What are the conventional methods to fragment bacterial DNA to get ~1-10 kb size fragments? Is there any review paper or other publications out there if it's a very broad set of methods? Any pointers are really appreciated. Is mechanical shearing the most preferred method?
I think for that size range, acoustic shearing (eg. Covaris) is the way to go. I've used aspiration through a 26G needle before but I think this method usually yields much bigger pieces than what you're looking for (). Then again, bacterial chromosomes might behave differently than mammalian chromosomes in this method so it might still be worth a try.
Our probe sonicator (80 watts 10 seconds) shears DNA to give fragments from~300bp to approx. 2kb. But I have no idea what the ends of the DNA are like.
Restriction endonucleases are going to give you well defined ends and I have seen claims that a 4 base cutter will produces average 256 base pairs, 5-base cutter 1024 bp, 6-base cutter 4096bp. Might be described in Devon et al 1995 NAR 23: 1644-1645
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