A non-radioactive DNA sequencing method using biotinylated dideoxynucleoside triphosphates and delta Tth DNA polymerase.

We synthesized a set of four biotinylated dideoxynucleoside triphosphates (biotin-9-ddNTPs) and optimized the reaction conditions for non-radioactive cycle sequencing using modified Tth DNA polymerase (delta Tth) and a chemiluminescent detection system. The resulting sequencing ladders showed lower background compared to those with the conventional non-radioactive sequencing method which uses 5'-biotinylated primers, especially when PCR products were analysed. With our method, DNA sequences can be determined at any primer positions without preparing 5'-biotinylated primers for dideoxy chain-termination.

Application of N-terminally truncated DNA polymerase from Thermus thermophilus (delta Tth polymerase) to DNA sequencing and polymerase chain reactions: comparative study of delta Tth and wild-type Tth polymerases.

N-Terminally truncated DNA polymerase from Thermus thermophilus (delta Tth polymerase) lacking 5'-3' exonuclease activity was used for DNA sequencing and polymerase chain reaction (PCR). In contrast to the high background of the sequencing ladder observed with the wild-type Tth polymerase, delta Tth polymerase gave readable sequencing patterns which extend up to more than 500 bases from the primer site on cycle sequencing and automated sequencing. The delta Tth polymerase was used for the standard and mutagenic PCR, and net amplification of the DNA and the mutations accumulated during PCR were analyzed. Under mutagenic PCR, the mutation rates were 7.0 x 10(-4) (Tth) and 8.3 x 10(-4) (delta Tth) per nucleotide per cycle of amplification, which were 4-9 times higher than the rates under standard PCR.

Cloning and nucleotide sequences of the BanI restriction-modification genes in Bacillus aneurinolyticus.

The genes of the BanI restriction-modification system specific for GGPyPuCC were cloned from the chromosomal DNA of Bacillus aneurinolyticus IAM1077, and the coding regions were assigned on the nucleotide sequence on the basis of the N-terminal amino acid sequences and molecular weights of the enzymes. The restriction and modification genes coded for polypeptides with calculated molecular weights of 39,841 and 42,637, respectively. Both the enzymes were coded by the same DNA strand. The restriction gene was located upstream of the methylase gene, separated by 21 bp. The cloned genes were significantly expressed in E. coli cells, so that the respective enzymes could be purified to homogeneity. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration indicated that the catalytically active form of the endonuclease was dimeric and that of the methylase was monomeric. Comparison of the amino acid sequences revealed no significant homology between the endonuclease and methylase, though both enzymes recognize the same target sequence. Sequence comparison with other related enzymes indicated that BanI methylase contains sequences common to cytosine-specific methylases.

Development of a novel method for operating magnetic particles, Magtration Technology, and its use for automating nucleic acid purification.

Magnetic particles are useful for simple and efficient nucleic acid extraction. To achieve fully automated nucleic acid extraction and purification using magnetic particles, a new method for operating magnetic particles, Magtration Technology, was developed. In this method, magnetic separation is performed in a specially designed disposable tip. This enables high recovery of magnetic particles with high reproducibility. The features of this technology are (i) a simple mechanism for process control and (ii) flexible software to enable adaptation to commercially available reagents. Automated instruments based on Magtration Technology were developed and used for nucleic acid extraction. Total DNA, total RNA and plasmids were purified by Magtration Technology at an efficiency comparable to that of manual methods.

Genetic and molecular analyses of Escherichia coli N-acetylneuraminate lyase gene.

Two plasmids containing the N-acetylneuraminate lyase (NALase) gene (nanA) of Escherichia coli, pNL1 and pNL4, were constructed. Immunoprecipitation analysis indicated that the 35,000-dalton protein encoded in pNL4 was NALase. The synthesis of NALase in E. coli carrying these plasmids was constitutive.

Serratia liquefaciens as a new host superior for overproduction and purification using the N-acetylneuraminate lyase gene of Escherichia coli.

Serratia liquefaciens was screened as a host strain for effective gene expression and easy purification of the target protein. A model gene, N-acetylneuraminate lyase gene (nanA), fused with the promoter region of Escherichia coli lac operon successfully overproduced the protein independently from the inducer. Since S. liquefaciens grew at lower temperature than E. coli and its proteins were more heat sensitive than those of E. coli, simple incubation at 60 degrees C could inactivate most enzymes but the nanA protein. Subsequent column works for purification, then, became simple and rapid.

Nucleotide sequence of the gene coding for the BanIII DNA methyltransferase in Bacillus aneurinolyticus.

