Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Domain Level Project Design

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=Domain Level Project Design=
 
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Consider 2D origami plane. On this plane is a random assortment of objects that have some
 
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meaning to us, something that we take some interest in keeping track of. Our goal for the summer is to
 
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develop and test a system that is capable of retrieving and sorting these objects in a meaningful way, to
 
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provide some order to what is currently a relatively chaotic system, and give us some ability to track
 
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these objects of interest.
 
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We see this technology being used effectively in a number of practical applications. The ability
 
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to sort on its own has plenty of uses. Additionally, when coupled with other mechanisms, the ability to
 
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sort has the possibility to lead to systems that automatically collect and remove byproducts from a
 
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reaction, purify a system and condense products into specified locations, and aid in controlled and
 
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detailed micro assembly machines. Additionally, our specific implementation of a solution to this
 
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problem is universal enough that it can be applied to not only DNA, but anything that can be tagged with
 
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a DNA identifier. For these reasons, we believe that this technology is worth developing such that it can
 
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be used as a tool by others in their applications.
 
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===Origami Layout===
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:Main Article: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Origami Layouts|List of Origami Layouts]]''
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== Domain Level Design ==
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==Random Walking Mechanism==
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:Main Article: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Random Walking|Random Walking Mechanism]]''
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=== Overall Domain Design ===  
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The backbone of our design is a random walker that moves across the surface of a rectangular
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origami. The mechanism by which said walker moves is simply strand displacement, whereby the walker
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[[Image: DomainLevelDesign.jpg | thumb|center|800px | Figure 1. Overall domain level desin]]
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contains a toehold on each end of the body, and the track strands on which it walks contains the
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complement of one of the two toeholds on the walker. This particular arrangement allows the walker to
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Probes are the extended part of staples which are complementary to the bottom part of the strands which should be anchored on the origami surface. Different kinds of probes were designed for each strand. Origami will be annealed with certain staples extended with probes at predetermined positions, and some strands, such as tracks or cargo goals, will be planted on those specific positions using interaction between probe regions.
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move randomly between track strands without modifying previously visited track segments.
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==Cargo Pick-Up Mechanism==
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=== Random Walking Mechanism ===
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:Main Article: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Cargo Pick-Up|Cargo Pick-Up Mechanism]]''
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The backbone of our design is a random walker that moves across the surface of a rectangular origami. The mechanism by which said walker moves is simply strand displacement, whereby the walker contains a toehold on each end of the body, and the track strands on which it walks contains the complement of one of the two toeholds on the walker. This particular arrangement allows the walker to move randomly between track strands without modifying previously visited track segments.
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==Cargo Drop-Off Mechanism==
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:Main Article: ''[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Cargo Drop-Off|Cargo Drop-Off Mechanism]]''
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The random Walker consists of a body which is a 15nt long domain (black), and two arms each which are 6nt short toeholds (red and blue toehold) at at each end of the body. Tracks on which it walks contain the complement of one of the two toeholds: track 1 with red domain and track 2 with blue domain. When a walker is on track 1, blue toehold is unpaired and searches for a complementary single strand. When track 2 is adjacent, it serves as a complementary sequence to which it can bind. After an blue toehold of the walker binds to an adjacent track 2, which serves as a "distal toehold", the hybridization extends by the rest of track 2. By this branch migration, the whole walker moves from track 1 to track 2. Similarly, a walker can move randomly from one kind of track to another kind.
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==See Also==
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[[Image: ssslide14.jpg | 600px | thumb|center | Figure 2 (a). Random walking mechanism from track 1 to track 2]]
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[[Image: ssslide15.jpg | 600px| thumb|center | Figure 2 (b). Random walking mechanism from track 2 to track 1]]
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===Cargo Pick-Up Mechanism===
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To accomplish a cargo-reorganizing-task, a walker is extended to have picking up arm which is complementary to cargos (green domain). When walker randomly walks and encounters a cargo molecule, it picks up the cargo by strand displacement using yellow toehold.
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[[Image: ssslide16.jpg | 600px| thumb|center |Figure 3. Cargo ick-up mechanism]]
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===Cargo Drop-Off Mechanism===
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It continues random walking after picking up, and when a walker gets to the cargo goal, cargo is dropped off at the cargo goal using purple toehold, which both cargo and cargo goal share. Therefore, random walking process is purely stochastic, yet a deterministic end result can be achieved by specific recognition between the cargo molecules and their destinations.
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[[Image: ssslide17.jpg | 600px| thumb|center |Figure 4. Cargo drop-off mechanism]]
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===Walking to the Walker Goal Mechanism (for verification of random walking) ===
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Another important stand is walker goal. Since walker goal contains both red and blue toeholds which are complementary to the both of the toeholds of the walker, walker stays on the walker goal when it gets there. Walker goal will be used in verifying random walking on origami, and its use will be explained in later section.
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[[Image: ssslide19.jpg | 600px| thumb|center| Figure 5. Walking to the walker goal mechanism]]
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=== Triggering Mechanism===
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While the system is under construction, (e.g. track being planted), a walker or cargo goal should be deactivated to prevent undesired random walking or cargo sorting. Walker inhibitor and cargo goal inhibitor are thus designed. Later, walker trigger and cargo goal trigger will rip off the inhibitors by strand displacement using corresponding toeholds.
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====Walker Triggering====
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[[Image: ssslide12.jpg | 600px| thumb|center| Figure 6. Walker triggering mechanism]]
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====Cargo Goal Triggering====
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[[Image: ssslide13.jpg | 600px| thumb|center|Figure 7. Cargo goal triggering mechanism]]
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===See Also===
*[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design|Sequence Design]]
*[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design|Sequence Design]]
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Domain Level Design

