4-State Device

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= Purpose =
= Purpose =
-
 
+
The 4-State Device (4SD) uses two inputs to sequentially switch through its four states. The four states are used to keep track of changes of the inputs. One state is connected to the output.
-
The 4-State Device (4-SD) uses two inputs to sequentially switch through its four states. The four states are used to keep track of changes of the inputs. One state is connected to the output.
+
= Design =
= Design =
== Suitable Strategies ==
== Suitable Strategies ==
 +
For realizing the design we need one repressor for each state. For this purpose there are several possibilities that can be considered:
 +
 +
* Silencing approach (antisense RNAs, short hairpin RNAs (shRNAs)) to reduce the pool of translatable mRNAs
 +
 +
* Existing Repressor-Operator (for example TetR-TetO)
-
For realizing the design we need one repressor for each state. For this purpose there are several possibilities that can be considered:
 
-
* Silencing approach (antisense RNAs, short hairpin RNAs (shRNAs)) to reduce the pool of translatable mRNAs,
 
-
* Existing Repressor-Operator (for example TetR-TetO)
 
* Designing new repressors (for example Zinc Finger Proteins)
* Designing new repressors (for example Zinc Finger Proteins)
== Selected System ==
== Selected System ==
 +
Considering the modularity as the first criterion for the selection of the system, we considered that the Zinc Finger Protein approach would be the optimal. Indeed, the operators could be as short as 9 nucleotide long and the specificity can be easily increased by either increasing the number of fingers in the ZFP or by coupling ZFP together via Leucine Zippers.
 +
The recognition sequence can then be scaled up to 18 nucleotides or even further.
-
Considering the modularity as the first criterium for the selection of the system, we considered that the Zinc Finger Protein approach would be the optimal. Indeed, the operators could be as short as 9 nucleotide long and the specificity can be easily increased by either increasing the number of fingers in the ZFP or by coupling ZFP together via Leucine Zippers. The recognition sequence can then be scaled up to 18 nucleotides or even further.
+
Known repressors such as tetR remain a possibility for our system because of the tunability that this repressor-operator can offer (via tetracycline for the TetR-TetO couple).
-
Known repressors such as tetR remain a possibility for our system because of the tunability that this repressor-operator can offer (via tetracyclin for the TetR-TetO couple).
+
The silencing approach has been dropped because of the lack of modularity and the difficulty to achieve full repression via silencing approaches in bacteria.
The silencing approach has been dropped because of the lack of modularity and the difficulty to achieve full repression via silencing approaches in bacteria.
-
We chose the approach use design new repressors using zinc finger domains. Furthermore, we put the binding sites for the repressors directly after start of transcription and before the ribosome binding site to prevent RNA polymerase to transcribe the gene. This would allow us to put any promotor in from of the binding site and allowing a very high degree of modularity.
+
We chose the approach to use design new repressors using zinc finger domains. Furthermore, we put the binding sites for the repressors directly after start of transcription and before the ribosome binding site to prevent RNA polymerase to transcribe the gene. This would allow us to put any promotor in from of the binding site and allowing a very high degree of modularity.
-
 
+
-
There is possibility to use several 4-SD connected to each order in order to count n^2. but for every new device four new repressors is needed. With zinc finger domains the construction of any binding site is possible and we would not run out of repressor.
+
-
A Zinc Finger (ZF) [http://en.wikipedia.org/wiki/Zinc_finger] is a protein domain [http://en.wikipedia.org/wiki/Protein_domain] that binds to three base pairs of double stranded DNA. A Zinc Finger Protein (ZFP) consists of one or several zinc finger domains.  Many protein-DNA interaction for ZF domains and triplet of base pairs have been described, therefore making it possible to to construct artificial transcription factors by combining ZF domains in a modular fashion.
+
If we want to use the possibility to use several 4SD connected to each order in order to count n^2, then for every new 4 state device four new repressors are needed. With zinc finger domains the construction of any binding site is possible and we will not run out of repressor.
= Actual Implementation =
= Actual Implementation =
Line 31: Line 31:
In the figure below is a parts-view of the device with PoPS interfaces (i/o).
In the figure below is a parts-view of the device with PoPS interfaces (i/o).
-
''Robins insertion start''
 
