, 2005a). Mass spectrometry analyses provided the molecular basis of these peculiar resistance

phenotypes: Erm(38) is a reluctant dimethyltransferase that leaves most of the rRNA molecules either monomethylated or unmethylated (Madsen et al., 2005b), and Erm(37) further methylates nucleotides A2057 and A2059 after monomethylation of A2058 (Madsen et al., 2005a). These phenotypic diversities of the Erm methylases suggest that frequent gene duplications and resultant paralog segregations eventually caused phylogenetic anomalies in the Erm clade of the Actinobacteria. The tree-constructing algorithms failed to ZVADFMK separate Erm proteins into either monomethylases (type I) or dimethylases (type II). Separate analysis of the Erm N-terminal and C-terminal domains or subdomains also could not distinguish monomethylase from dimethylase activities in the phylogenetic trees (data not shown). This research was supported by the Research Program for New Drug Target Discovery (2008-2005325) and the Basic Science Research Program (2010-0011442) through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (to H.J.J.). Fig. S1. Sequence alignments of representative amino acid sequences of Erm methylases and KsgA/Dim1 proteins. Selleck PD0325901 Table S1. List of sequences of KsgA/Dim1 used in phylogenetic

analyses. Please note: Wiley-Blackwell is not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. “
“In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis

and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated RAS p21 protein activator 1 the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n(T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence.