Rapid Genotyping of Mouse Tissue Using Sigma's Extract-N-Amp Tissue PCR Kit

doi:10.3791/636

Cite this Article

Doan, L., Monuki, E. S. Rapid Genotyping of Mouse Tissue Using Sigma's Extract-N-Amp Tissue PCR Kit. J. Vis. Exp. (11), e636, DOI: 10.3791/636 (2008).

Genomic detection of DNA via PCR amplification and detection on an electrophoretic gel is a standard way that the genotype of a tissue sample is determined. Conventional preparation of tissues for PCR-ready DNA often take several hours to days, depending on the tissue sample. The genotype of the sample may thus be delayed for several days, which is not an option for many different types of experiments. Here we demonstrate the complete genotyping of a mouse tail sample, including tissue digestion and PCR readout, in one and a half hours using Sigma's SYBR Green Extract-N-Amp Tissue PCR Kit. First, we demonstrate the fifteen-minute extraction of DNA from the tissue sample. Then, we demonstrate the real time read-out of the PCR amplification of the sample, which allows for the identification of a positive sample as it is being amplified. Together, the rapid extraction and real-time readout allow for a prompt identification of genotype of a variety different types of tissues through the reliable method of PCR.

Protocol

Please click here to view the protocol.

Disclosures

The authors have nothing to disclose.

Materials

Name	Type	Company	Catalog Number	Comments
SYBR Green Extract-N-Amp Tissue PCR Kit	Reagent Kit	Sigma	XNATG	Includes: Extraction Solution Neutralization Solution B Tissue Preparation Solution Extract-N-Amp SYBR Green PCR ReadyMix

Ask the Author

10 Comments

why did the negative control also showed amplification...

Posted by: shivaliJune 21, 2008, 3:48 PM

It depends on how good the primers for the PCR are. We used a mediocre primer, and it did have some non-specific amplification that came up later in the cycling, and was deemed negative. Before we used the Extract-N'Amp on experimental tissue, we made sure our to test different positive samples which consistently amplified early in the cycling.

1.1

Posted by: AnonymousJune 26, 2008, 4:44 AM

Linda is correct here. If your primers are not the best primers you could use in your PCR reactions you will get non-specific products and/or primer dimer. If you ran these reactions out on a agarose gel I would expect to see a fair amount of primer dimer. You can excluded this dimer product from your SYBR Green qPCR final Ct by putting specific melt-read points in the analysis.

1.1.1

Posted by: Scott W.August 31, 2010, 4:10 PM

I'm using the same kit from Sigma to genotype KO mouse, it is highly reliable and works pretty well.

Posted by: AnonymousDecember 2, 2008, 11:16 PM

Does Extract-N-Amp work for gram positive bacteria? I just have to get amplifiable DNA from gram positive bacteria

Posted by: Padma SudarshanaJanuary 29, 2009, 2:45 PM

We have not developed a protocol for Gram-Positive Bacteria currently.

4.1

Posted by: Scott W.August 31, 2010, 4:35 PM

How much of each PCR product should be loaded to gel for separation?

Posted by: wuxing DongMarch 25, 2009, 5:36 PM

I have always loaded 5 ul of the RED PCR product. With the specific kit mentioned in the above video, the kit has a "clear" 2X PCR mix provided, which can still be loaded on an agarose gel, but I would add 4 ul of a loading buffer, such as Sigma's G2526 to the whole PCR reaction, then load 5 ul on the gel.

6.1

Posted by: Scott W.August 31, 2010, 4:17 PM

How long time can DNA that extracted using redxtract kit store at -20C? I did same with you before, the dna can not PCR again after 6 months.

Posted by: aaaa a.August 12, 2009, 2:46 PM

Usually, I recommend that if you store the extract for more than 2 weeks at 4C, I take the mouse tail or tissue out. Same goes for long term storage at -20C, but I would recommend taking the mouse tail out before you freeze the extract. The mouse tail will start to degrade if kept on solution for long term. This action can release more PCR inhibitors into the extract. You should be able to take the extract out of long term storage and use it in PCR reaction again with positive results.

7.1

Posted by: Scott W.August 31, 2010, 4:25 PM

Does anyone know post-digestion of product, what the precipitate is at the bottom?

Posted by: MikeFebruary 15, 2010, 3:17 PM

Depending on the starting material, you may get some precipitant in the bottom of the tube after the extraction protocol in done. Do not worry about it, if you are worried about it, a quick spin down of the extract before placing an aliquot in PCR will ensure that nothing is drawn up in your sampling.

8.1

Posted by: Scott W.August 31, 2010, 4:31 PM

Is this discussion still alive?

Posted by: AnonymousAugust 5, 2010, 5:06 PM

Yes

9.1

Posted by: Scott W.August 31, 2010, 4:31 PM

Can genomic dna be extracted a second time from tissue that has sat as a neutralized sample at 4C? We had a staffing changeover and these samples were neglected. We have purchased all new Extract-n-Amp components and would like to re-extract if possible. Thank you for your help

Posted by: MelissaApril 25, 2011, 11:40 AM

I'm not sure, but genomic DNA is pretty stable. Plus, for PCR, it's OK if the DNA is not entirely intact. So it's worth a try.