==== Basic Functionality ====
==== Basic Functionality ====
-
The 4-State Device uses two inputs to sequentially switch through its four states. Note that this behaviour can be observed abstractly in the concept section.  
+
The 4-State Device uses two inputs to sequentially switch through its four states. Note that this behavior can be observed abstractly in the concept section.  
-
To achieve such behaviour in our system, we use four interconnected gates. In the following, we call them ''NOR gates''. Each of our NOR gates has three inputs. All of them have to be low for the output to be high.  
+
To achieve such behavior in our system, we use four interconnected gates. In the following, we call them ''NOR gates''. Each of our NOR gates has three inputs. All of them have to be low for the output to be high.
===== Electrical NOR gate =====
===== Electrical NOR gate =====
A NOR gate is a very common part in electrical engineering.
A NOR gate is a very common part in electrical engineering.
-
          ______________
+
 
-
rs1---->¦              ¦
+
[[Image:NORcircuit.gif]]
-
rs2---->¦  NOR gate    ¦---->
+
 
-
rs3---->¦______________¦
+
-
     
+
===== Biological NOR gate =====
===== Biological NOR gate =====
Biologically, a NOR gate can be implemented through a promoter with high basal activity that is repressed by three effectors. If there is at least one of the three repressors, transcription is inhibited.
Biologically, a NOR gate can be implemented through a promoter with high basal activity that is repressed by three effectors. If there is at least one of the three repressors, transcription is inhibited.
-
After each of the four NOR gates, there is a coding region for a protein. These four different proteins are called R1 to R4 in the following. (Note that such a biological NOR gate has no POPs interfaces)
+
Each NOR gates, expresses a repressor protein. (Note that such a biological NOR gate has no POPs interfaces)
-
biological picture of NOR gate
+
[[Image:NORcircuit.gif]]
===== 4-State Device circuit diagram =====
===== 4-State Device circuit diagram =====
-
circuit diagram
+
[[Image:4SDcircuit.gif]]
===== 4-State Device parts diagram =====
===== 4-State Device parts diagram =====
-
parts diagram
+
[[Image:4SD.gif]]
-
By design of the Event Processing Device, input 1 and input 2 have opposite activity, meaning that either R1/R3 or R2/R4 is active. Furthermore, since R1/R3 (respectively R2/R4) are repressing each other, only one of the two is active. Therefore, in a stable situation, only 1 of the 4 repressor proteins is expressed.
+
In the design of the Event Processing Device, input 1 and input 2 have opposite activity, meaning that either R1/R3 or R2/R4 is active. Furthermore, since R1 and R3 (respectively R2 and R4) are repressing each other, only one of the two is active. Therefore, in a stable situation, only 1 of the 4 repressor proteins is expressed.
Let us assume that R1 is being expressed. Input 2 must then be low, and therefore input 1 high. This situation is stable and remains until there is a change in the inputs. Now, if input 1 decreases, and input 2 increases, the expression of R1 will come to a halt. Since input 1 is now low, either R2 or R4 will be expressed. At this stage, R1 is still present in relatively high concentration and by repressing R4, it tips the balance in favor of R2, leading to a new stable state in which only R2 is expressed.  
Let us assume that R1 is being expressed. Input 2 must then be low, and therefore input 1 high. This situation is stable and remains until there is a change in the inputs. Now, if input 1 decreases, and input 2 increases, the expression of R1 will come to a halt. Since input 1 is now low, either R2 or R4 will be expressed. At this stage, R1 is still present in relatively high concentration and by repressing R4, it tips the balance in favor of R2, leading to a new stable state in which only R2 is expressed.  
Line 64: Line 61:
Note that electrical engineers call such a device a "J-K flip flop". It can also be seen as a combination of two toggle switches ([[Atkinson03]]), each being able to store one bit.
Note that electrical engineers call such a device a "J-K flip flop". It can also be seen as a combination of two toggle switches ([[Atkinson03]]), each being able to store one bit.
-
''Robins insertion end''
+
=== Biological Details ===
In the design of the repressor protein we use the following domains:  
In the design of the repressor protein we use the following domains:  
-
Zinc Finger (ZF)  
+
- ''Zinc Finger (ZF)''
-
DNA-binding domain
+
DNA binding domain
-
NTD  
+
- ''NTD''
The N-terminal polymerase domain from NusA. This protein has a RNA polymerase halting properties.
The N-terminal polymerase domain from NusA. This protein has a RNA polymerase halting properties.
-
 
