4-State Device

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Back to the [[ETH Zurich]] main page.
Back to the [[ETH Zurich]] main page.
-
=Organisation=
+
= Organisation =
-
===Group Members===
+
=== Group Members ===
*[[Alexander Roth]](coordinator),  [[User:realUACM|Urs A. Müller]],  [[Simon Barkow]],  [[User:Tamara|Tamara Ulrich]],  [[Robin Künzler]], Herve, Dominic, Christophe ...
*[[Alexander Roth]](coordinator),  [[User:realUACM|Urs A. Müller]],  [[Simon Barkow]],  [[User:Tamara|Tamara Ulrich]],  [[Robin Künzler]], Herve, Dominic, Christophe ...
-
===Meetings===
+
=== Meetings ===
  '''2005.08.17, Wednesday, 15:30 @ Alex' bureau (CAB F62)''' [[Summary]]
  '''2005.08.17, Wednesday, 15:30 @ Alex' bureau (CAB F62)''' [[Summary]]
  '''2005.08.18, Thursday, 13:15 @ Alex' bureau (CAB F62)'''
  '''2005.08.18, Thursday, 13:15 @ Alex' bureau (CAB F62)'''
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  '''2005.09.06, Tuesday 08:00 @ Alex' bureau (CAB F62)'''
  '''2005.09.06, Tuesday 08:00 @ Alex' bureau (CAB F62)'''
-
=Description of NOR module=
+
= Description of the NOR module =
This module behaves like a NOR gate. It has two inputs and one output. The output is high only when neither input 1 nor input 2 is high.
This module behaves like a NOR gate. It has two inputs and one output. The output is high only when neither input 1 nor input 2 is high.
-
==NOR-module Schematic==
+
== NOR Gate ==
-
Below a preliminary parts-view of the module with PoPS interfaces (i/o).
+
In the figure below is a parts-view of the NOR gate module with PoPS interfaces (i/o).
               ---------------------------------
               ---------------------------------
Line 33: Line 33:
               ---------------------------------
               ---------------------------------
-
=Design=
+
== Interconnected NOR module ==
-
=== Zinc Fingers ===
 
-
A zinc finger [http://en.wikipedia.org/wiki/Zinc_finger]  is a protein domain that binds to double stranded DNA. The idea is to use a zinc finger protein (ZFP) as a repressor by putting a ZFP binding site upstream of the coding region and thereby preventing RNA polymerase to transcribe the gene. A ZFP consistists of one or several Zinc Finger Domains that binds to three base pairs each. Many domain-DNA interaction for a triplet of base pairs have been described, therefore making it possible to to construct artificial transcription factors by combining domains.
 
-
===== Zinc Finger Proteins =====
 
-
In total for the counter we will need four ZFPs. We have two different designs of the ZFPs.
 
-
1.  Three domains to recognize nine base pairs.
 
-
2.  two zinc finger 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.
+
= Design =
-
===== Zinc Finger Protein Binding Sites =====
+
== Repressors ==
-
Since we are going to synthesize parts of our module, we have the possibility to design our own ZFP binding sites, as well as our ZFPs.
+
The Interconnected NOR module consists of four repressors. We considered several alternatives but finally decided to put all out bets on a approach based on zinc finger proteins.  
-
We have to different candidates for placing the binding sites.  
+
-
1. Binding sites in the promoter. This would prevent the polymerase from binding to the promotor.
+
RNA polymerase...
-
2. Binding sites directly after the start of transcription and before the ribosome binding site. This alternative is quite 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.
+
=== Zinc Finger Proteins ===
 +
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. The idea is to use a ZFP as a repressor by putting a binding site for a ZFP upstream of the coding region and thereby preventing RNA polymerase to transcribe the gene.
-
===Tester for Zinc Finger===
+
We use several different designs of ZFPs.  
-
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 .
+
-
===System Variants===
+
- Three ZF domains to recognize nine base pairs.
-
Currently, we have two systems, and we hope that at least one of them is going to work.  
+
- 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.
-
The first system, cryptically labelled "3dZFp-R" below, consists of 4 proteins with 4 operator regions. Each protein has four domains: a) 3 zink fingers that bind to specific sites on the helical DNA, and b) one repression (R) domain. We call the whole system (i.e. a+b) "Zinc Hand" (ZH) to distinguish it clearly from the individual zinc finger domains.
+
- Six ZF domains to recognize twelve base pairs.
-
In the second system, labelled "2dZFp-LZ-R" (LZ = leucine zipper), each protein has also 4 domains: 2 zink fingers, 1 leucine zipper (LZ) and 1 repression (R) domain.
+
- Three ZF domains fused to negative transcription factors. (e.g. NTD and ERD)
-
The operator regions in both systems are made of 2 binding regions, each of which lets a specific Zinc Hand bind to it and thus each consisting of the corresponding 3 codons that match the 3 zinc fingers in that Zinc Hand. The operator regions (i.e. the "roadblocks" that will prevent the binding of the RNApolymerase) form a BioBrick that should be inserted between the promoter region and the ribosome binding site in order to keep the design modular. Since we always use 2 Zinc Hands to block a promoter site (i.e. the promoters Pr and Prm of the lambda-system) and since we have 4 such promoter sites (i.e. 2xPr and 2xPrm), we need to have 4 operators = 4 permutations of Zinc Hand pairs.
 
