Design Considerations

   Over the years, the Group I intron from Tetrahymena thermophila as well as related
   self-splicing RNAs have enjoyed diverse engineering attempts to repurpose them as in vivo
   RNA editing tools . The main step
   towards engineering these self-splicing ribozymes consist of turning the ribozymes' self-splicing
   activity into trans-splicing activity . Conveniently, the structure
   of T. thermophila group I intron is fairly amenable to such engineering attempts by virtue of
   its modular structure . The ribozyme consists of a compact catalytic core
   (Figure 1, core) – this should not be disturbed when attempting to engineer the ribozyme –
   flanked on the 5' and 3' ends respectively by a pair of hairpin loops (Figure 1, 5': P2 and P2.1; 3': P9.2 and P9.1),
   The P2 substructure is followed by an internal guide sequence (IGS) directly interacting with the ribozyme core
   and an external guide sequence (EGS), which positions the 5' exon for the splicing reaction (Figure 1, EGS).
   On the 3' end, the P9 substructure is followed by the 3' splice site and the 3' exon itself (Figure 1, 3' active site).
   For a properly functioning ribozyme, the P2 and P9 substructures may be engineered, but must be able
   to form a tertiary interaction between P2.1 and P9.1 for high activity .

   Engineering a trans-splicing version of the T. thermophila group I intron is almost trivially easy –
   intuitively all one has to do is to detach the 5' exon from the group I intron and extend the EGS to include at
   least 10 bases complementary to the target RNA sequence. This usually suffices to yield at least minimal trans-splicing
   activity .

EGS / IGS Design

   To achieve high-efficiency trans-splicing using the T. thermophila group I intron requires careful design of the
   external guide sequence (EGS). First and foremost, a valid target sequence for trans-splicing needs to contain
   an uracil (U) base at the splice site. This is a hard, non-negotiable sequence requirement – no U, no activity.
   Secondly, the target RNA sequence needs to be accessible – it must not form stable secondary structures
   in the region complementary to the ribozyme EGS as well as at the splice site itself .
   This can be checked in silico by predicting the secondary structure of the target RNA within a sliding window
   around potential splice sites. Experimentally, splice site preferences may be measured by preparing a splice site library
   of ribozymes with different target sites and measuring splicing efficiency .

   A further consideration to make trans-splicing as efficient as possible is the length of the EGS, together with the
   size of the bulge formed between the IGS and EGS upon 5' substrate binding . Here, the
   literature tells us that the optimal size of the EGS-bulge should be in the range between 5 and 6 bases .
   In addition, the bulge on the side of the ribozyme should be able to form base base pairs with the start of the 3' exon, just after
   the 3' splice site (P10 extension). For our experiments we designed a fixed EGS/IGS and corresponding splice-site for the sake of
   simplicity. These were designed according to all design principles mentioned above to ensure high trans-splicing activity.

Split Trans Splicing Ribozymes

 Taking another look at our overview of the T. thermophila ribozyme in Figure 1, we may notice that the both the
 P2.0 and P9.2 stems are not structurally essential for ribozyme activity. Therefore, we may safely split the ribozyme
 across these two stems to yield a split ribozyme core (
   <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K3657048">BBa_K3657048</a>
 ) a 5' guide sequence, directing the ribozyme to a target 5' exon (
   <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K3657047">BBa_K3657047</a>
    for our choice of IGS/EGS and target sequence
 ) and a 3' exon guide sequence tethering a chosen 3' exon to the trans-splicing ribozyme (
   for example
   <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K3657050">BBa_K3657050</a>
   for a 3' exon containing the sequence of the mScarlet fluorescent protein
 ). Splitting the ribozyme in this way makes the base Tetrahymena ribozyme more modular, allowing a single
 ribozyme core to do the work of splicing on multiple 3' and 5' exons, thereby improving on earlier
 T. thermophila ribozymes in the iGEM registry (e.g.
   <a href="https://parts.igem.org/Part:BBa_I4285">BBa_I4285</a>
 ).

Single Guide Trans Splicing Ribozymes

 Taking note of the property of the tertiary interaction between P2.1 and P9.1, we make take our engineering strategy
 one step further. We may split out ribozyme along the P2.1 and P9.1 stem and insert a linker between the split 5' and 3' parts,
 which results in P9.1 and P2.1 being kept in spatial proximity by base-pairing interactions and fusing the 5' and 3' guide sequences
 into a single-guide sequence for a split trans-splicing ribozyme core. We provide parts for this type of ribozyme
 core and single-guide sequence as well (
   <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K3657041">BBa_K3657041</a> for the core and
   <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K3657042">BBa_K3657042</a> for the guide.
 )

Source

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Part:BBa_K3657038:Design

Design Notes

Design Considerations

EGS / IGS Design

Split Trans Splicing Ribozymes

Single Guide Trans Splicing Ribozymes

Source

References