single-stranded DNA in S1 mapping

[Klaus Salger]

Toshiharu Ishizuka (tishizuk at AQUARIUS.BEKKOAME.OR.JP) wrote:
: Dear netters
:         I'm afraid this is a primitive question. Does anybody know why we
: have to add single-stranded calf-thymus DNA to the S1 nuclease digestion
: buffer in S1 nuclease mapping of mRNA. Without the DNA, what will happen ?
: I will greatly appreciate it if somebody teach me. Sorry again for this
: stupid question ?

I hope this is not a stupid answer...
Isn't it something like blocking? I mean the nonspecific ssDNA should be
much more than your specific probe. So almost everything that unspecifically
binds to ssDNA will bind to the calf-thymus (or whatever) DNA and not to your
probe. If you leave out the calf-thymus DNA, I would expect a higher
background which results from protection of non-hybridized DNA stretches by
some sort of junk.
This is just a guess.

  Klaus

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