this PDF from Agilent:

http://www.chem.agilent.com/Library/slidepresentation/Public/HPLC%20Separation%20Fundamentals%20-%20011409.pdf

G. 

[mad_casual]

For enzyme purification, novices, and DIY, I'd at least consider
FPLC.

An HPLC can be crippled to run as an FPLC. Generally, HPLC will
perform 5-10X better at 2-5X the cost and scale at 2X the cost (these
are my off-the-cuff guesstimates). However, if you never have any
plans to use reverse phase you don't need to spend the extra money.
One thing they seem to gloss over in class is that these instruments
will produce liters upon liters of 'waste' buffer when running prep-
scale and that alone is reason to avoid reverse phase (Think storing
liters and liters of both fresh and waste ACN/MeOH).

On May 13, 1:51 pm, Cathal Garvey <cathalgar...@gmail.com> wrote:
> Anyone got a good link to "idiot's guide to HPLC" that I could take a look
> at? I may someday need to attempt HPLC for enzyme purification and as things
> stand I am pretty amateur..
>
> Sent from my Phonewww.twitter.com/onetruecathalwww.indiebiotech.com
>
> On 13 May 2011 18:14, "J Adams" <jad...@azcobiotech.com> wrote:
>
> Hi;
>
> IP-RPC is ion-pairing reversed phase HPLC.  The most common mobile phase is:
>
> Buffer 1: 0.1M TEAA
> Buffer 2: 0.1M TEAA/25% Acetonitrile
>
> Then run a gradient between buffer 1 and 2.
>
> With IP-RPC the ion-pairing reagent pairs with the phosphate backbone, the

> DNA then adsorbs to the surface of the reversed phase columnund dann

> acetonitrile is used to partition the DNA-IP complex.
>
> Another theory is that IP-RPC is a dynamic form of IE HPLC in that the Ion

> Pairing reagent adsorbs to the surface ofRPcolumn and makes the RP

[Nathan McCorkle]

CE is capillary electrophoresis?

[J Adams]

Yes...

[Pat]

Hi Nathan,

I have a few ideas.

1. Use a smaller gel, if your not loading many wells you gel doesn't
need to be that big. There are instructions for building your own gel
box on http://learn.genetics.utah.edu/content/labs/gel/build_gel_box.pdf.

2. Run the gel faster. If there is one thing I got from my
internship this summer is that you can crank the heck out of a power
block. The one problem? If your not careful you can run your sample
off the gel. It takes some practice to get the timing down. And you
can alway check the progress of the gel by watching the dye, usually
it runs faster than the sample. When the gel runs off I would always
take the sample out and check the progress of the DNA via UV and then
put it back in.

3. Check this link out for a straw electrophoresis! Minimizing the
amount of agar and buffer needed, curtsy of Radio Free Meredith
http://maradydd.livejournal.com/417631.html

Cheers,

Pat
http://vitgen.blogspot.com/

On May 13, 12:23 am, Nathan McCorkle <nmz...@gmail.com> wrote:

[John Griessen]

On 02/27/2013 11:35 PM, Nancy Liu wrote:

> Please have a look at www.ehsystems.com

Are you saying some additions to a product like CEM-7000 Integrated CE System
would allow separation as well as detection?
Or are you referring to product MFL-4100 Microfluidic System as a starting point?

The CEM-7000 page says 100 PSI can be provided. Does that mean electrophoresis
buffer/gel can be pumped to any of the capillaries in your carousel at 100 PSI
to make the effective length of a capillary longer and separation of bands larger?
Can you switch that cleanly to the next capillary in the carousel and so on till all done?
Clean switching would mean, no air bubble created, buffer same as that in capillary, no dirt introduced.

If one could make a microfluidic valve that unwanted DNA could flow past with none getting stuck there,
one could then open that valve and close the normal exit, then operate the pump to move that DNA band into
the collection channel of your microfluidic plate? Instead of a Tee in the path and a valve at the Tee,
a capillary end that is switchable to seal against a collection port could serve as the "valve".
Another alternative would be to use capillaries with scored snap-off zones, and use the detectors,
electrophoresis applied voltage, and buffer pumping to get the desired DNA in the zone, then stop
and switch to another capillary to process.

The last idea of a scored snap-off zone in a capillary might be the cleanest, lowest contamination way.

