[BBF Standards] question on PoPS devices

[Deepak Chandran]

Hello Reshma,

Yes, having a device that is not on a contiguous piece of DNA would be 
able to have multiple outputs. However, such a device would be very 
difficult to assemble (ligate) with other devices, or is there a clever 
way of making the assembly easier?

As for Anil's comment on the cis vs trans, I do not understand how 
cross-talk is prevented when the device is on a contiguous piece of DNA. 
For an inverter device, the repressor protein is still free to diffuse 
to any other part of the cell -- or is this not this sort of crosstalk 
that you are referring to? However, there might be some issue about 
"PoPS crosstalk" if one "piece" of the device is placed in an area where 
it can potentially receive PoPS from some other source. For example, 
suppose there is an inverter with three outputs:

---rbs--geneA--stop--promoterA--...{1}....----promoterA--....{2}.....---promoterA    
(by promoterA, I am also including the operator site)

if the region {1} or {2} has some leaky PoPS, then this might make the 
three outputs unequal. However, this can probably be avoided by careful 
design.


--Deepak

Reshma Shetty wrote:
> Hey Deepak,
>
> On Wed, May 21, 2008 at 1:06 PM, Deepak Chandran
> <deepakc at u.washington.edu> wrote:
>
>   
>> A PoPS device can only have one input and one output -- is that correct?
>>     
>
> No.  PoPS devices can have multiple inputs and/or multiple outputs.
> For example, an inverter can have multiple outputs simply by having
> multiple copies of the cognate promoter regulating different
> downstream devices.  To engineer a device with multiple inputs, simply
> use multiple copies of the RBS, coding region and terminator under the
> control of different upstream devices.  Stated differently, PoPS
> devices do not need to be on contiguous pieces of DNA.
>
> If
>   
>> so, is it possible to create a network similar to natural regulatory
>> networks (i.e. with one gene regulating multiple genes) solely through the
>> use of the PoPS interface?
>>     
>
> Sure.  See above.
>
> Let me know if I am unclear on the above.
>
> Thanks,
>
> Reshma
>