+
- ''ERD''
-
ERD
+
ERF repressor domain. a repressor domain in eukaryotes.
ERF repressor domain. a repressor domain in eukaryotes.
-
LZ
+
-''LZ''
-
 
+
Leucine zipper. For dimerization.
Leucine zipper. For dimerization.
-
 
-
 
If it turns out that repression has been used in all the literature we can find, then we would be better off to play safe and include them:
If it turns out that repression has been used in all the literature we can find, then we would be better off to play safe and include them:
-
 
* Beerli PNAS 1998: they fused ZF to KRAB repressor and it has a stronger effect compare to ZF alone (see p14632 graph A)
* Beerli PNAS 1998: they fused ZF to KRAB repressor and it has a stronger effect compare to ZF alone (see p14632 graph A)
Line 94: Line 86:
-
table of parts.
+
The different designs of repressors
 +
{| border="1" cellpadding="2"
 +
|+ Synthesized Sequences
 +
! BioBrick Part !! Number of ZF domains !! LZ domain !! TF domain
 +
|-
 +
| BBa_J05101 || 3  || -    ||    -
 +
|-
 +
| BBa_J05108 || 3* || CREBH || -
 +
|-
 +
| BBa_J05109 || 3* || ATF6  || -
 +
|-
 +
| BBa_J05110 || 3* || YAP7  || -
 +
|-
 +
| BBa_J05111 || 3* || cMaf  || -
 +
|-
 +
| BBa_J05112 || 3  || -    || ERD
 +
|-
 +
| BBa_J05113 || 3* || ATF6  || KRAB
 +
|-
 +
| BBa_J05114 || 3* || ATF6  || NTD
 +
|-
 +
| BBa_J05115 || 6  || -    || -
 +
|}
-
We use several different designs of ZFPs.
 
-
- Three ZF domains to recognize nine base pairs.
 
-
- Two ZF domains and a leucine zipper domain. The leucine zipper will be cause the protein to home-dimerize and hence it will recognize 12 base pairs.
+
==== BioBrick parts ====
-
- Six ZF domains to recognize twelve base pairs.
+
{| border="1" cellpadding="2"
 +
|+ BBa_J05040 4-State Device
 +
! State !! Repressor  !! Regulator !! Comments
 +
|-
 +
| R1 || BBa_J05311 || BBa_J05215 ||
 +
|-
 +
| R3 || BBa_J05312 || BBa_J05216 ||
 +
|-
 +
| R2 || BBa_J05313 || BBa_J05217 ||
 +
|-
 +
| R4 || BBa_J05314 || BBa_J05218 ||
 +
|}
-
- Three ZF domains fused to negative transcription factors. (e.g. NTD and ERD)
 
{| border="1" cellpadding="2"
{| border="1" cellpadding="2"
-
|+ Ordered Sequences
+
|+ Synthesized Sequences
-
 
