Ghost band (was Re: How to get a single stranded DNA as long as 2-3kb?)

[Jose de las Heras]

"peter" <peter.ianakiev from gmail.com> wrote in message 
news:1181703849.449545.163540 from x35g2000prf.googlegroups.com...
> On Jun 12, 5:31 pm, "Jose de las Heras" <jose... from tiscali.co.uk> wrote:
>> "peter" <peter.ianak... from gmail.com> wrote in message
>>
>> news:1181593924.822581.168770 from q75g2000hsh.googlegroups.com...
>>
>>
>>
>> > On Jun 11, 4:22 pm, Nick Theodorakis <nick_theodora... from hotmail.com>
>> > wrote:
>> >> ChenHA wrote:
>>
>> >> [...]
>>
>> >> > Perhaps I misremember, was it XL1 blue cells that produces the ghost
>> >> > band of ssDNA instead?
>>
>> >> I seem to remember a discussion about NaOH irreversibly altering the
>> >> plasmid conformation to generate a ghost band during alkaline preps, 
>> >> but
>> >> perhaps there is more than one kind of ghost band.
>>
>> >> Nick
>>
>> >> --
>> >> Nick Theodorakis
>> >> nick_theodora... from hotmail.com
>> >> contact form:http://theodorakis.net/contact.html
>>
>> > Guys keep it focussed ... the original poster asked a specific
>> > question - 2-3 kb ssDNA out of a plasmid with 3 kb insert. There is no
>> > such thing like "ghost" bands. If the culture is overgrown the plasmid
>> > does not have time to separate and you have occasionally  concatenates
>> > -  thats all.
>> > my2c
>>
>> actually, "ghost" bands do exist.
>>
>> They do seem to be related to a change in conformation of the plasmid DNA
>> under alkaline conditions.
>> I remember vaguely an old paper, from the 70s, describing what 
>> conformation
>> circular DNA can take, and it was defined as "type V" DNA, or something 
>> like
>> that...
>> I might be able to fish it out...
>>
>> Jose
>
> Jose, Why do you think I should believe to a paper from the 70s?  Do
> you know how many crappy papers were published in the past that are
> pure BS when we look at retrospect....
> my2c


oh, and I HAVE had that ghost band appearing in plasmid preps (using Nova 
Blue bugs) sometimes. Very faint, but visible. It's resistant to every 
restriction site I tried (well, just a handful) and the paper mentioned 
shows a change in conformation that may explain why restriction enzymes 
might have a hard time recognising their site.
I'll get the paper... give me a day.

Jose