Probing lambda libraries with oligonucleotides

[Roger Anderson]

>Steven Goldberg <goldberg at bms.com> writes: 
> 
>>1.  Transferring and fixing phage DNA:  Some procedures say immerse 
>>the filters in the denaturation and neutralization; others claim this 
>>gives diffuse signals. 
 
Having done this procedure many many times I find that for Lambda it did 
not make a difference.  
 
>>2.  End-labeling oligonucleotides:  How much DNA is needed, how much 
>>label (again, I've seen anywhere from 5 t0 25 ul of gamma-dATP rec- 
>>commended).  How about the ECL 3' labeling kit or similar?   
 
I labelled 100 ng of probe and I used 40 - 60 uL of gamma-ATP. I thought 
it seemed like a lot at first but remember this drives the reaction. If 
you are thinking of costs, the cost of repeating the experiment is much 
more. Beside 1000 uCi is about the same price as 500 from some suppliers. 
> 
>>3.  Pre-hybridization and hybridization conditions.  Some use SSPE, 
>>others SSC; some include pyrophosphate; others leave out Denhardt's 
>>in the hybridization. 
> 
 
SSPE is much better buffer but it works either way. Calculate the TM and 
subtract 15 degrees. In fact if you do the washes right you can go a bit 
lower. Not too low you need to have hybridization. 
 
>>4.  Wash conditions.   
> 
 
USE Tetramethylammoniumchloride. This allows you to set VERY specifically 
the degree of divergence allowed. I screened several libraries using a 28 
mer and allowed for only 2 - 3 bases mismatch. It worked perfectly every 
time. In fact I even used a 21 mer with the same result. 
 
I published a paper showing the number of repeat copies in a sea urchin 
genome using this technique  
Anderson et al (1994) Development Biology 163, 11-18 
 
If you have any questions feel free to write and ask. 
 
>>Thanks for any suggestions. 
> 
>>Steve Goldberg 
>--  
        
 
Roger Anderson 
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