+
! Nickname              !! Length !! SacI !! KpnI !! NheI !! EcoRI  !! XbaI   !! SpeI   !! PstI
-
! Nickname              !! Length !! SacI !! KpnI !! NheI !! EcoRI  !! XbaI     !! SpeI     !! PstI  
+
|-
|-
-
| BBa_J05215+BBa_J05108 || $874.35 ||  1  ||  91  ||  598 || 7, 97  || 22, 112 || 71, 578 || 85, 592
+
| BBa_J05215+BBa_J05108 || 603  ||  1  ||  91  ||  598 || 7, 97  || 22, 112 || 71, 578 || 85, 592
|-
|-
-
| BBa_J05216+BBa_J05109 || $843.9 ||  1  ||  91  ||  577 || 7, 97  || 22, 112 || 71, 557 || 85, 571
+
| BBa_J05216+BBa_J05109 ||  582  ||  1  ||  91  ||  577 || 7, 97  || 22, 112 || 71, 557 || 85, 571
|-
|-
-
| BBa_J05217+BBa_J05110 || $883.05 ||  1  ||  91  ||  604 || 7, 97  || 22, 112 || 71, 584 || 85, 598
+
| BBa_J05217+BBa_J05110 || 609  ||  1  ||  91  ||  604 || 7, 97  || 22, 112 || 71, 584 || 85, 598
|-
|-
-
| BBa_J05218+BBa_J05111 || $870    ||  1  ||  91  ||  595 || 7, 97  || 22, 112 || 71, 575 || 85, 589
+
| BBa_J05218+BBa_J05111 || 600  ||  1  ||  91  ||  595 || 7, 97  || 22, 112 || 71, 575 || 85, 589
|-
|-
-
| BBa_J05221+BBa_J05101 || $722.1 ||  1  ||  112 ||  493 || 7, 118 || 22, 133 || 92, 473 || 106, 487  
+
| BBa_J05221+BBa_J05101 ||  498  ||  1  ||  112 ||  493 || 7, 118 || 22, 133 || 92, 473 || 106, 487
|-
|-
-
| BBa_J05114            || $1238.3 ||  1  ||  849 ||  -   ||    7  || 22       || 829     || 843
+
| BBa_J05114            || 854  ||  1  ||  849 ||  -   ||    7  || 22     || 829     || 843
|-
|-
-
| BBa_J05112            || $759.8 ||  1  ||  519 ||  -   ||    7  || 22       || 499     || 513
+
| BBa_J05112            ||  524  ||  1  ||  519 ||  -   ||    7  || 22     || 499     || 513
|-
|-
-
| BBa_J05222+BBa_J05115 || $980.2 ||  1  ||  87  ||  671 || 7, 93  || 22, 108 || 67, 651 || 81, 665
+
| BBa_J05222+BBa_J05115 ||  676  ||  1  ||  87  ||  671 || 7, 93  || 22, 108 || 67, 651 || 81, 665
|}
|}
-
describe the trick we use to reduce cost, that is, putting small parts together with big parts.
+
The provider of the synthesized DNA used for the zinc fingerers has a lower cost limit of $500. To reduce cost per base pair for short sequences we put the short sequences together with a long sequence with restriction sites between them. the trick we use to reduce cost, by having an extra step of cloning.
binding of ZFP. describe choice of binding sites. Describe the function of RNA pol II. emphasize: modularity!
binding of ZFP. describe choice of binding sites. Describe the function of RNA pol II. emphasize: modularity!
Another important aspect is the overall goal of keeping the design modular - one of the most important aspects of the this contest.
Another important aspect is the overall goal of keeping the design modular - one of the most important aspects of the this contest.
-
 