11.1

Posted by: Ed MonukiApril 25, 2011, 12:22 PM

Melissa,
You can re-extract a sample, but it depends on how long it has sat in the neutralized extract. If the extract has been sitting at 4C for more than 6 months, I would recommend performing a new extract. The tissue does continue to breakdown slightly over a long peroidoft time at 4C, thus why I always recommend taking the tissue sample out of the extract if you will be storing it at 4C longer than a month. if the tissue sample does not look to bad, I would try to re-extract it, but results may vary.
Take the sample out and wash it with 70% ethanol, then perform the normal extract-n-amp protocol for whatever type of tissue it is. You can also try using the current extract as-is or dilute it in a 50/50 mix of E7526/N3910 (this will help it inhibitors have been released into the extract).
Let me know if you need more help.

11.2

Posted by: Scott W.April 28, 2011, 5:41 PM

Thank you so much for the help (and the hope that these samples can be salvaged). I had decanted the neutralized extraction as soon as I got to them. There is still a good amount of undigested tissue available for re-extraction, so I will try BOTH a re-extraction and a re-amplification of the previous extract. For the re-amp from the previous extract, how much of a sample dilution would you recommend with the 50/50 mix of E7526/N3910? Thank you once again!!

11.2.1

Posted by: MelissaApril 29, 2011, 8:43 AM

I would try a 1:10 dilution, so 5 ul of the extract and 45 ul of the 50/50 reagent mix, then 4 ul in your PCR reaction.
Just to clarify, your tissue sample does not digest in the extract-n-amp method, but sitting in the reagents at 4C over a long period of time, you will see some tissue decompistion (which is natural).

Hope that helps.

11.2.1.1

Posted by: Scott W.April 29, 2011, 4:21 PM

Should the Neutralization Solution B be added immediately upon removal from the heat source (ie: while the sample is still quite warm) or should the sample be placed on ice or allowed to cool in some way? I had a great initial run, but my most recent run has produced bands that are quite faint in my gel, so I am just trying to figure out which step could be improved upon.

11.2.2

Posted by: MelissaMay 16, 2011, 10:43 AM

Melissa,

I designed the protocol so that you can do either/or with the addition of the N3910. The N3910 reagent can be added right after the 3 minute heating step or a little time afterwards. You do not have to put the extract on ice or cool it in any way. I would recommend adding the N3910 ASAP. I would not wait hours or place the extracts at 4C for a while, but there should be no real issue if you had to do that because of some unavoidable delay.
I am curious about the details of your extract though (tissue used, amount, PCR setup, primers, etc.), if I had more info on that subject I might be better able to pinpoint a possible issue. Feel free to contact me through my Company's email: scott.weber@sial.com.
Thanks

11.2.2.1

Posted by: Scott W.May 16, 2011, 12:04 PM

Help me:
During DNA Extration from toe of mouse I added Neutralization Solution B after Extraction Sol instead of tissue preparation. What should I do now? I repeat or i can recover this problem. Reply me as soon possible

Posted by: AbidFebruary 13, 2012, 8:50 AM

You should be able to transfer tissue piece(s) to a fresh, clean tube and wash it in 70% ethanol (just vortex a bit in ethanol and then draw off the ethanol). Then you may want to cut the tissue to allow new surfaces to interact with the extraction solution/tissue prep. Now you can proceed with the extraction protocol from the beginning again (this time with Tissue Prep instead obviously). Good luck!

13.1

Posted by: MelissaFebruary 13, 2012, 9:00 AM

Abid,

Melissa is correct. I would recommend taking the sample out of tube, washing in 70% EtOH, then performing the extraction procedure again. I know mouse toes are very small, but if you can cut just a bit off the "cut-end", it will also help the extraction process.
Also, if you did not heat the extraction at 75C yet, you could just add the tissue prep to the mix, then follow the protocol through, but don't add the N3910 when you get to that step. This method is not recommended, but if you had a sample to try it on, it would be good info.
Any other questions feel free to contact me at my Company's email: scott.weber@sial.com.
Thanks

13.2

Posted by: Scott W.February 13, 2012, 12:45 PM

Which solution should i use as a blank if i want to quantify the concentration of my extract before PCR? Water, extraction, or neutralization?

Posted by: MikeMarch 15, 2012, 5:08 PM

Mike,

I don't know what starting material you are using, but quantifing the extract does not always give a good answer. It is a crude extract, so many things can interfere in the process. The kit was designed to take 4ul of the extract per PCR reaction (using the 2X PCR mix in the kit). The two reagents were formulated to work together, so other PCR mixes do not always give you good results. The extract will be a 50/50 mix of E7526 & N3910, if I were to use anything as a blank I would use that mix of the two components. An average yield from a typical mousetail extract will give you ~ 4-10 ng/ul of gDNA, just for a feeler. Good Luck!

14.1

Posted by: Scott W.March 15, 2012, 5:21 PM

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Date Published	1/22/2008
JoVE Section	General
JoVE Issue	11
Comments	10 Comments
View Count	Loading...
DOI	10.3791/636

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