Part:BBa_K4245132

Black Hole Quencher 1 (BHQ1) DNA Probe

This part is a quencher molecule labeled with a Black Hole Quencher (BHQ1) at the 3’ end designed by researchers of Key Lab at Shaanxi Normal University (Zhou et. al, 2014). When used with BBa_K4245130, a fluorophore molecule labeled with a 6-caryboxy-uroescein (FAM) at the 5’ end, the parts form a reporter mechanism known as linear DNA probes. Quenchers are molecules that absorb energy from a fluorophore and re-emit a large portion of that energy as either heat or visible light (Ogawa et al., 2009). When a fluorophore and quencher are in proximity, the quencher absorbs the energy released by the excited fluorophore, preventing fluorescence emission (see Fig. 1). When the two molecules are far apart, the quencher can no longer absorb the fluorophore's emission, allowing detection of the fluorescence emission.

Figure 1. Diagram showing FRET between the fluorophore and quencher.

The fluorophore and quencher can bind to a complementary sequence BBa_K4245131, which aligns the probes head-to-head. This proximity allows the quencher to suppress the natural fluorescence emitted by the fluorophore, resulting in no fluorescence output. Therefore, an increase in BBa_K4245131 results in a decrease in fluorescence.

References
Ogawa, M., Kosaka, N., Longmire, M. R., Urano, Y., Choyke, P. L., & Kobayashi, H. (2009). Fluorophore-quencher based activatable targeted optical probes for detecting in vivo cancer metastases. Molecular pharmaceutics, 6(2), 386–395. https://doi.org/10.1021/mp800115t

Zhou, F., Li, B., & Ma, J. (2014). A linear DNA probe as an alternative to a molecular beacon for improving the sensitivity of a homogenous fluorescence biosensing platform for DNA detection using target-primed rolling circle amplification. RSC Advances, 5(6), 4019–4025. https://doi.org/10.1039/c4ra14467h

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]