Skip to main content

Table 1 Description of the Beacon designer sequences used to quantify gene expression and real-time reaction efficiencies of PCR assays

From: Dynamic compression counteracts IL-1β induced inducible nitric oxide synthase and cyclo-oxygenase-2 expression in chondrocyte/agarose constructs

Gene Accession number Sequences Product size (base pairs) Efficiency
iNOS U14640 Probe: 5'-FAM-CGCGATCCCTGCTTGGTGGCGAAGATGAGCGATCGCG-DABCYL-3' Forward: 5'-GTAACAAAGGAGATAGAAACAACAGG-3' Reverse: 5'-CAGCTCCGGGCGTCAAAG-3' 81 1.98 ± 0.06
COX-2 AF031698 Probe: 5'-FAM-CGCGATCGTCAGAAATTCGGGTGTGGTACAGTTGATCGCG-DABCYL-3' Forward: 5'-CGAGGTGTATGTATGAGTGTAGG-3' Reverse: 5'-GTTGGGAGTGGGTTTCAGG-3' 82 1.99 ± 0.03
Aggrecan U76615 Probe: 5'-FAM-CGCGATCCACTCAGCGAGTTGTCAGGTTCTGAGATCGCG-DABCYL-3' Forward: 5'-TGGTGTTTGTGACTCTGAGG-3' Reverse: 5'-GATGAAGTAGCAGGGGATGG-3' 79 1.97 ± 0.05
Collagen type II X02420 Probe: 5'-FAM-CGCGATGCGTCAGGTCAGGTCAGCCATATCGCG-DABCYL-3' Forward: 5'-AAACCCGAACCCAGAACC-3' Reverse: 5'-AAGTCCGAACTGTGAGAGG-3' 70 2.00 ± 0.05
GAPDH U85042 Probe: 5'-HEX-CGCGATCCACCATCTTCCAGGAGCGAGATCCGATCGCG-DABCYL-3' Forward: 5'-TTCAACGGCACAGTCAAGG-3' Reverse: 5'-TTCAACGGCACAGTCAAGG-3' 75 2.03 ± 0.01
  1. The Beacon Designer software was used to design forward and reverse primer and probe sequences for molecular beacon applications and were synthesized by Sigma Genosys Ltd, Cambridge, UK. Secondary structures were avoided using the Mfold programme and sequences were analyzed using Basic Local Alignment Search Tool to verify specificity. Probes contain fluorescein (FAM) or 6-carboxyhexafluorescein (HEX) as a 5'-reporter dye and 4-(4'-dimethylaminophenylazo)benzoic acid (DABCYL) as 3'-quencher. Note that the arm sequences are underlined. COX, cyclo-oxygenase; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; iNOS, inducible nitric oxide synthase.