Difference between revisions of "Part:BBa K2918013"

Revision as of 22:10, 7 October 2019

BBa_B0032 RBS and SarJ

BioBrick BBa_B0032 (RBS) along with ribozyme (SarJ).

Sequence and Features

Usage and Biology

Although promoters end at the Transcription Start Site (TSS), there are often additional sequences downstream of the TSS that become part of the transcript. These additional sequences are shown to affect the behavior of parts downstream (Lou et al. 2012). Therefore, to insulate the parts behavior from the influence of neighboring parts, ribozymes can be used. Ribozymes have self cleavage properties and can be used upstream of ribosome binding sites to cleave sequences that occur downstream of the TSS. By the action of ribozymes, outputs of genetic circuits will be insulated by the effect of the sequence between the promoter and the genetic circuit (Lou et al. 2012). This BioBrick consists of SarJ and BBa_B0032 .

Strain Construction

The DNA sequence of the part was synthesized by IDT with flanking BpiI sites and respective Modular Cloning (MoClo) compatible 5'UTR overhangs. The RBS was then cloned in a level 0 MoClo backbone pICH41246 and the sequence was confirmed by sequencing. The cloning protocol can be found in the modular cloning section below.

Modular Cloning

Modular Cloning (MoClo) is a system which allows for efficient one pot assembly of multiple DNA fragments. The MoClo system consists of Type IIS restriction enzymes that cleave DNA 4 to 8 base pairs away from the recognition sites. Cleavage outside of the recognition site allows for customization of the overhangs generated. The MoClo system is hierarchical. First, basic parts (promoters, UTRs, CDS and terminators) are assembled in level 0 plasmids in the kit. In a single reaction, the individual parts can be assembled into vectors containing transcriptional units (level 1). Furthermore, MoClo allows for directional assembly of multiple transcriptional units. Successful assembly of constructs using MoClo can be confirmed by visual readouts (blue/white or red/white screening). For the protocol, you can find it here.

Note: The basic parts sequences of the Sci-Phi 29 collection in the registry contain only the part sequence and therefore contain no overhangs or restriction sites. For synthesizing MoClo compatible parts, refer to table 2. The complete sequence of our parts including backbone can be found here.

Table 1: Overview of different level in MoClo

For synthesizing basic parts, the part of interest should be flanked by a BpiI site and its specific type overhang. These parts can then be cloned into the respective level 0 MoClo parts. For level 1, where individual transcriptional units are cloned, the overhangs come from the backbone you choose. The restriction sites for level 1 are BsaI. However, any type IIS restriction enzyme could be used.

Table 2: Type specific overhangs and backbones for MoClo. Green indicates the restriction enzyme recognition site. Blue indicates the specific overhangs for the basic parts