Table 1

Description of the LNA probe and primer sequences used to quantify gene expression

Gene

Gene ID

Sequences

Product length

Efficiency


iNOS

4843

Probe: 5'-FAM-ACTTCTTTCCCGTCTCC-BHQ1-3'

305

1.99

± 0.8

Sense: 5'-TCCAGATAAGTGACATAAGTG-3'

Antisense: 5'-CAGCTTGACCAGAGATTC-3'

COX-2

5743

Probe: 5'-AAACTGCTCAACACCG-BHQ1-3'

216

1.99

± 2.8

Sense: 5'- GGACAGGATTCTATGGAG-3'

Antisense: 5'- GGATGTCAACACATAACTC-3'

Aggrecan

176

Probe: 5-'FAM-CCAACTCTTCAAGGTGA-BHQ1-3'

109

1.98

± 0.4

Sense: 5'-GACTGAAGTTCTTGGAGAA-3'

Antisense: 5'-CACGAAAACCCAGAGTAA-3'

Collagen type II

1280

Probe: 5'-FAM-TCTGTCTCCTTGCTTGCCA-BHQ1-3'

200

1.99

± 0.9

Sense: 5'-GGAGTCAAGGGTGATCGT-3'

Antisense: 5'-CTTGTGCACCAGCTTCTC-3'

GAPDH

2597

Probe: 5'-HEX-CAGTCAGCCGCATCTTCT-BHQ1-3'

160

1.98

± 4.3

Sense: 5'-TCTCTGCTCCTCCTGTTC-3'

Antisense: 5'-CGCCCAATACGACCAAAT-3'


Primers used in PCR experiments with Locked Nucleic Acid (LNA) probes produced amplicons between 109 and 305 base pairs and efficiency values between 1.98 and 1.99. Probes contain fluorescein (FAM) or 6-carboxyhexafluorescein (HEX) as the 5'-reporter dye and Black Hole Quencher 1 (BHQ1) as the 3'-quencher. Nucleotides highlighted in bold denote the LNA base.

Ramachandran et al. Arthritis Research & Therapy 2011 13:R145   doi:10.1186/ar3459

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