The gene coding for the ATCGAT specific BanIII DNA methyltransferase (M-BanIII) of Bacillus aneurinolyticus was cloned and its nucleotides sequenced. The coding region was assigned on the nucleotide sequence on the basis of the N-terminal amino acid sequence and molecular weight of the enzyme. The M-BanIII gene coded for a protein of 580 amino acid residues (MW 66,344). Comparison with other methylases indicated that the M-BanIII sequence contained a segment of tetra-amino acids, NPPY, characteristic of N6-adenine methylases. In addition, some homologous regions were found in the sequences of type II adenine methylases PaeR7I(CTCGAG), TaqI(TCGA) and PstI(CTGCAG), containing TCGA within the recognition sequences.

Cloning and nucleotide sequences of the AccI restriction-modification genes in Acinetobacter calcoaceticus.

The genes of the AccI restriction-modification system specific for GT(A/C) (G/T)AC were cloned from the chromosomal DNA of Acinetobacter calcoaceticus, and their nucleotides sequenced. The restriction and modification genes coded for polypeptides with calculated molecular weights of 42,494 and 63,078, respectively. Both the enzymes were coded by the same DNA strand and the restriction gene was upstream of the methylase gene, separated by 2 bp. The restriction gene was significantly expressed in E. coli cells, so that the AccI restriction endonuclease could be purified to homogeneity. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration indicated that the catalytically active form of the endonuclease was tetrameric. Sequence comparison with related enzymes indicated that AccI methylase contained a segment of tetra-amino acids, NPPY, characteristic of N6-adenine methylases. In addition, some homologous regions were found in the sequence of HincII methylase specific for GT(C/T) (A/G)AC.

3-Chloro-D-alanine chloride-lyase (deaminating) of Pseudomonas putida CR 1.1. Purification and characterization of a novel enzyme occurring in 3-chloro-D-alanine-resistant pseudomonads.

A novel enzyme catalyzing cleavage of 3-chloro-D-alanine to pyruvate, ammonia, and chloride ion is distributed in some pseudomonads which have a resistance to high concentrations of 3-chloro-D-alanine. Pseudomonas putida CR 1-1 (AKU 867) was found to have the highest activity of enzyme, which was inducibly formed by the addition of 3-chloro-D-alanine to the medium. The enzyme, tentatively called 3-chloro-D-alanine chloride-lyase, was purified from P.l putida CR 1-1 in seven steps. After the last step, the enzyme appeared to be homogeneous by the criteria of polyacrylamide gel electrophoresis, analytical ultracentrifuge, and double diffusion in agarose. The enzyme has a molecular weight of about 76,000 and consists of two subunits identical in molecular weight (approximately 38,000). The enzyme exhibits absorption maxima at 278 nm and 418 nm, which are independent of the pH (6.0-9.0), and contains 2 mol of pyridoxal 5'-phosphate/mol of the enzyme. The holoenzyme is resolved to the apoenzyme by incubation with phenylhydrazine and reconstituted by the addition of pyridoxal-P. The apoenzyme can be crystallized by adding ammonium sulfate. 3-Chloro-D-alanine chloride-lyase catalyzes an alpha, beta-elimination reaction of 3-chloro-D-alanine and also, but to a lesser extent, D-cysteine and D-cysteine. The enzyme also catalyzes a beta-replacement reaction of chlorine of 3-chloro-D-alanine with hydrosulfide to yield D-cysteine. The important role of this novel beta-lyase enzyme in the detoxication of e-chloro-D-alanine by P. putida CR 1-1 is also discussed.

Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR.

The DNA polymerase gene from the archaeon Pyrococcus sp. strain KOD1 (KOD DNA polymerase) contains a long open reading frame of 5,013 bases that encodes 1,671 amino acid residues (GenBank accession no. D29671). Similarity analysis revealed that the DNA polymerase contained a putative 3'-5' exonuclease activity and two in-frame intervening sequences of 1,080 bp (360 amino acids; KOD pol intein-1) and 1,611 bp (537 amino acids; KOD pol intein-2), which are located in the middle of regions conserved among eukaryotic and archaeal alpha-like DNA polymerases. The mature form of the DNA polymerase gene was expressed in Escherichia coli, and the recombinant enzyme was purified and characterized. 3'-5' exonuclease activity was confirmed, and although KOD DNA polymerase's optimum temperature (75 degrees C) and mutation frequency (3.5 x 10(-3)) were similar to those of a DNA polymerase from Pyrococcus furiosus (Pfu DNA polymerase), the KOD DNA polymerase exhibited an extension rate (100 to 130 nucleotides/s) 5 times higher and a processivity (persistence of sequential nucleotide polymerization) 10 to 15 times higher than those of Pfu DNA polymerase. These characteristics enabled the KOD DNA polymerase to perform a more accurate PCR in a shorter reaction time.