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  • 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

  • #2
    I don't know about any kits, but DNA can be fragmented with reduced CuSO4

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    • #3
      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.

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      • #4
        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.

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        • #5
          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

          Comment

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