Part:BBa_K4118001

hsa_circ_0070354 H1 probe

The H1 probe is a hairpin-shaped structure used to detect the Backsplice Junction (BSJ) site of hsa_circ_0070354. It contains an ten-nucleotide BSJ site detection dangling end, a twenty-nucleotide long stem with a fourteen-nucleotide loop, and a final twelve-nucleotide long dangling end for hybridization to the RCA backbone. With a Toehold Mediated Strand Displacement reaction (TMSD), the BSJ site hybridizes to the corresponding dangling end and the stem enabling the H2 hybridization site. The length of the stem is responsible for the stability of the probe.

Based on the BSJ sequence, we the H1 probe consists of the following domains: A domain complementary to the BSJ sequence to "identify" the target circRNA among the various RNAs present in the sample (1) The loop domain (2) A domain complementary to 20 bases of sequence (1) to create a 20-base hairpin stem (3) A domain complementary to the RCA product (4)

When designing the above structure special care must be taken, so that no artifacts are present it the secondary structure. Unexpected secondary structures can affect the probe's ability to detect the targeted BSJ.

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
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]