[Automated-sequencing] Weird chromat, part 2

Phillip San Miguel pmiguel at purdue.edu
Thu Jun 23 15:09:10 EST 2005


Hi Jean,

	Nice! It never occured to me to think of viscosity.
	I tend to think about electrophoresis as only involving charged 
products migrating through a matrix because of an applied electrical 
field. But DNA is charged and can be viscous. Those capillaries have a 
narrow diameter. So drag caused by viscosity could play a role.
	Maybe the skewing I see is from surface interactions at the interface 
between the capillary inner surface and the polymer.

Thanks,
Phillip

Jean Renaud wrote:
> The solution to obtain good chromatogram is to increase dilution with 
> formamide in order to decrease viscosity of sample.
> Jean
> 
> 
> Hi Phillip,
> 
> Sometimes, presence of genomic DNA in the prep may give some viscosity 
> to it and cause trailing of peaks. Effect is more important as molecular 
> weight of fragments increase.
> 
> Jean
> 
> 
>> Take a look at this screen capture:
>>
>> http://data.genomics.purdue.edu/~pmiguel/technical/06-22-2005read.htm
>>
>>
>> (It is only a 74 kbyte .png file.)
>>
>> Anyone have an idea of what is going on? Note that the peaks look 
>> pretty good around 200 bases, but by 500 bases something is clearly 
>> wrong. The right-side edge of the peaks come up pretty high above 
>> baseline. But the left-side edge looks much better. I guess the peaks 
>> are "skewed".
>>
>> Has anyone seen this before?
>>
>> -- 
>> Phillip
>>
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> 
> 
> 




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