Biomod/2011/TeamJapan/Sendai/Computational design/Legs design: Difference between revisions

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Our molecular robot requires three different kinds of legs for performing its rolling motion. Therefore, the robot utilizes three different substrates and field sequences (Figure 1) for its motion mechanism.  
Our molecular robot requires three different kinds of legs for performing its rolling motion. Therefore, the robot utilizes three different substrates and field sequences (Figure 1) for its motion mechanism.  
For robustness, the system is designed to have two legs of the same type in each of the three edges of the prism shape robot (Figure 2).
For robustness, the system is designed to have two legs of the same type in each of the three peaks of the prism shape robot (Figure 2).
The DNA sequences of these legs were calculated by carrying out a Monte-Carlo optimization using the Java version of [http://www.dna.caltech.edu/DNAdesign/ DNA Design Toolbox].
The DNA sequences of these legs were calculated by carrying out a Monte-Carlo optimization using the Java version of [http://www.dna.caltech.edu/DNAdesign/ DNA Design Toolbox].


Revision as of 07:44, 30 October 2011

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About the design

Figure 1. Simplified view of the leg DNA sequence

Our molecular robot requires three different kinds of legs for performing its rolling motion. Therefore, the robot utilizes three different substrates and field sequences (Figure 1) for its motion mechanism. For robustness, the system is designed to have two legs of the same type in each of the three peaks of the prism shape robot (Figure 2). The DNA sequences of these legs were calculated by carrying out a Monte-Carlo optimization using the Java version of DNA Design Toolbox.


For design purpose we initially tried to get a simplified version of the three legs. This simplified design is based on the previous work done by Lund et al. (Nature, 2010), where they used three legs which consisted of the same sequence. Our initial guess used that sequence for the leg A as is shown in Figure B. For leg B and C, unknown sequences have been considered.

Figure 2. The three different DNA-based legs of the molecular robot


The program needs the input of each strand and define which helices exist, from here each leg and its respective field and substrate were defined as a helix. These constrains help us to describe the system in such a way that we state the conditions in which the legs could be near the body without making base paring between them. As legs should not form base pairs with the robot body we include the whole robot body sequence. Here, we decided to include a second sequence (sticky motif robot), in addition to the prism robot sequence, as a guarantee in case that the prism robot were not successful. Thus, in that case making only the sticky motif structure with the calculated legs.


Unknown values for the nucleotides are represented as N (any base: A, C, G or T) according to the IUPAC notation. For carrying out the Monte-Carlo optimization, it is needed to set a random number (seed). Unfortunately, there is no relation between how good the optimized sequence is and the given random number that generate it [1]. Therefore, we selected five seeds and found between them the corresponded sequence which generated the lowest best score.


We included a 'temporary' sequence defined as the sticky part and to be complementary with the base pairing common area between the substrate and leg. This sequence was used for the sake of maintaining a unique melting temperature in all the leg sequence and, consequently, being thermostable sequences. Without this 'trick' the sequence tends to form a low GC content. Then, leading to a low melting temperature (Tm). For calculating the melting temperature of those preliminary single strand DNA sequences we used the online program DINAMelt. You can download those results by clicking here.


Furthermore, in order to cut costs we decided to use a T-mer sequence instead of the BioTEG//iSp18//iSp18 linker [2] that binds to the streptavidin protein body. This linker is about 6nm. Therefore, the T-mer is made of 20 thymine base pairs (Figure 3). We are inclined to believe that our linker has as well flexible properties.


Figure 3. Robot body with the legs

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