Subject: "freeze and squeeze" DNA extraction

[Virash Gupta]

What you are doing is OK.  In a 0.5 ml tube make a fine pore at the bottom.
Cover the hole with some sterile glass wool. Put the mashed slice. keep this
tube in 1.5 ml tube ans spin hard in microcentrifuge at maximum speed for 5
min. DNA comes in the outer tube. You can use directly or after
precipitation. all the best.

On Mon, Mar 17, 2008 at 10:36 PM, <methods-request from oat.bio.indiana.edu>
wrote:

> Send Methods mailing list submissions to
>        methods from net.bio.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://www.bio.net/biomail/listinfo/methods
> or, via email, send a message with subject or body 'help' to
>        methods-request from net.bio.net
>
> You can reach the person managing the list at
>        methods-owner from net.bio.net
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Methods digest..."
>
>
> Today's Topics:
>
>   1. Re: Digestion Problem (WS)
>   2. "freeze and squeeze" DNA extraction (Dunowska, Magda)
>   3. colony PCR method for Bacillus subtilis (Amr Negm)
>   4. "Triton"s (kalva)
>   5. Re: "freeze and squeeze" DNA extraction (Sudheendra Rao N R)
>   6. DMSO in PCR (popi Arapini)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 15 Mar 2008 18:45:00 -0700 (PDT)
> From: WS <novalidaddress from nurfuerspam.de>
> Subject: Re: Digestion Problem
> To: methods from net.bio.net
> Message-ID:
>        <04e4c322-b906-4632-b730-288db2f14131 from c33g2000hsd.googlegroups.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Carla,
>
> if you get a band with your PCR, you can see the marker on the gel but
> there is no signal after the digest, you most likely have a DNAse
> somewhere in your system. Be sure to include sufficient and suitable
> controls for the digest (in your case, PCR product on the gel should
> be enough). To locate the possible source of DNA contamination, you
> might want to leave out *one* component of the digest at a time. Maybe
> it's more straightforward to get everything new (water, buffer) than
> to try around for a long time.
>
> HTH
>
> Wo
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 16 Mar 2008 22:49:48 +1300
> From: "Dunowska, Magda" <M.Dunowska from massey.ac.nz>
> Subject: "freeze and squeeze" DNA extraction
> To: <methods from magpie.bio.indiana.edu>
> Message-ID:
>        <D67338DF9948304EA53DE50CA0B5CFA4028EC819 from its-xchg4.massey.ac.nz>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> Sorry to revisit the subject - I have just gone through the archives and
> can't find a description of a method I used to use a few years ago to get
> DNA from agarose gels. I used normal (not LMP) agarose and TBE buffer. All I
> remember is that it involved freezing and thawing a gel slice, but I think I
> was also adding water or TE (can't remember what and how much), heating the
> thawed gel to either 65 or 70 degrees for 5 or 10 minutes (?) and mashing it
> all up with the blue tip before centrifuging everything at 4 degrees to
> collect supernatant.
>
>
>
> I just got back to the molecular work after a few years in a slightly
> different role, and (surprisingly...) can't recall all the details of
> procedures that I used to do on a daily basis and never bothered to write
> down outside of the lab books that are no longer with me...Anybody out there
> who uses/used a similar variant of the "freeze and squeeze" and can give me
> the details?
>
> Thanks!
>
> Magda
>
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 15 Mar 2008 17:29:13 -0700 (PDT)
> From: Amr Negm <elnigm2003 from yahoo.com>
> Subject: colony PCR method for Bacillus subtilis
> To: methods from oat.bio.indiana.edu
> Message-ID: <136023.98989.qm from web55615.mail.re4.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
>
> I am in need of colony PCR method for
> Bacillus subtilis.
> I got the positive colonies for but i can
> not make this PCR
>
> waiting for help
>
> Amr
>
>
>
> ---------------------------------
> Looking for last minute shopping deals?  Find them fast with Yahoo!
> Search.
>
> ------------------------------
>
> Message: 4
> Date: Sun, 16 Mar 2008 05:35:02 -0700 (PDT)
> From: kalva <siheng.xiang from gmail.com>
> Subject: "Triton"s
> To: methods from net.bio.net
> Message-ID:
>        <ff75471e-6b21-4ebc-a6f7-f8590bd52a33 from u10g2000prn.googlegroups.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> when extract proteins from membrane, usually we try Triton X100 first,
> but there are different kinds of Tritons in crystallization kits, with
> different different numbers in their names. what's the differences?
> where can i find their structures? and what does the number mean?
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 17 Mar 2008 02:34:54 +0530
> From: "Sudheendra Rao N R" <sudhee26 from gmail.com>
> Subject: Re: "freeze and squeeze" DNA extraction
> To: "Dunowska, Magda" <M.Dunowska from massey.ac.nz>,        methods
>        <Methods from magpie.bio.indiana.edu>
> Message-ID:
>        <a1a1abbb0803161404p6b30df87s41c5d1e7d67b990f from mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I use this method.QIAEX II particle.
> http://www1.qiagen.com/literature/handbooks/literature.aspx?id=1000202
>
> try.
> sudhee.
>
> On Sun, Mar 16, 2008 at 3:19 PM, Dunowska, Magda <M.Dunowska from massey.ac.nz>
> wrote:
>
> > Hi,
> >
> > Sorry to revisit the subject - I have just gone through the archives and
> > can't find a description of a method I used to use a few years ago to
> get
> > DNA from agarose gels. I used normal (not LMP) agarose and TBE buffer.
> All I
> > remember is that it involved freezing and thawing a gel slice, but I
> think I
> > was also adding water or TE (can't remember what and how much), heating
> the
> > thawed gel to either 65 or 70 degrees for 5 or 10 minutes (?) and
> mashing it
> > all up with the blue tip before centrifuging everything at 4 degrees to
> > collect supernatant.
> >
> >
> >
> > I just got back to the molecular work after a few years in a slightly
> > different role, and (surprisingly...) can't recall all the details of
> > procedures that I used to do on a daily basis and never bothered to
> write
> > down outside of the lab books that are no longer with me...Anybody out
> there
> > who uses/used a similar variant of the "freeze and squeeze" and can give
> me
> > the details?
> >
> > Thanks!
> >
> > Magda
> >
> >
> >
> >
> > _______________________________________________
> > Methods mailing list
> > Methods from net.bio.net
> > http://www.bio.net/biomail/listinfo/methods
> >
>
>
>
> --
> Think before agree
> Think before you nod
> but STOP thinking
> and You Are God
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 17 Mar 2008 11:41:51 +0200
> From: "popi Arapini" <karapini from gmail.com>
> Subject: DMSO in PCR
> To: methods from magpie.bio.indiana.edu
> Message-ID:
>        <f68d9faa0803170241u65937821ld0bc7ce898befaae from mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> hI! everybody,
> I'am using DMSO to standardize my PCR (high GC content)
> I've read in a protocol that, once DMSO in the thermowell tube, it shall
> not  be spinned  down . Does anybody  know why??
>
> Popi
>
>
> ------------------------------
>
> _______________________________________________
> Methods mailing list
> Methods from net.bio.net
> http://www.bio.net/biomail/listinfo/methods
>
> End of Methods Digest, Vol 34, Issue 17
> ***************************************
>



-- 
Dr V K Gupta
Sr Microbiologist (Molecular Biology)
Insect Molecular Biology Lab
Department of Entomology
Punjab Agricultural University
Ludhiana (Pb)-141004- India
M: 09815963210