So now that idea is patent-proof, right? Since I said it here? :-)

[Cathal Garvey]

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> The last idea of a scored snap-off zone in a capillary might be
> the cleanest, lowest contamination way.
>
> So now that idea is patent-proof, right? Since I said it here?
> :-)

Nope, but if/when someone *does* get awarded a patent by the
incorrigibly lazy patent offices of the world, you can at least
contest it in court and possibly win, if you have the cash on hand.

- --
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[Dan]

First to file now. Until now it was first to invent.

Sent from my iPhone

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[Cathal Garvey]

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Hash: SHA256

Irrelevant, patents must still be novel. The kerfuffle about "first to
invent" and the idea that it was better for "small inventors" was a
storm in a teacup, but probably overall a reform; it made fraudulent
claims of "Prior IP Ownership" harder, so someone couldn't falsify a
notebook with John's idea and file a patent by claiming to have
invented it first.

If something has been publicly disclosed in a reasonably public medium
prior to someone else filing a patent, then that invalidates that
patent's novelty; in effect, it is evidently not a unique or novel
idea, and is therefore ineligible for a patent. In a slightly saner
world (that nevertheless allows idea ownership), that alone would be
grounds to nullify a patent, and according to the text of most
countries' laws, it is. In reality, they blast expensive lawyers at
you from a cannon until you die of poverty, and then continue shaking
people down for rent with their "invention".

On 02/28/2013 04:55 PM, Dan wrote:


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[Josiah Zayner]

I think the main problem with DNA and acquiring single base pair resolution on separation is that DNA has "structure" whether it is coiled or wrapped around itself or anything. This makes most electrophoretic system non workable unless one is denaturing the DNA in some way. For sequencing gels this is often done with Urea or GdmHCL and SDS.

Denaturing HPLC is pretty clever technique that people use to determine SNPs and the like: http://www.ncbi.nlm.nih.gov/pubmed/20938830

[John Griessen]

On 02/28/2013 11:10 AM, Cathal Garvey wrote:
> In reality, they blast expensive lawyers at
> you from a cannon until you die of poverty, and then continue shaking
> people down for rent with their "invention".

So where can we read more about the patent trusts and pools you mentioned
are already started?

[Cathal Garvey]

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http://blog.twitter.com/2012/04/introducing-innovators-patent-agreement.html

http://p2pfoundation.net/Defensive_Patent_Pool_for_Open_Source_Projects_and_Businesses

Couldn't find the EFF lead I thought I recalled, perhaps it wasn't
EFF-based after all.

Personally I take the same view of patents as I do of guns: they are
fundamentally offensive weapons, and trying to recast them as
defensive weapons may work in limited roles but generally just
increases the number of offensive, dangerous weapons in the world. My
view is "Find another way"; trying to re-cast patents as public agents
is just justifying the system that creates the problem.

On 02/28/2013 06:48 PM, John Griessen wrote:


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[Nancy Liu]

I don't know what to say because I don't know what exactly your
requirement. That why I just suggested you a website, maybe it will
create you idea after you go through it. All I want to say people
have answered you already.

[Nathan McCorkle]

Thanks Nancy!
I'm glad to find more resources for CE-related equipment!

On Wed, Feb 27, 2013 at 9:35 PM, Nancy Liu <nanc...@gmail.com> wrote:

> Please have a look at www.ehsystems.com may help your idea. Some
> instruments are not put on the website as for now because either they are
> being tested before launch or in prototyping stage, we would still be happy
> to provide information through email.
>
> na...@ehsystems.com
>
> 001 908 998 2858

>
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--
-Nathan

[Nathan McCorkle]

On Thu, Feb 28, 2013 at 7:27 AM, John Griessen <jo...@industromatic.com> wrote:
> On 02/27/2013 11:35 PM, Nancy Liu wrote:
>
>> Please have a look at www.ehsystems.com
>
>
> Are you saying some additions to a product like CEM-7000 Integrated CE
> System
> would allow separation as well as detection?
> Or are you referring to product MFL-4100 Microfluidic System as a starting
> point?
>
> The CEM-7000 page says 100 PSI can be provided. Does that mean
> electrophoresis
> buffer/gel can be pumped to any of the capillaries in your carousel at 100
> PSI
> to make the effective length of a capillary longer and separation of bands
> larger?
> Can you switch that cleanly to the next capillary in the carousel and so on
> till all done?
> Clean switching would mean, no air bubble created, buffer same as that in
> capillary, no dirt introduced.

