Part:BBa_K4118000
RCA Domain
RCA Domain is one of the multiple repeats a Rolling Circle Amplification product possesses. Alongside the full RCA product, it is the backbone of the Linear DNA Nanostructure. It contains two hairpin probe hybridization sites and two spacer domains. Of the hairpin probe binding sites, the first one corresponds to the H1 hairpin probe and the second to the H2 hairpin probe. The spacer domains are present so that both the two probes and the probe groups are appropriately distanced to ensure minimum background fluorescence. The distance between H1 and H2 probes is eight nucleotides, while the distance between two alternating groups is nineteen. A correctly designed RCA domain will correspond to a functional DNA backbone for Nanostructure.
Ligand density is directly affected by the spacer domains. The shorter the spacer domains, the greater the ligand density, hence the shorter the distances between the probes. Spacer domains that consist of polyT sequences, rather than random sequences in the RCA domain, could reduce the nonspecific interactions. The distances between the H1 and H2 probes or H1/H2 groups on the RCA product are crucial to reaction efficiency in the Linear DNA Nanostructure system and should be optimized carefully. Probes too close to each other will produce a steric hindrance effect, while a long distance will make the H1 and H2 hybridization challenging. A short distance between the groups affects the free diffusion rate of the target, while a long distance reduces the collision efficiency between the target and H1. Both will reduce the reaction efficiency and result in a weak fluorescence signal (1).
The RCA domain originates from a phosphorylated DNA template sequence and a primer complementary to the two ends of the template in order to bring them closer, creating a padlock DNA template.
Properties: Melting Temperature:
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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