 +
===== Zinc Finger Protein Binding Sites =====
 +
Since we are going to synthesize parts of our module, we have the possibility to design our own ZFP binding sites, as well as our ZFPs.
 +
We have two alternatives for placing the binding sites.
-
ZHR stands for '''Z'''ink '''H'''ands '''R'''egulatory proteins, and ZHO for '''Z'''ink '''H'''ands '''O'''perators. The +1/+10 indication reflects the starting position of the 2 ZH-binding regions within the operator on the DNA. Both lie between the promoter region (<0) and the ribosome binding site (RBS, around +20). There has been some discussion about having the operator around 0 (-9/+1)
+
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.
-
{| border="1"
+
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.
-
! || Type || Size (bp) per Unit || . || . || . || . || TOTAL SYSTEM SIZE (bp)
+
 
-
|-  
+
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.
-
!3dZFp-R
+
 
-
| Repressor (protein) || 400 || ZHR1 || ZHR2 || ZHR3 || ZHR4 || 1600
+
{| border="1" cellpadding="2"
 +
! Repressor !! Binding motif !! K_d (nM) !! freq. in genome !! freq. hamming dist=1
 +
|-
 +
| R1        || ggaggggac    || 4        || 1              || 132
 +
|-
 +
| R2        || ggaggcggg    || 30      || 5              || 396
 +
|-
 +
| R3        || gggggcgag    || 3        || 8              || 303
 +
|-
 +
| R4        || ggggccgga    || 45      || 23              || 433
 +
|-
 +
| R1 lz    || gtccccggggac  || N/A      || 0              || 2
|-
|-
-
| . || Operator +1/+10 (target sequence) || 30 || ZHO1.1 || ZHO2.1 || ZHO3.1 || ZHO4.1 || 120
+
| R2 lz    || ctcgccggcgag  || N/A      || 0              || 7
-
|-
+
-
!2dZFp-LZ-R
+
-
| Repressor (protein) || 400 || ZHR5 || ZHR6 || ZHR7 || ZHR8 || 1600
+
|-
|-
-
| . || Operator +1/+10 (target sequence) || 30 || ZHO5 || ZHO6 || ZHO7 || ZHO8 || 120
+
| R3 lz    || cccgccggcggg  || N/A      || 0              || 19
|-
|-
-
! TOTAL || . || . || . || . || . || . || 3440
+
| R4 lz    || tccggcgccgga  || N/A      || 0              || 27
|}
|}
 +
We need to have 4 operators = 4 permutations of ZFP.
 +
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.
-
====Repression====
+
=== Tester for Zinc Finger ===
 +
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.
 +
 
 +
=== Interconnected NOR System ===
 +
The NOR 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.
 +
 
 +
 
 +
 
 +
==== Repression ====
Note that in both cases, it is still under discussion as whether the repression domain should really be included or not. If it turns out that repression has been used in all the literature we (well, actually Hervé) can find, then we would be better off to play safe and include them:
Note that in both cases, it is still under discussion as whether the repression domain should really be included or not. If it turns out that repression has been used in all the literature we (well, actually Hervé) 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 93: Line 107:
An alternative could be a negative transcription domain fused to the ZFP.
An alternative could be a negative transcription domain fused to the ZFP.
-
====Degradation====
+
==== Degradation ====
We considered adding a variant with degradation tag, since the system might be slow otherwise. However, due to the fact that we have limited resources - in terms of money, manpower, and time - and the fact that the degradation is decoupled and it will be clearly visible if the system turns out to be too slow, we decided against it for now.
We considered adding a variant with degradation tag, since the system might be slow otherwise. However, due to the fact that we have limited resources - in terms of money, manpower, and time - and the fact that the degradation is decoupled and it will be clearly visible if the system turns out to be too slow, we decided against it for now.
-
====Additional Comments====
+
==== Additional Comments ====
We changed our strategy a couple of times in heated debates. There is quite obviously a trade-off between probability of success through redundancy, i.e. trying multiple approaches in parallel, and limited resources, i.e. financial, manpower, and time. Thus we decided against certain additional variants and cloning steps since we simply won't have the time for it.
We changed our strategy a couple of times in heated debates. There is quite obviously a trade-off between probability of success through redundancy, i.e. trying multiple approaches in parallel, and limited resources, i.e. financial, manpower, and time. Thus we decided against certain additional variants and cloning steps since we simply won't have the time for it.
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.
The modification of the promoter regions of the lambda-system, i.e. Pr and Prm, although a valid approach will probably be dropped, since it is too much work and cost and no longer modular (as opposed to having the operators after the promoter).
The modification of the promoter regions of the lambda-system, i.e. Pr and Prm, although a valid approach will probably be dropped, since it is too much work and cost and no longer modular (as opposed to having the operators after the promoter).
-
===Assembly===
+
There has been some discussion about having the operator around 0 (-9/+1)
 +
 