Line 144: Line 164:
2. Binding sites directly after the start of transcription and before the ribosome binding site. This alternative is attractive, since it would allow for a high degree of modularity. In theory the ZFP would act as an extra "roadblock-operator" and any promotor could be used in front of the protein.
2. Binding sites directly after the start of transcription and before the ribosome binding site. This alternative is attractive, since it would allow for a high degree of modularity. In theory the ZFP would act as an extra "roadblock-operator" and any promotor could be used in front of the protein.
-
The ZFP roadblock operator regions (from now on refered to as: operators) consists of binding motifs for two repressors. The two bindning motifs are usually spaced with 5 base pairs (gcgcg). Some data of the binding strength were available and we have chosen operators with the affinity estimated to K_d = 3-40 nM.
+
The ZFP roadblock operator regions (from now on referred to as: operators) consists of binding motifs for two repressors. The two binding motifs are usually spaced with 5 base pairs (gcgcg). Some data of the binding strength were available and we have chosen operators with the affinity estimated to K_d = 3-40 nM.
{| border="1" cellpadding="2"
{| border="1" cellpadding="2"
-
!    Part  !!  Binding Site Seq !! # exact matches !! Hamming Dist 1 !! Hamming Dist 2 !! Hamming Dist 3
+
!    Part  !!  Binding Site Seq !! est Kd [nM] !! # exact matches !! Hamming Dist 1 !! Hamming Dist 2 !! Hamming Dist 3
|-
|-
-
| BBa_J05100 || ggaggggac          || 1 || 132 || 3125 || 32788
+
| BBa_J05100 || ggaggggac          || 4  || 5  || 267 || 6196  || 65733
|-
|-
-
| BBa_J05102 || ggaggcggg          || 5 || 396 || 6293 || 47897
+
| BBa_J05102 || ggaggcggg          || 30  || 17 || 799 || 12589 || 95996
|-
|-
-
| BBa_J05101 || gggggcgag          || 8 || 303 || 4955 || 41302
+
| BBa_J05101 || gggggcgag          || 3  || 15 || 634 || 10173 || 82956
|-
|-
-
| BBa_J05103 || ggggccgga          || 23|| 433 || 5606 || 45492
+
| BBa_J05103 || ggggccgga          || 45  || 44 || 848 || 11317 || 91422
|-
|-
-
| BBa_J05108 || gtcccctccggaggggac || 0 || 0  || 0   || 0
+
| BBa_J05108 || gtcccctccggaggggac || N/A || 0 || 0  || 0     || 1
|-
|-
-
| BBa_J05109 || ctcgcccccgggggcgag || 0 || 0  || 0   || 2
+
| BBa_J05109 || ctcgcccccgggggcgag || N/A || 0 || 0  || 0     || 2
|-
|-
-
| BBa_J05110 || cccgcctccggaggcggg || 0 || 0  || 0   || 3
+
| BBa_J05110 || cccgcctccggaggcggg || N/A || 0 || 0  || 0     || 4
|-
|-
-
| BBa_J05111 || tccggccccggggccgga || 0 || 0  || 0   || 3
+
| BBa_J05111 || tccggccccggggccgga || N/A || 0 || 0  || 0     || 6
|-
|-
-
| BBa_J05115 || gggggcgaggggggcgag || 0 || 0  || 0   || 1
+
| BBa_J05115 || gggggcgaggggggcgag || N/A || 0 || 0  || 0     || 3
|}
|}
-
Kd values of interactions. put in table above.
 
-
Degradation...?
+
Degradation rates????
Tests: design all tests.
Tests: design all tests.
Line 178: Line 197:
{| border="1" cellpadding="2"
{| border="1" cellpadding="2"
-
|+Repression Tests
+
|+ BBa_J05000 Zinc Finger Protein Tester
-
! Repressor  !! Operator !! Comments
+
! Repressor  !! Regulator !! Comments
|-
|-
-
| J05100    || J05212  || ...
+
| BBa_J05112 R3-e2+ERD || Regulator for R3-ATF6 ||
|-
|-
-
| J05100    || J05212  || ...
+
| BBa_J05113 R3-ATF6+ NTD || BBa_J05221 Triple Binding Site for R3-ATF6 ||
 +
|-
 +
| BBa_J05114 R3-ATF6+NTD || Regulator for R3-ATF6 ||
 +
|-
 +
| BBa_J05101 R3-e2 || Regulator for R3-ATF6 ||
 +
|-
 +
| BBa_J05115 ZF-2*e2 || ZF-2*e2 Binding Site ||
|}
|}
 +
assembly diagram of test.
assembly diagram of test.
[[Image:TesterParts.gif]]
[[Image:TesterParts.gif]]
-
 

Revision as of 21:40, 31 October 2005

Back to the ETH Zurich main page.

Contents

Purpose

The 4-State Device (4SD) uses two inputs to sequentially switch through its four states. The four states are used to keep track of changes of the inputs. One state is connected to the output.

Design

Suitable Strategies

For realizing the design we need one repressor for each state. For this purpose there are several possibilities that can be considered:

  • Silencing approach (antisense RNAs, short hairpin RNAs (shRNAs)) to reduce the pool of translatable mRNAs
  • Existing Repressor-Operator (for example TetR-TetO)
  • Designing new repressors (for example Zinc Finger Proteins)

Selected System

Considering the modularity as the first criterion for the selection of the system, we considered that the Zinc Finger Protein approach would be the optimal. Indeed, the operators could be as short as 9 nucleotide long and the specificity can be easily increased by either increasing the number of fingers in the ZFP or by coupling ZFP together via Leucine Zippers. The recognition sequence can then be scaled up to 18 nucleotides or even further.

Known repressors such as tetR remain a possibility for our system because of the tunability that this repressor-operator can offer (via tetracycline for the TetR-TetO couple). The silencing approach has been dropped because of the lack of modularity and the difficulty to achieve full repression via silencing approaches in bacteria.

