In vitro transcription of DNA templates was carried out with 20–40 U of T7 RNA polymerase per reaction and α-32P UTP (800 Ci·mmol−1; 10 mCi·ml−1). Probes for TS and GFP siRNA were generated by in vitro transcription reactions from plasmid templates [500 μg ml−1 of pTSa linearized with Sal1 or pKSGFP5 as described in (11 (link))]. These reactions were supplemented with 100 μM unlabelled UTP and carried out at 37°C. Where oligonucleotide or ‘mirVana’ templates were used, the only source of UTP was from the radioactively labelled solution ([final] = ∼3 μM). Templates to make probes for mmu-mir-292-as, mmu-mir-294, hsa-mir-21, hsa-mir-16 were prepared using the mirVana™ miRNA Probe Construction Kit (Ambion, USA) with oligonucleotides aagtgccgccaggttttgagtgtcctgtctc (mmu-mir-292as), aaagtgcttcccttttgtgtgtcctgtctc (mmu-mir-294), tagcagcacgtaaatattggcgcctgtctc (hsa-mir-16) and tagcttatcagactgatgttgacctgtctc (hsa-mir-21) respectively according to the manufacturer's instructions. Resulting templates were used for RNA probe synthesis following manufacturer's instructions. The probes for ath-mir-159b and pi-R1 were prepared by annealing oligonucleotides aagagctcccttcaatccaaacctatagtgagtcgtatta (ath-mir-159) or tgacatgaacacaggtgctcagatagctttcctatagtgagtcgtatta (pi-R1) with the oligonucleotide taatacgactcactatagg. These were used at 250 nM as templates for in vitro transcription with α-32P UTP by T7 RNA polymerase at 22°C.
All in vitro transcriptions were treated with TurboDNAse® (Ambion) prior to addition to the hybridization solution to eliminate the DNA template.
End-labelling of oligonucleotides: (1 pmol per labelling) with or without LNA modifications were carried out with T4 polynucleotide kinase and γ32P ATP (6000 Ci·m mol−1; 10 mCi·ml−1). Pre-designed LNA oligonucleotides for hsa-mir-21 and hsa-mir-16 were obtained from Exiqon (Denmark). Unmodified oligonucleotide probe sequences were 5′ tcaacatcagtctgataagcta 3′ (hsa-mir-21) and 5′ cgccaatatttacgtgctgcta 3′ (hsa-mir-16) (Sigma).
All in vitro transcriptions were treated with TurboDNAse® (Ambion) prior to addition to the hybridization solution to eliminate the DNA template.
End-labelling of oligonucleotides: (1 pmol per labelling) with or without LNA modifications were carried out with T4 polynucleotide kinase and γ32P ATP (6000 Ci·m mol−1; 10 mCi·ml−1). Pre-designed LNA oligonucleotides for hsa-mir-21 and hsa-mir-16 were obtained from Exiqon (Denmark). Unmodified oligonucleotide probe sequences were 5′ tcaacatcagtctgataagcta 3′ (hsa-mir-21) and 5′ cgccaatatttacgtgctgcta 3′ (hsa-mir-16) (Sigma).