Stu I problems

[Alan KAY]

In article <slrn5s7ig3.f7l.aiyar at ebv.oncology.wisc.edu>, 
aiyar at ebv.oncology.wisc.edu says...
>
>On 9 Jul 1997 13:04:34 GMT,
>Alan KAY (kay at lyon151.inserm.fr) wrote:
>>In article <Pine.A32.3.91.970708110055.75636A-100000 at swan.u
>spnet.usp.br>, 
>>mdamarin at usp.br says...
>>>
>>>
>>>Hi there,
>>>
>>>          I have a problem with a Stu I digestion. I have 
>an insert which 
>>>contains a Stu I site that in the 5' end is overllaping wi
>th a metilation 
>>>site...it forms ccAGGCCT...the ccAGG is the metilaiton sit
>e and the 
>>>AGGCCT the Stu I site. 
>
>>According to the New England Biolabs catalogue, which is wh
>at I usually refer 
>>to when I think I may have a methylation problem, Stu I wil
>l be blocked by 
>>overlapping dcm methylation, but apparently only in the con
>text of AGGCCTGG, 
>>so that it is the second C in the recognition site which is
> methylated. In 
>>your sequence context, Stu I should not be inhibited.
>
>The complement of ccAGGCCT is AGGCCTgg, which as you have po
>inted out,
>is a sequence that is not cleaved by StuI, when dcm methylat
>ed.
>
>So it is extremely likely that dcm methylation is the reason
> why the StuI
>site in question is recalcitrant to digestion.
>
>Later,
>Ashok
>-- 
>Ashok Aiyar, Ph.D.
>McArdle Laboratory for Cancer Research
>aiyar at ebv.oncology.wisc.edu

Dear Ashok,

As you correctly point out, and I stand ashamed, this context will create a 
dcm methylation site in the sense opposite to that which was stated. 
Palindromes will not always be pals, I hope we will be.

Yours


Alan Kay