extra bands in SSCP'S

Ian Howell ihowell at ozemail.com.au
Fri Jun 21 06:46:11 EST 1996

We are in the early stages of optimising  Single Stranded
Conformational Polymorphism assays to detect mutations in several
genes.  Occasionally we see an extra single stranded (?)  band.   Can
single stranded DNA fragments fold into more than one stable
conformation and thus produce more than one band on a non-denaturing
gels? If this is true, what are the factors that affect the formation
of more than one conformation?

(We are running 10% polyacrylamide gels +/- 5% glycerol at room
temperature, at 20 V/cm in 1 x TBE followed by silver staining.
Fragment sizes are generally between 150-220bp.  Double stranded DNA
is denatured by 0.5M NaOH at 42C, and loaded with formamide containing
loading dye)

Viive Howell and Bruce Bennett
Westmead Hospital, Sydney, Australia

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