Table 1.
The design of oligonucleotide probes
| Oligonucleotide probe | Sequences, fluorophore and quencher | Tm (°C) |
|---|---|---|
| Random MB with Cy3 | 5′-Cy3-CGACGCGACAAGCGCACCGATACGTCG-BHQ-3′ | 50.9 |
| Random MB2 with Cy3 | 5′-Cy3-CGACGCTCTGCCTAAGTGATGTCCGTCG-BHQ-3′ | 53.5 |
| Random 2′-O-methyl MB with Cy3a | 5′-Cy3-CGACGCGACAAGCGCACCGATACGTCG-BHQ-3′ | 68.2 |
| Random linear probe with Cy3 | 5′-Cy3-CCTGCCGACAAGCGCACCGATACGTCC-3′ | – |
| Random DSO with dye and quencher | 5′-Cy3-CGACGCGACAAGCGGCTTGTCGCGTCG-BHQ-3′ | 84.5 |
| Random DSO with dye only | 5′-Cy3-CGACGCGACAAGCGGCTTGTCGCGTCG-3′ | 84.5 |
| Random linear probe with Alexa 488 | 5′-Alexa488-CCTGCCGACAAGCGCACCGATACGTCC-3′ | – |
| Random linear probe with Alexa 546 | 5′-Alexa546-CCTGCCGACAAGCGCACCGATACGTCC-3′ | – |
| Random MB with Alexa 546 | 5′-Alexa546-CGACGCGACAAGCGCACCGATACGTCG-BHQ-3′ | 50.9 |
| Random linear probe with Cy5 | 5′-Cy5-CCTGCCGACAAGCGCACCGATACGTC-3′ | – |
| Short-linear probe with Cy3 | 5′-Cy3-CCTG-3′ | – |
| Long-linear probe with Cy3 | 5′-Cy3-CTGCCGACAAGCGCACCGATACGTCCCCTGCCGACAAGC-3′ | – |
| Random linear target with quencher | 5′-GACGTATCGGTGCGCTTGTCGGCAGG-BHQ-3′ | – |
| BMP4 MB with Cy3 | 5′-Cy3-CGCAGCCTCTACCACCATCTCCCTGCG-BHQ-3′ | 55.4 |
aItalic letters indicate 2′-O-methyl backbone chemistry; MB, molecular beacon; DSO, double-stranded oligonucleotide probe.