We chose the approach to use design new repressors using zinc finger domains. Furthermore, we put the binding sites for the repressors directly after start of transcription and before the ribosome binding site to prevent RNA polymerase to transcribe the gene. This would allow us to put any promotor in from of the binding site and allowing a very high degree of modularity.

If we want to use the possibility to use several 4SD connected to each order in order to count n^2, then for every new 4 state device four new repressors are needed. With zinc finger domains the construction of any binding site is possible and we will not run out of repressor.

Actual Implementation

The central part of the counter is the 4SD. When input changes the next state is reached and the repressor is expressed. Every Repressor represses all other states except for the next. For example R1 represses R3 and R4, but not R2. This forces a progression of states R1 to R4 during the cycles of the input.

In the figure below is a parts-view of the device with PoPS interfaces (i/o).

Basic Functionality

The 4-State Device uses two inputs to sequentially switch through its four states. Note that this behavior can be observed abstractly in the concept section.

To achieve such behavior in our system, we use four interconnected gates. In the following, we call them NOR gates. Each of our NOR gates has three inputs. All of them have to be low for the output to be high.

Electrical NOR gate

A NOR gate is a very common part in electrical engineering.

NORcircuit.gif

Biological NOR gate

Biologically, a NOR gate can be implemented through a promoter with high basal activity that is repressed by three effectors. If there is at least one of the three repressors, transcription is inhibited. Each NOR gates, expresses a repressor protein. (Note that such a biological NOR gate has no POPs interfaces)

NORcircuit.gif

4-State Device circuit diagram

4SDcircuit.gif

4-State Device parts diagram

4SD.gif

In the design of the Event Processing Device, input 1 and input 2 have opposite activity, meaning that either R1/R3 or R2/R4 is active. Furthermore, since R1 and R3 (respectively R2 and R4) are repressing each other, only one of the two is active. Therefore, in a stable situation, only 1 of the 4 repressor proteins is expressed.

Let us assume that R1 is being expressed. Input 2 must then be low, and therefore input 1 high. This situation is stable and remains until there is a change in the inputs. Now, if input 1 decreases, and input 2 increases, the expression of R1 will come to a halt. Since input 1 is now low, either R2 or R4 will be expressed. At this stage, R1 is still present in relatively high concentration and by repressing R4, it tips the balance in favor of R2, leading to a new stable state in which only R2 is expressed.

Note that electrical engineers call such a device a "J-K flip flop". It can also be seen as a combination of two toggle switches (Atkinson03), each being able to store one bit.

Biological Details

In the design of the repressor protein we use the following domains:

- Zinc Finger (ZF) DNA binding domain

- NTD The N-terminal polymerase domain from NusA. This protein has a RNA polymerase halting properties.

- ERD ERF repressor domain. a repressor domain in eukaryotes.

-LZ Leucine zipper. For dimerization.

If it turns out that repression has been used in all the literature we can find, then we would be better off to play safe and include them:

  • Beerli PNAS 1998: they fused ZF to KRAB repressor and it has a stronger effect compare to ZF alone (see p14632 graph A)
  • Beerli Nat Biotech review feb2002 : if you read the complete paragraph on gene repression (p 132), it gives strong evidence that we should fuse the ZF to a repressor (apparently at the N-Term of the ZF)

It is stated that polymerase blockade through ZF only is not very efficient. We can not be sure that the 45 amino acid long KRAB domain will work, if it doesn't exist in prokaryotes. KRAB domains have a very specific interaction with a co-repressor molecule. It might be better to find something already known to work in bacteria or skip the repressor approach altogether.


