P1-tcyA: GCTGATTTCAACTAAGGGACG, P2-tcyA: GTAAGGTAAAAGCGACCAAGG, P3-tcyA: TCAGCAGTATTTAGCGGGTG, P4-tcyA: GGTAAACCTGAGCAGTTGTCATC, P1-tcyB: CAACAGACTCAGATACAGCTCC, P2-tcyB: CCGTTAGGTAAACTGGCAAC, P3-tcyB: AAGCTGTGGAAGGAGGTGTG, P4-tcyB ACGATAAAGAATCCAACCCG, P1-tcyC: CCGATCTTGGTTCAACTGATG, P2-tcyC: CCGACAAGGGCTACAACTTC,

P3-tcyC: ATTCTTGAGCAGGGAACGCC, P4-tcyC: CGGAAAAAAGCACCATCAC, P1-tcyR: TGGACTGGGCAATCTCATCACC, P2-tcyR: TGGTAACTGCTGGTTGTGTAATGTG, P3-tcyR: GAATCTCCTTTTTCTATCGCAG, P4-tcyR: TCTGTCAGGCTTCCACTATTG, Erm-F: GGCGCGCCCCGGGCCCAAAATTTGTTTGAT, Erm-R: GGCCGGCCAGTCGGCAGCGACTCATAGAAT. Note: An AscI restriction site was added at the 5′-end of the P2 primers, while an FseI restriction Staurosporine site was added at the 5′-end of the P3 primers. Primers were designed and analyzed with MacVector 7.2 software. Streptococcus mutans cells grown to mid-log phase (OD600 nmc. 0.4–0.5) were harvested by centrifugation (4000 g, 15 min, 4 °C), and total RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer’s instructions. Five micrograms of each RNA samples and ladder (Invitrogen) were prepared by electrophoresis on a 1% agarose-formaldehyde gel and transferred http://www.selleckchem.com/products/Bortezomib.html to a nylon membrane (Even et al., 2006). The tcyA, tcyB, and tcyC probes generated using primers labeled with digoxigenin-dUTP with the PCR DIG Probe Synthesis kit

(Roche) as specified by the manufacturer. Transcripts were diluted with the chemiluminescent substrate CDP-star (Roche) and exposed to X-ray films (Kodak). Primers used for probe preparation are as follows (5′–3′): TcyA-PF: CAGGAAACAATCACTGTAGCAAC, TcyA-PR: GAATAGCAGCATAGTTAGAACCAGC, TcyB-PF: CCTCAATCAAAAGATGGGGAC, TcyB-PR: CGATAAGACGACCAACTTGTTC, TcyC-PF: TTCTGGTGCTGGGAAATCAAC, TcyC-PR: TGACCTCCTGAAAGATGGCG. The 5′ RACE-PCR Alectinib research buy technique was used to define the transcriptional start site (TSS) of the tcyABC

locus. Overnight cultures of S. mutans UA159 were diluted 1 : 50 in fresh THYE broth and incubated at 37 °C until an OD600 nm of approximately 0.4 was reached. Total RNA was extracted using RNeasy Mini Kit. Ten micrograms of DNA-free RNA was reverse transcribed using RACE outer primer (5′-CGATAACTGATAACGTCCTG-3′) and Superscript II Reverse Transcriptase (Invitrogen) according to the supplier’s instructions. RNaseH (USB) and RNase T1 (Roche) were then added and incubated at 37 °C for 30 min. The cDNA was purified using the StrataPrep PCR Purification kit (Stratagene) following the manufacturer’s instructions. Tailing of purified cDNA using terminal deoxynucleotidyl transferase (Sigma) and dGTP/dTTP was performed according to instructions. Tailed cDNAs were amplified by PCR using RACE universal primers (5′-GAATTCGAATTCCCCCCCCCCCC-3′, 5′-GAATTCGAATTCAAAAAAAAAAAA-3′) and RACE inner primer (5′-GCTGTATCTGAGTCTGTTGCTAC-3′). Amplicons were analyzed by agarose gel electrophoresis and sequenced using the RACE inner primer.