method for transcription start determination

Nick Theodorakis nicholas_theodorakis at urmc.rochester.edu
Wed Feb 2 15:13:50 EST 2000


In article <879nn9$isk$1 at rzsun03.rrz.uni-hamburg.de>,
behrends at plexus.uke.uni-hamburg.de (soenke behrends) wrote:
>
>
>Dear netters,
>
>what is the easiest and most straightforward
>method of transcription start analysis. We
>have isolated cDNA and 2000 bp of 5 prime
>flanking genomic DNA with potential TATA
>Signals.
>
>
>Primer extension analysis?
>RNase protection analysis?

Usually, a combination of these two (or S1 nuclease). Nuclease
protection will not distinguish between the 5'-end or an intron.
And primer extrension can show stops if there is strong secondary
structure in the RNA.

N

Nick Theodorakis

nicholas_theodorakis at urmc.rochester.edu

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