sodium acetate in sequencing gel buffers!

Hiranya Roychowdhury hroychow at NMSU.EDU
Fri Mar 7 10:48:20 EST 1997

At 06:16 PM 3/5/97 -0800, zarir wrote:
>Hi people,
>i want to know the reason for adding sodium acetate to the lower buffer
>tank while doing manual sequencing. I know it reduces compressions, by
>altering the voltage gradient, but how? what is the chemistry involved?
>Please reply urgently.also some reference where it is documented.
>zarir E.V.
>dept. of agronomy,
>purdue university.
>zarir at

No, acetate does not do anything for compressions. The acidic anolyte reduces the electrophoretic  mobility of the DNA closer to the anode in the gel virtually to a crawl. This essentially achieves the effect of a pH gradient across the gel. The result is that the lower portion of the gel stacks up the smaller fragments, affording more read per gel without letting too much of the sequence close to the primer escape. However, it does take much longer to run. 

Dr. Hiranya Sankar Roychowdhury
Plant Genetic Engineering Lab.
New Mexico State University
Las Cruces, NM 88003
Ph. (505) 646-5785
hroychow at

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