Overall Domain Design

Figure 1. Overall domain level desin
Figure 1. Overall domain level desin

Probes are the extended part of staples which are complementary to the bottom part of the strands which should be anchored on the origami surface. Different kinds of probes were designed for each strand. Origami will be annealed with certain staples extended with probes at predetermined positions, and some strands, such as tracks or cargo goals, will be planted on those specific positions using interaction between probe regions.

Random Walking Mechanism

The backbone of our design is a random walker that moves across the surface of a rectangular origami. The mechanism by which said walker moves is simply strand displacement, whereby the walker contains a toehold on each end of the body, and the track strands on which it walks contains the complement of one of the two toeholds on the walker. This particular arrangement allows the walker to move randomly between track strands without modifying previously visited track segments.

The random Walker consists of a body which is a 15nt long domain (black), and two arms each which are 6nt short toeholds (red and blue toehold) at at each end of the body. Tracks on which it walks contain the complement of one of the two toeholds: track 1 with red domain and track 2 with blue domain. When a walker is on track 1, blue toehold is unpaired and searches for a complementary single strand. When track 2 is adjacent, it serves as a complementary sequence to which it can bind. After an blue toehold of the walker binds to an adjacent track 2, which serves as a "distal toehold", the hybridization extends by the rest of track 2. By this branch migration, the whole walker moves from track 1 to track 2. Similarly, a walker can move randomly from one kind of track to another kind.

Figure 2 (a). Random walking mechanism from track 1 to track 2
Figure 2 (a). Random walking mechanism from track 1 to track 2
Figure 2 (b). Random walking mechanism from track 2 to track 1
Figure 2 (b). Random walking mechanism from track 2 to track 1


Cargo Pick-Up Mechanism

To accomplish a cargo-reorganizing-task, a walker is extended to have picking up arm which is complementary to cargos (green domain). When walker randomly walks and encounters a cargo molecule, it picks up the cargo by strand displacement using yellow toehold.

Figure 3. Cargo ick-up mechanism
Figure 3. Cargo ick-up mechanism

Cargo Drop-Off Mechanism

It continues random walking after picking up, and when a walker gets to the cargo goal, cargo is dropped off at the cargo goal using purple toehold, which both cargo and cargo goal share. Therefore, random walking process is purely stochastic, yet a deterministic end result can be achieved by specific recognition between the cargo molecules and their destinations.

Figure 4. Cargo drop-off mechanism
Figure 4. Cargo drop-off mechanism


Walking to the Walker Goal Mechanism (for verification of random walking)

Another important stand is walker goal. Since walker goal contains both red and blue toeholds which are complementary to the both of the toeholds of the walker, walker stays on the walker goal when it gets there. Walker goal will be used in verifying random walking on origami, and its use will be explained in later section.

Figure 5. Walking to the walker goal mechanism
Figure 5. Walking to the walker goal mechanism

Triggering Mechanism

While the system is under construction, (e.g. track being planted), a walker or cargo goal should be deactivated to prevent undesired random walking or cargo sorting. Walker inhibitor and cargo goal inhibitor are thus designed. Later, walker trigger and cargo goal trigger will rip off the inhibitors by strand displacement using corresponding toeholds.

Walker Triggering

Figure 6. Walker triggering mechanism
Figure 6. Walker triggering mechanism

Cargo Goal Triggering

Figure 7. Cargo goal triggering mechanism
Figure 7. Cargo goal triggering mechanism



See Also

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