DNA sequence analysis with a modified bacteriophage T7 DNA polymerase

DNA sequence analysis with a modified bacteriophage T7 DNA polymerase

July 1987 | STANLEY TABOR and CHARLES C. RICHARDSON
A chemically modified T7 DNA polymerase is ideal for DNA sequencing by the chain-termination method due to its high processivity, lack of 3' to 5' exonuclease activity, and efficient use of nucleotide analogs. This enzyme, derived from T7 DNA polymerase, consists of two proteins: the 84-kDa T7 gene 5 protein and the 12-kDa E. coli thioredoxin. The gene 5 protein is responsible for catalytic activity, while thioredoxin enhances processivity by binding to the primer-template. The modified enzyme has a high processivity (synthesizing thousands of nucleotides without dissociating), a rapid synthesis rate (>300 nucleotides per second), and efficiently incorporates nucleotide analogs. It lacks exonuclease activity, which reduces background noise and improves the resolution of DNA sequencing gels. The modified T7 DNA polymerase is used in a two-step sequencing procedure: a labeling reaction where the primer is radioactively labeled, followed by a processive extension reaction using ddNTPs for termination. The labeling reaction uses a low concentration of dNTPs to limit processivity, resulting in radioactive fragments ranging from a few to 150 nucleotides. The termination reaction uses high dNTP concentrations and increased temperature to ensure processive synthesis until a ddNTP is incorporated. This method produces highly uniform radioactive intensity and minimal background, allowing for accurate sequence determination. The modified T7 DNA polymerase outperforms other DNA polymerases, such as the Klenow fragment of E. coli DNA polymerase I and avian myeloblastosis virus reverse transcriptase, in terms of processivity, synthesis rate, and lack of exonuclease activity. It is particularly effective in eliminating band compressions, which occur due to secondary structure stabilization at the 3' end of DNA fragments. Replacing dGTP with dITP in the labeling and termination reactions helps to avoid these compressions, resulting in uniform fragment migration. The modified T7 DNA polymerase is also efficient in incorporating nucleotide analogs such as dc7GTP and dITP, which are useful for improving gel resolution. It shows minimal discrimination against ddNTPs, allowing for the use of low concentrations of these analogs. The enzyme's high processivity and lack of exonuclease activity make it ideal for DNA sequencing and other applications requiring high fidelity and efficiency.A chemically modified T7 DNA polymerase is ideal for DNA sequencing by the chain-termination method due to its high processivity, lack of 3' to 5' exonuclease activity, and efficient use of nucleotide analogs. This enzyme, derived from T7 DNA polymerase, consists of two proteins: the 84-kDa T7 gene 5 protein and the 12-kDa E. coli thioredoxin. The gene 5 protein is responsible for catalytic activity, while thioredoxin enhances processivity by binding to the primer-template. The modified enzyme has a high processivity (synthesizing thousands of nucleotides without dissociating), a rapid synthesis rate (>300 nucleotides per second), and efficiently incorporates nucleotide analogs. It lacks exonuclease activity, which reduces background noise and improves the resolution of DNA sequencing gels. The modified T7 DNA polymerase is used in a two-step sequencing procedure: a labeling reaction where the primer is radioactively labeled, followed by a processive extension reaction using ddNTPs for termination. The labeling reaction uses a low concentration of dNTPs to limit processivity, resulting in radioactive fragments ranging from a few to 150 nucleotides. The termination reaction uses high dNTP concentrations and increased temperature to ensure processive synthesis until a ddNTP is incorporated. This method produces highly uniform radioactive intensity and minimal background, allowing for accurate sequence determination. The modified T7 DNA polymerase outperforms other DNA polymerases, such as the Klenow fragment of E. coli DNA polymerase I and avian myeloblastosis virus reverse transcriptase, in terms of processivity, synthesis rate, and lack of exonuclease activity. It is particularly effective in eliminating band compressions, which occur due to secondary structure stabilization at the 3' end of DNA fragments. Replacing dGTP with dITP in the labeling and termination reactions helps to avoid these compressions, resulting in uniform fragment migration. The modified T7 DNA polymerase is also efficient in incorporating nucleotide analogs such as dc7GTP and dITP, which are useful for improving gel resolution. It shows minimal discrimination against ddNTPs, allowing for the use of low concentrations of these analogs. The enzyme's high processivity and lack of exonuclease activity make it ideal for DNA sequencing and other applications requiring high fidelity and efficiency.
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