What are the conventional methods of DNA extraction from bacteria (lysis & purification) that would ensure the DNA strands does not fragment during lysis & purification? Is there a preferred method among conventional lysis like mechanical, chemical etc. which would ensure DNA is not fragmented?
Methods which ensure DNA/RNA is not fragmented to less than 10-40 kb. I mean lysis/DNA extraction methods that do not fragment the DNA (cut it down to small pieces or even sub 10 kb) or ensure fidelity. Like alkaline lysis?
The key to not fragmenting chromosomal DNA too much is to handle the prep gently (i.e. no shaking or jerking of the tube) so as to decrease shearing as much as possible. Choice of specific protocol makes no significant difference in this regard.
Alkaline lysis is not a good choice, as you will denature the strands and, given the high sequence complexity of chromosomal DNA, reannealing them will be next to impossible and you will end up with a supramolecular aggregate once pH is neutralized.
Commercial Calf thymus DNA (Sigma) that has been re-extracted with phenol (x2) by vigorous and extensive vortex mixing followed by ethanol precipitation has (on agarose gels) a mean size well in excess of 20kb as far as I can judge. Even when I sonicate it with a probe sonicator, the size only reduces to approx. 700bp. So for your purposes, really any extraction procedure should be fine. If you have any doubt about the method you use, just check the DNA on 1% agarose with an appropriate marker.
Note that there is a common misperception abouto the extreme fragility of DNA that originated during the time that Southern blotting was about the only molecular analysis you could apply. For that technique, especially using 6-base or rare cutting restriction endonucleases, very high molecular weight DNA (~50+kb) was essential. Nowadays, for sequencing (even long range) and for most PCR applications, you would need to try very hard (or sonicate -but even then its probably OK for most PCRs!) to make the DNA useless.
Note also that as you are sequencing, the DNA will need at some point to be singlestranded, so an alkaline lysis method should be perfectly acceptable (although I wouldn't use one as my DNA often contains lots of alkali-labile sites!)
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