 +
= Synthesis of sequences =
 +
 
 +
{| border="1" cellpadding="2"
 +
|+Multiplication table
 +
! Seq nickname  !! Length !! Cost    !! SacI !! KpnI !! NheI !! EcoRI !! XbaI  !! SpeI  !! PstI
 +
|-
 +
| J05211+J05100 || 460    || $736.00  || 1    || 74  || 455  || 7,80  || 22,95 || 54,435 || 68,449
 +
|-
 +
| J05212+J05102 || 460    || $736.00  || 1    || 74  || 455  || 7,80  || 22,95 || 54,435 || 68,449
 +
|-
 +
| J05213+J05101 || 460    || $736.00  || 1    || 74  || 455  || 7,80  || 22,95 || 54,435 || 68,449
 +
|-
 +
| J05214+J05103 || 460    || $736.00  || 1    || 74  || 455  || 7,80  || 22,95 || 54,435 || 68,449
 +
|-
 +
| J05218+J05108 || 515    || $824.00  || 1    || 81  || 510  || 7,87  || 22,102|| 61,490 || 75,504
 +
|-
 +
| J05109        || 414    || $662.40  || 1    || 409  ||-    || 7    || 22    || 389    || 403
 +
|-
 +
| J05222+J05115 || 676    || $1081.60 || 1    || 87  ||671  || 7,93  || 22,108|| 67,651 || 81,665
 +
|-
 +
| J05221+J05114 || 728    || $1164.80 || 1    || 133  || 723  || 7,139 || 22,154|| 113,703|| 127,717
 +
|-
 +
| J05112        || 524    || $838.40  || 1    || 519  || -    || 7    || 7    || 499    || 513
 +
|}
 +
 
 +
= Assembly =
 +
 
 +
== ZFP Tester ==
* Cut each system into BioBricks Pieces using different restriction enzymes.
* Cut each system into BioBricks Pieces using different restriction enzymes.
* Assemble in parallel for each genes 1-4 in two variants: promoter+operator, rbs+gene
* Assemble in parallel for each genes 1-4 in two variants: promoter+operator, rbs+gene
Line 107: Line 150:
* ...
* ...
-
[[Image:CounterParts.gif]]
+
[[Image:TesterParts.gif]]
-
(please complete the above and add the test/debugging steps)
+
==== Tests ====
 +
{|
 +
| Repressor  || Operator || Comments
 +
|-
 +
| J05100    || J05212  || ...
 +
|-
 +
| J05100    || J05212  || ...
 +
|}
 +
(complete this...)
 +
 
 +
== Interconnected NOR device ==
 +
 
 +
[[Image:CounterParts.gif]]
=References=
=References=
Line 143: Line 198:
[[Newman03]] ("Leucine Zippers")
[[Newman03]] ("Leucine Zippers")
-
 
-
=Design=
 
-
==Overall Design==
 
-
[[Image:OverallDesign.png.png]]
 
-
==What to order==
 
-
[[Image:WhatToOrder.png.png]]
 

Revision as of 15:35, 22 September 2005

Back to the ETH Zurich main page.

Contents

Organisation

Group Members

Meetings 

2005.08.17, Wednesday, 15:30 @ Alex' bureau (CAB F62) Summary
2005.08.18, Thursday, 13:15 @ Alex' bureau (CAB F62)
2005.08.22, Monday, 13:45 @ Alex' bureau (CAB F62) Summary 050822
2005.08.25, Thursday 15:30 @ Alex' bureau (CAB F62)
2005.08.29, Monday 14:00 @ Alex' bureau (CAB F62)
2005.08.30, Tuesday 16:00 @ Alex' bureau (CAB F62)
2005.09.06, Tuesday 08:00 @ Alex' bureau (CAB F62)

Description of the NOR module

This module behaves like a NOR gate. It has two inputs and one output. The output is high only when neither input 1 nor input 2 is high.

NOR Gate

In the figure below is a parts-view of the NOR gate module with PoPS interfaces (i/o). 

