SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
looking to outsource DNA shearing delbar Core Facilities 16 10-25-2012 08:48 PM
DNA Shearing Lj Lee Sample Prep / Library Generation 4 04-12-2012 02:01 PM
g-TUBE for DNA Shearing coffee52 Sample Prep / Library Generation 0 02-06-2012 11:46 PM
DNA shearing suludana Illumina/Solexa 18 03-01-2010 07:30 PM
DNA Shearing for 454 alanc 454 Pyrosequencing 3 02-26-2009 03:27 AM

Reply
 
Thread Tools
Old 11-13-2017, 06:12 AM   #1
JamieWizard
Member
 
Location: London

Join Date: Sep 2013
Posts: 10
Default Chemical shearing of DNA specifically (not RNA)

Hi,

I just wondered, are there any sequencing protocol kits around for shearing DNA by chemical means? I know that heating RNA in presence of divalent cations can be used to fragment RNA (i.e. Illumina TruSeq protocol kits). Do similar kits exist/or are methods applied for fragmenting DNA prior to sequencing?

Cheers,
Jamie
JamieWizard is offline   Reply With Quote
Old 11-13-2017, 11:30 AM   #2
torben
Junior Member
 
Location: Norway

Join Date: Oct 2012
Posts: 8
Default

I don't know about any kits, but DNA can be fragmented with reduced CuSO4
https://beng.soe.ucsc.edu/sites/defa...esis_Final.pdf
torben is offline   Reply With Quote
Old 11-13-2017, 11:37 AM   #3
JamieWizard
Member
 
Location: London

Join Date: Sep 2013
Posts: 10
Default

Cheers for that Torben. I saw that article, but thought it looks like a masters and because it's not referenced elsewhere might therefore not be a standard method that is used in labs that do sequencing.
JamieWizard is offline   Reply With Quote
Old 11-13-2017, 04:17 PM   #4
jwfoley
Senior Member
 
Location: Stanford

Join Date: Jun 2009
Posts: 176
Default

If enzymes count as chemicals, NEB has its "Fragmentase" mix, which appears to be a combination of a dsDNA nicking enzyme that's had its sequence specificity engineered out of it and a second enzyme that turns nicks into blunt ends.
jwfoley is offline   Reply With Quote
Old 11-14-2017, 05:07 AM   #5
JamieWizard
Member
 
Location: London

Join Date: Sep 2013
Posts: 10
Default

Thanks JW. The reason I am asking is I'm interested in the biases introduced by different fragmentation methods. Enzymatic methods, such as restriction endonucleases are a different class.

Essentially what I'm trying to establish, is that are metal cations also used to fragment DNA (I know they are used for RNA). I know the phosphate backbone of DNA/RNA carries a significant negative charge which facilitates this method. I believe RNA is slightly less stable than DNA, and I wondered if the method is also used for fragmenting DNA, but I can't seem to find reference to it online or in sequencing protocols.

Cheers
JamieWizard is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:42 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO