Chemical gene synthesis: strategies, softwares, error corrections, and applications

Abstract

Chemical synthesis of DNA sequences provides a powerful tool for modifying genes and for studying gene structure, expression and function. Modified genes and consequently protein/enzymes can bridge genomics and proteomics research or facilitate commercial applications of gene and protein technologies. In this review, we will summarize various strategies, designing softwares and error correction methods for chemical gene synthesis, particularly for the synthesis and assembly of long DNA molecules based on polymerase cycling assembly. Also, we will briefly discuss some of the major applications of chemical synthesis of DNA sequences in basic research and applied areas.

Patch oligodeoxynucleotide synthesis (POS): a novel method for synthesis of long DNA sequences and full-length genes

“…Xiong et al have reported a PCR-based two-step DNA synthesis method (Xiong et al 2004). Although the use of overlap-extension PCR to construct doublestranded DNA templates minimizes the number of oligonucleotides, error rate may be a concern due to two steps of PCR in this strategy (Xiong et al 2008).…”

Pemurnian Pretrombin-2 Manusia Rekombinan di Escherichia coli untuk Produksi Trombin sebagai Komponen Lem Fibrin

“…Nukleotida PT2 sintetik, selain banyak memiliki kodon jarang juga kandungan GC nya tinggi, sehingga diperlukan optimasi kodon gen sesuai preferensi kodon E. coli melalui memanfaatkan teknologi gen sintetik. Pemanfaatan teknologi gen sintetik mampu mengubah bias kodon dari gen target menjadi cocok dengan kodon preferensi inang rekombinan (Graslund et al, 2008;Xiong et al, 2008). Setiap gen dalam genom memiliki nilai numerik yang disebut indeks adaptasi kodon (Codon Adaptation Index,CAI).…”

Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology

“…Since this time, dozens of different methods have been created to assemble double-stranded DNA from singlestranded oligonucleotides via PCR-like methods. A summary of many of these methods has been reviewed in the literature (Xiong et al 2008a;Czar et al 2009;Hughes et al 2011;Ma et al 2012) and will not be reviewed extensively here. All of these methods use single-stranded synthetic oligonucleotides with complementary overlapping sequences between adjacent oligonucleotides to assemble doublestranded DNA synthons using a thermostable DNA polymerase and PCR.…”