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

Jose de las Heras via methods%40net.bio.net (by josenet from tiscali.co.uk)
Wed Jun 13 05:10:36 EST 2007


"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

don't throw away a paper based on the date, but on the science in it.

It's a paper on DNA structure, including crystalography, physical chemistry, 
good ol' physics and maths. While I am not as well versed in those areas as 
I am in "modern" molecular biology, the paper has remained cited right till 
these days (I didn't read it in the 70s, but sometime in the 21st century, 
in fact).

When did they work out which codon coded for which aminoacid? Was that 
bullshit too?

Let's not be prejudiced, this is science.

Jose




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