Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Sequence Design
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Tuesday, September 2, 2014

Sequence Design
Design ProcessAfter having designed our mechanism at the domain level, we needed to fill in our domains with actual sequences. To start, we picked specific lengths for each of our domains. We decided to stick with the general precedent that toeholds be 6 nucleotides in length, then decided that any domain that was part of a probe be 20 nucleotides in length, as this length is both not wastefully long and long enough to ensure that no spontaneous dissociation would occur. We then decided that any domain longer than a toehold, but not part of the probe system should be 15 base pairs in length, as this would not spontaneously dissociate, but could be easily strand displaced. After these numbers were decided, we consulted a list of 20 nucleotide sequences that are known to be relatively inert and chose sequences from this list to fill in our 20 and 15 nucleotide domains. We used NUPACK and a little trial and error to find our 7 necessary relatively inert toeholds. We then ran a number of simulations in NUPACK to check for unwanted secondary structures and interactions in our designed sequences. List of DomainsProbe DomainsThe length of these sequences is 20 nucleotides.
† The lp domain is 27 nucleotides long.
Toehold DomainsThe length of these sequences is 7 nucleotides.
† The a_{2}' domain is a subset of the a_{2} domain and is 4 nucleotides long.
Other DomainsThe length of these sequences is 15 nucleotides.
List of Strands