              ---------------------------------
              |  ------------\                |
PoPS_in1 ---->|  | Repressor1 | --------      |
              |  ------------/          |     |
              |                         =     | 
              |                       --------|------> PoPS_out
              |                         =     | 
              |  ------------\          |     |
PoPS_in2 ---->|  | Repressor2 | --------      |
              |  ------------/                |
              ---------------------------------

Interconnected NOR module

Design

Repressors

The Interconnected NOR module consists of four repressors. We considered several alternatives but finally decided to put all out bets on a approach based on zinc finger proteins.

RNA polymerase...

Zinc Finger Proteins

A Zinc Finger (ZF) [1] is a protein domain [2] 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. The idea is to use a ZFP as a repressor by putting a binding site for a ZFP upstream of the coding region and thereby preventing RNA polymerase to transcribe the gene.

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.

- Six ZF domains to recognize twelve base pairs.

- Three ZF domains fused to negative transcription factors. (e.g. NTD and ERD)


Zinc Finger Protein Binding Sites

Since we are going to synthesize parts of our module, we have the possibility to design our own ZFP binding sites, as well as our ZFPs. 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.

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.

Repressor Binding motif K_d (nM) freq. in genome freq. hamming dist=1
R1 ggaggggac 4 1 132
R2 ggaggcggg 30 5 396
R3 gggggcgag 3 8 303
R4 ggggccgga 45 23 433
R1 lz gtccccggggac N/A 0 2
R2 lz ctcgccggcgag N/A 0 7
R3 lz cccgccggcggg N/A 0 19
R4 lz tccggcgccgga N/A 0 27

We need to have 4 operators = 4 permutations of ZFP. 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.

Tester for Zinc Finger

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.

Interconnected NOR System

The NOR 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.


Repression

Note that in both cases, it is still under discussion as whether the repression domain should really be included or not. If it turns out that repression has been used in all the literature we (well, actually Hervé) 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) (either KRAB or SID repressor). It is stated that polymerase blockade through ZF only is not very efficient.

However, the discussion is ongoing: As Alex pointed out we can not be sure that the 45 amino acid long KRAB domain will work, if it don't exists 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. An alternative could be a negative transcription domain fused to the ZFP.

Degradation

We considered adding a variant with degradation tag, since the system might be slow otherwise. However, due to the fact that we have limited resources - in terms of money, manpower, and time - and the fact that the degradation is decoupled and it will be clearly visible if the system turns out to be too slow, we decided against it for now.

Additional Comments

We changed our strategy a couple of times in heated debates. There is quite obviously a trade-off between probability of success through redundancy, i.e. trying multiple approaches in parallel, and limited resources, i.e. financial, manpower, and time. Thus we decided against certain additional variants and cloning steps since we simply won't have the time for it. Another important aspect is the overall goal of keeping the design modular - one of the most important aspects of the this contest. The modification of the promoter regions of the lambda-system, i.e. Pr and Prm, although a valid approach will probably be dropped, since it is too much work and cost and no longer modular (as opposed to having the operators after the promoter).

There has been some discussion about having the operator around 0 (-9/+1)

Synthesis of sequences

Multiplication table
Seq nickname Length Cost SacI KpnI NheI EcoRI XbaI SpeI PstI
J05211+J05100 460 $736.00 1 74 455 7,80 22,95 54,435 68,449
J05212+J05102 460 $736.00 1 74 455 7,80 22,95 54,435 68,449
J05213+J05101 460 $736.00 1 74 455 7,80 22,95 54,435 68,449
J05214+J05103 460 $736.00 1 74 455 7,80 22,95 54,435 68,449
J05218+J05108 515 $824.00 1 81 510 7,87 22,102 61,490 75,504
J05109 414 $662.40 1 409 - 7 22 389 403
J05222+J05115 676 $1081.60 1 87 671 7,93 22,108 67,651 81,665
J05221+J05114 728 $1164.80 1 133 723 7,139 22,154 113,703 127,717
J05112 524 $838.40 1 519 - 7 7 499 513

Assembly

ZFP Tester

  • Cut each system into BioBricks Pieces using different restriction enzymes.
  • Assemble in parallel for each genes 1-4 in two variants: promoter+operator, rbs+gene
  • Assemble the two constructs
  • ...

TesterParts.gif

Tests

Repressor Operator Comments
J05100 J05212 ...
J05100 J05212 ...

(complete this...)

Interconnected NOR device

CounterParts.gif

References

Kim & Wang (??)

Park et al. 2005 (Activation of transcription)

Chou et al. 1998

Mani05

Beerli98

Beerli00 (Linker)

Beerli02

Isalan01

Greisman97

Segal03

Segal99 ("GNN-paper")

Dreier01 ("ANN-paper")

Dreier05 ("CNN-paper")

Yang95 (Kinetics!!)

Klug05 (Minireview)

Newman03 ("Leucine Zippers")

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