Re: [DIYbio] Re: Low cost PCR(under development)

On Mon, Jun 30, 2014 at 8:48 AM, John Griessen <john@industromatic.com> wrote:
> On 06/30/2014 06:05 AM, Cathal Garvey wrote:
>>
>> t's rare that you'll need decreasing ramp rates faster than 1C, in any
>> case. Have you a special experiment in mind?

I'd say that you always want faster, unless you want your PCR to be
sloppier. Sloppiness depends on a lot of factors, ramp rate is one,
but a properly designed primer is another.

>
> Are there some good research reasons to go for more delta T rate?

Yes, it gives the molecules less time to be random and jiggle around.
You transition through all the other possible molecular states faster,
all the possible base-pairing of a primer to a target sequence
(avoiding sequences that don't match the best)... the math is probably
something about the speed of the temperature delta being closer/faster
than than the speed of diffusion... thought there are the electronics
of basepairing too, but that'd be where I'd generally start to think
about a model of this.

> My stirred air cooled PCR cycler concept is likely to do more
> when I get around to doing it and testing it. And for evenness,
> it will be top performing inherently.

Yep, instantaneous with nice power metering, and you can probably
start to do some neat target detection stuff with something like
differential scanning calorimetry (maybe pair this with qPCR?)
http://en.wikipedia.org/wiki/Differential_scanning_calorimetry

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