TOPO primer choice for sequencing - (Feb/27/2008 )

Hi,

I normally use my gene specific primers when I sequence my clones, however due to too many primer dimers I'd like to use either the M13 or T3/7 primers which come with the TOPO kit. Is either primer set good to use? Have any of you found one set is better than the other?

Thanks in advance,
Bunsen
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You can use either set (T3/T7 or M13F/M13R) or even combinations between the two sets. It won't make much difference, unless you're desperate for longer sequencing read, in which case you can choose the primers that anneal closer to your insert. Just make sure that none of the primers you'll use can anneal to your insert, rather than only on the vector.

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Both sets work equally good.

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Yeah, it's better to use those than your specific primers. The thing is that, when you do the sequencing, it's common that the first 10-20bp won't come out that good. So, if you're using your sequence-specific primers, you won't be able to have a very precise read on the first bps.

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