Part:BBa_K4674008

RCORI-65

RCORI-65 serves as the stop point of RepA medated circular ssDNA synthesis in rolling circle replication

The RCR mechanism: RepA protein, RCORI105 and RCORI65

Rolling Circle Replication (RCR) is a fundamental molecular process that plays an important role in DNA replication and various molecular biology applications. It involves one-way amplification of circular DNA samples, producing long single-stranded or double-stranded DNA products with repetitive sequences.

In RCR, each replication initiator enzyme (e.g. RepA) recognizes its corresponding double-stranded origin (DSO) of the target plasmid (e.g. pC194), and creates a nick on one of the DNA strands. The DNA polymerase uses an unnicked strand as a template to elongate the nicked strand. Finally, the elongated nicked strand is completely replaced by the newly synthesised strand, and the replication initiator enzyme will then ligate the elongated nicked strand into a circular ssDNA. The circular ssDNA could server as a template for secondard strand synthesis (Ruiz-Masó et al 2015).

Fig. The mechanism of RCR replication

The design of RCR mediated ssDNA production

To produce ssDNA, we decided to construct the RCR mechanism in E. Coli. We selected the replication initiator enzyme RepA, and the corresponding DSO, RCORI, from the target R-plasmid pC194 (Noirot-Gros et al., 1994). The last 105 nucleotides of pC194 DSO (RCORI-105) serves as the start point of RCR replication, while the first 65 nucleotides is applied as stop point. The cis-auto splicing sequence and tetrahedral ssDNA sequence are inserted between RCORI-105 and RCORI-65. For the activation of RCR, we cloned the RepA gene into pET15b, by which the protein expression could be regulated by lac operator. Furthermore, we insert another ribosome binding sequence (RBS) and the coding sequence of E. Coli ssDNA binging protein (SSBP) to protect the RCR-generated ssDNA. Finally, to purify the SSBP bound ssDNA, we fused a 6xHis-tag to SSBP.

Fig. The design of RCR mediated circular ssDNA generation

References Ruiz-Masó J, et al. (2015) Plasmid rolling-circle replication. microbial spectrum.3;10.1128

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal NgoMIV site found at 44
  
• 1000
  COMPATIBLE WITH RFC[1000]