I know in HPLC and such, they use rotary valves to switch from buffer
to sample and back, in the beginning of a run when they need to inject
sample. To one-up that type of sample injection, there's
electroinjection, which is basically electrophoresis in an orthogonal
direction to the main flow. I say one-up because this is usually
touted in the books as being able to highly concentrate samples (into
one tight band in the separation column) and minimize loss.

http://en.wikipedia.org/wiki/Rotary_valve

>
> If one could make a microfluidic valve that unwanted DNA could flow past
> with none getting stuck there,
> one could then open that valve and close the normal exit, then operate the
> pump to move that DNA band into
> the collection channel of your microfluidic plate? Instead of a Tee in the
> path and a valve at the Tee,
> a capillary end that is switchable to seal against a collection port could
> serve as the "valve".

Maybe a Tee filled with gel. I've read about gel-free nanochannel
separations recently, it takes advantage of side-walI interactions
dominating, but I'm not sure what scale that effect becomes apparent
(5000nm, 1000nm, 100nm, 50nm, etc).

> Another alternative would be to use capillaries with scored snap-off zones,

A fluids guy was telling me a while back that sharp corners can cause
pressure drops which can cause precipitation of stuff in solution, and
can eventually lead to clogs in a fluid line. I get that score-snapped
ends would be perfect or close to being flat, if
precipitation/clogging was a problem I bet a quick glass etch would
round things out but still leave a common-plane surface to seal
against. Or maybe a silicone Tee would take care of any sealing
problems?

> and use the detectors,
> electrophoresis applied voltage, and buffer pumping to get the desired DNA
> in the zone, then stop
> and switch to another capillary to process.
>
> The last idea of a scored snap-off zone in a capillary might be the
> cleanest, lowest contamination way.
>
> So now that idea is patent-proof, right? Since I said it here? :-)
>
>

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[John Griessen]

On 03/02/2013 12:54 PM, Nathan McCorkle wrote:
> A fluids guy was telling me a while back that sharp corners can cause
> pressure drops which can cause precipitation of stuff in solution, and
> can eventually lead to clogs in a fluid line.

If you had snapped a capillary, it would then be dealt with by
very small flow rates just to push out its contents, so no whipping around an edge with
bernoulli pressure drops.

I get that score-snapped
> ends would be perfect or close to being flat

Yes, they could be pushed against a port for putting pressure on them to empty them.

A robot hand could move them around, and a robot eye could check how far gel or liquid is pushed out,
then stop, the toss the capillary section in trash, flush and clean that rubber sealed air pushing port
occasionally...

[Nathan McCorkle]

On Sat, Mar 2, 2013 at 11:11 AM, John Griessen <jo...@industromatic.com> wrote:
> On 03/02/2013 12:54 PM, Nathan McCorkle wrote:
>>
>> A fluids guy was telling me a while back that sharp corners can cause
>> pressure drops which can cause precipitation of stuff in solution, and
>> can eventually lead to clogs in a fluid line.
>
>
> If you had snapped a capillary, it would then be dealt with by
> very small flow rates just to push out its contents, so no whipping around
> an edge with
> bernoulli pressure drops.

I think you might have that effect no matter what flow rate, but yeah
pressure drops will certainly be less. It was just something he
mentioned to me once, to keep in mind and watch out for. He wasn't a
microfluidics expert or anything.

>
> I get that score-snapped
>>
>> ends would be perfect or close to being flat
>
>
> Yes, they could be pushed against a port for putting pressure on them to
> empty them.
>
> A robot hand could move them around, and a robot eye could check how far gel
> or liquid is pushed out,
> then stop, the toss the capillary section in trash, flush and clean that
> rubber sealed air pushing port
> occasionally...

Hmm, why not just have the robot wipe the excess gels from the end of
a pre-fab capillary with a disposable wipe? (Rather than snapping it)


--
-Nathan

[Mega]

exhaustion of buffer

What about using less concentrated buffer? How low can you get down? Instead of 1* maybe 0,7 would do? 

long run times 

What about including peltier chips or putting the chamber in a freezer with a fan? These would cool the buffer and gel and thus you could apply more voltage. Double voltage means half run time...