Re: [DIYbio] How important is it for primers to have 40-60% GC content?

Simply, the length and GC ratio influence the melting temp (Tm), less
simply the secondary, tertiary, maybe quaternary structure also
influence the Tm.

On Mon, May 6, 2013 at 11:52 AM, Jeswin <phillyj101@gmail.com> wrote:
> On Friday, May 03, 2013 11:02:06 PM, Zeb Haradon wrote:
>>
>>
>> I did find some primers that have a "buffer" of only 167 base pairs,
>> so I can run it next to a 100 bp ladder and it will be fairly easy to
>> visualize (max size - a sample with 10 repeats - will be 647 bp). The
>> problem is that the reverse primer has a GC content of 66.67%. What
>> I'm reading online says to try to aim for 40-60%. So my question, for
>> someone with more PCR experience than me (none) - how likely is it
>> that this primer will work? Is there anything I can do to compensate
>> for it (raise the temperature)? I can provide more detail if needed.
>>
>
> I haven't found it to be a big deal. I think most primers I used had at
> least 50% G/C. I think the melting temperature is more important when
> designing a primer.
>
>
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--
-Nathan

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