The different designs of repressors

Synthesized Sequences
BioBrick Part Number of ZF domains LZ domain TF domain
BBa_J05101 3 - -
BBa_J05108 3* CREBH -
BBa_J05109 3* ATF6 -
BBa_J05110 3* YAP7 -
BBa_J05111 3* cMaf -
BBa_J05112 3 - ERD
BBa_J05113 3* ATF6 KRAB
BBa_J05114 3* ATF6 NTD
BBa_J05115 6 - -


BioBrick parts

BBa_J05040 4-State Device
State Repressor Regulator Comments
R1 BBa_J05311 BBa_J05215
R3 BBa_J05312 BBa_J05216
R2 BBa_J05313 BBa_J05217
R4 BBa_J05314 BBa_J05218


Synthesized Sequences
Nickname Length SacI KpnI NheI EcoRI XbaI SpeI PstI
BBa_J05215+BBa_J05108 603 1 91 598 7, 97 22, 112 71, 578 85, 592
BBa_J05216+BBa_J05109 582 1 91 577 7, 97 22, 112 71, 557 85, 571
BBa_J05217+BBa_J05110 609 1 91 604 7, 97 22, 112 71, 584 85, 598
BBa_J05218+BBa_J05111 600 1 91 595 7, 97 22, 112 71, 575 85, 589
BBa_J05221+BBa_J05101 498 1 112 493 7, 118 22, 133 92, 473 106, 487
BBa_J05114 854 1 849 - 7 22 829 843
BBa_J05112 524 1 519 - 7 22 499 513
BBa_J05222+BBa_J05115 676 1 87 671 7, 93 22, 108 67, 651 81, 665


The provider of the synthesized DNA used for the zinc fingerers has a lower cost limit of $500. To reduce cost per base pair for short sequences we put the short sequences together with a long sequence with restriction sites between them. the trick we use to reduce cost, by having an extra step of cloning.

binding of ZFP. describe choice of binding sites. Describe the function of RNA pol II. emphasize: modularity! Another important aspect is the overall goal of keeping the design modular - one of the most important aspects of the this contest.


We have two alternatives for placing the binding sites.

1. Binding sites in the promoter. This would prevent the polymerase from binding to the promotor. Although this might be most likely to work, we have chosen to not pursue this alternative, while we are quite intrigued by the possibility of a roadblock. The operator regions (i.e. the "roadblocks" that will prevent of the RNApolymerase to transcribe the gene) form a BioBrick that should be inserted between the promoter region and the ribosome binding site in order to keep the design modular.

2. Binding sites directly after the start of transcription and before the ribosome binding site. This alternative is attractive, since it would allow for a high degree of modularity. In theory the ZFP would act as an extra "roadblock-operator" and any promotor could be used in front of the protein.

The ZFP roadblock operator regions (from now on referred to as: operators) consists of binding motifs for two repressors. The two binding motifs are usually spaced with 5 base pairs (gcgcg). Some data of the binding strength were available and we have chosen operators with the affinity estimated to K_d = 3-40 nM.

Part Binding Site Seq est Kd [nM] # exact matches Hamming Dist 1 Hamming Dist 2 Hamming Dist 3
BBa_J05100 ggaggggac 4 5 267 6196 65733
BBa_J05102 ggaggcggg 30 17 799 12589 95996
BBa_J05101 gggggcgag 3 15 634 10173 82956
BBa_J05103 ggggccgga 45 44 848 11317 91422
BBa_J05108 gtcccctccggaggggac N/A 0 0 0 1
BBa_J05109 ctcgcccccgggggcgag N/A 0 0 0 2
BBa_J05110 cccgcctccggaggcggg N/A 0 0 0 4
BBa_J05111 tccggccccggggccgga N/A 0 0 0 6
BBa_J05115 gggggcgaggggggcgag N/A 0 0 0 3


Degradation rates????

Tests: design all tests. To test whether our assumptions about using multiple zinc finger proteins (ZFP) as repressors (i.e. roadblocks) will actually work, we will build a tester/debugging device in parallel with the counter.


BBa_J05000 Zinc Finger Protein Tester
Repressor Regulator Comments
BBa_J05112 R3-e2+ERD Regulator for R3-ATF6
BBa_J05113 R3-ATF6+ NTD BBa_J05221 Triple Binding Site for R3-ATF6
BBa_J05114 R3-ATF6+NTD Regulator for R3-ATF6
BBa_J05101 R3-e2 Regulator for R3-ATF6
BBa_J05115 ZF-2*e2 ZF-2*e2 Binding Site


assembly diagram of test. TesterParts.gif


4SD system The 4SD system consists of 4 proteins with 4 operator regions. It has an interface boundary with input module (Pr and Prm). Repressor R3 is connected to a reporter to be able to count to modulo two. assembly diagram of device. CounterParts.gif

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