We just received the 3700 and are trying to optimize the reaction
We are encountering two kinds of problems.
1. Our sequences start with a good intensity in the beginning. After about
200bp the intensity suddenly drops.
2. In couple of places we see a broad peak of G or T covering 3-5 bases.
Initially we thought problem maybe due to formamide. Changing formamide did
not help. We considered problems with purification. We are using 56%
isopropanol. Increasing or decreasing isopropanol concentration did not make
any difference. We also tried spin columns and problem still persists.
I would appreciate input from experienced users.
Also I would like to know advantages of using water over formamide in
suspending sequencing reactions and also amount of water to use.
T. V. (Venky) Venkatesh, Ph D
Senior Scientist (Bioinformatics and Molecular Biology)
Synaptic Pharmaceutical Corporation
215 College Road
Paramus NJ 07652 - 1431
Tvenkatesh at synapticcorp.com