View source for Part:BBa K4207005


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Toehold switch for the detection of BYDV genomic RNA


===Usage and Biology===

Toehold switches are engineered riboregulators that control the expression of a downstream protein coding sequence. They can be designed to detect virtually any sequence. Toehold switches are designed <i>in silico</i> so that they fold into a pre-determined secondary structure. This structure contains a stable stem-loop that sequesters the ribosome binding site (RBS) and the start codon, thus preventing translation. After a specific trigger RNA binds to the binding site of the toehold, the lower part of the stem-loop unfolds, revealing the start codon. A weak stem remains, but this structure unfolds upon ribosome binding to the RBS, starting translation (Green et al., 2017). This toehold switch was designed to detect conserved sequences in the X genome. The structural change of the toehold switch is illustrated in Figure 1.

[[[[[Animation]]]]]
<b>Figure 1</b>. Toehold switch mechanism. This animation illustrates the operation of the toehold switch. Initially, the structure is in an inactive state and the RBS and the start codon are hidden in the stem-loop. When a specific trigger binds to the binding site, the stem-loop structure opens and the ribosome binding site and start codon are revealed.

To use this toehold switch, it should be assembled in a construct containing a promoter, the toehold switch, a protein-coding sequence, and optionally a terminator if the sensor is not to be used as linear. To prevent frame-shifting, the last nucleotide is omitted from the sequence and this part is compatible with iGEM Type IIS standard assembly.

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<span class='h3bb'>Sequence and Features</span>
<partinfo>BBa_K4207005 SequenceAndFeatures</partinfo>

===Design===

This toehold switch was designed according to the B-series ideal structure from Pardee et al. (2016). This structure was improved from the original toehold switch structure (Green et al., 2014) to reduce translational leakage. We screened the BYDV genome for conserved sequences. Each sequence was divided into 36-nucleotide long subsequences and we designed toehold switches designed to specifically bind to the sequence. This toehold switch was designed using the 30-nucleotide linker found in the 27B sensor (Pardee et al., 2016). We assigned a score for each toehold switch based on the three-parameter fit from Ma et al. (2018) and selected the best-ranking toehold switches for our library.


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===Functional Parameters===
<partinfo>BBa_K4207005 parameters</partinfo>
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