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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.
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Arthritis Research & Therapy

ISSN: 1478-6362

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