Louis, MO) with occasional mixing for 1 h at 37°C, followed by 2% wt/vol SDS (Gibco, Carlsbad, CA), and proteinase K (0.2 mg/ml) (Sigma Aldrich, St. Louis, MO) for 1 h at 37°C. DNA was extracted with phenol:chloroform:isoamyl alcohol, precipitated with two volumes of ice-cold www.selleckchem.com/products/baricitinib-ly3009104.html ethanol, washed with 70% ice-cold ethanol, and suspended in TE, pH 8.0 buffer containing

0.2 Selleckchem RG7112 mg/ml RNase A (Invitrogen, Carlsbad, CA). DNA amplification by PCR Primers used in PCR reactions are listed in Table 1 and Additional File 2 (Table S2). PCR was used to investigate the presence and organization of the RD2 element in streptococcal strains. The PCR primers #1-#4 detect a chromosomal and extrachromosomal circular form, and tile across the entire RD2. Confirmation of RD2 presence by tailing and detection of genes encoding extra-chromosomal proteins was performed as described previously [1, 2] Table 1 PCR primers used in this study A. Primers used for detection of multiple RD2 genes, Q-PCR and tiling. Primer name Primer sequence Source emm sequencing   CDC emm1 TATT(C/G)GCTTAGAAAATTAA [19] CDC emm2 GCAAGTTCTTCAGCTTGTTT [19] Detection of circular form   #1 GAAAACAAAAGTTTCTTCATGCGTTTGGCG

learn more this work #2 CAATTAATAGAAACATATGGTCATTTG this work #3 GGAATTAGCCCACTAGAATATAAGC this work #4 TAGCAAGTAAACCCTAGATTGTCTATGTTC this work Detection of genes encoding extracellular RD2 proteins   M28_Spy1306F ACTAAGCCAAGCGAGGACAA [1] M28_Spy1306R CCAAAACCGTGTAGCCTGTA [1] M28_Spy 1307F TCATCGTCAAAAGCCATCTC [1] M28_Spy 1307R TTGCTCTGATAAACCTCAAG [1] M28_Spy1308F TACGACAGAAGCAGGTGGAG Sitaxentan [1] M28_Spy1308R ACCGAGTTTCGCAGGATTG [1] M28_Spy1325F TGAATGATGCGGGGACTTAT

[1] M28_Spy1325R TGTAAAAGGCTGCTGGGTCT [1] M28_Spy1326F ACACCGACTGAGATTGCTGA [1] M28_Spy1326R TTGGCTTGTGAGGTTTGAGA [1] M28_Spy1332F ATGCCAAAAACCAAAGGAAG [1] M28_Spy1332R TCATACTTTTCAGGTACACAAGCA [1] M28_Spy1336F GATACTTCACAGACGAAACAACG [1] M28_Spy1336R ATCACGACTCCCATCACTCC [1] Quantitative PCR (Taqman)   proS_F TGAGTTTATTATGAAAGAGGCTATAGTTTC [15] proS_R AATAGCTTCGTAAGCTTGACGATAAT [15] proS_P TCGTAGGTCACATCTAATCTTCATAGTTG [15] M28_Spy1306 F CGTTGTTCCTGCTACTGGATCTGCTAC this work M28_Spy1306 P ACGATTGCAAGTATTGCTTTG this work M28_Spy1306 R CAATCGGTGTCGTTGGTTG this work M28_Spy1325 F ACCGTCGCAAGGACCTTGTCTTTCTG [8] M28_Spy1325 P CAGCATACGCATGACCTC [8] M28_Spy1325 R AGTGATAACACTACCATCTGATAAAG [8] M28_Spy1336 F ACAGAAGCTGCACCAAACTTGAACTTCTTAATTGA this work M28_Spy1336 P GTAGATGCAGCAACTATTGAC this work M28_Spy1336 R ATGATACTTCACAGACGAAACAAC this work M28_Spy0784_RD0 F AGCAGAGTATGAAGGCGGTTTT this work M28_Spy0784_RD0 P ATATTCTATCTGAAACGGCTCG this work M28_Spy0784_RD0 R AACATCTCTGCGAGTCGTTCTATACTT this work M28_Spy0980_6180.1 F TCGTTAGGACTGGCGGTAGAG this work M28_Spy0980_6180.1 P TGCAACTGCTGTCTTAA this work M28_Spy0980_6180.