Cost-Effective Method of Gene Synthesis by Sequencing from Microchip-Derived Oligos for Droplet Cloning

Gene synthesis has provided important contributions in various fields including genomics and medicine. Current genes are 7 - 30 cents depending on the assembly and sequencing methods performed. Demand for gene synthesis has been increasing for the past few decades, yet available methods remain expensive. A solution to this problem involves microchip-derived oligonucleotides (oligos), an oligo pool with a substantial number of oligo fragments. Microchips have been proposed as a tool for gene synthesis, but this approach has been criticized for its high error rate during sequencing. This study tests a possible cost-effective method for gene synthesis utilizing fragment assembly and golden gate assembly, which can be employed for quicker manufacturing and efficient execution of genes in the near future. The droplet method was tested in two trials to determine the viability of the method through the accuracy of the oligos sequenced. A preliminary research experiment was performed to determine the efficacy of oligo lengths ranging from two to four overlapping oligos through Gibson assembly. Of the three oligo lengths tested, only two fragment oligos were correctly sequenced. Two fragment oligos were used for the second experiment, which determined the efficacy of the droplet method in reducing gene synthesis cost and speed. The first trial utilized a high-fidelity polymerase and resulted in 3% correctly sequenced oligos, so the second trial utilized a non-high-fidelity polymerase, resulting in 8% correctly sequenced oligos. After calculating, the cost of gene synthesis lowers down to 0.8 cents/base. The final calculated cost of 0.8 cents/base is significantly cheaper than other manufacturing costs of 7 - 30 cents/base. Reducing the cost of gene synthesis provides new insight into the cost-effectiveness of present technologies and protocols and has the potential to benefit the fields of bioengineering and gene therapy.

Identification of miRNAs and target genes regulating catechin biosynthesis in tea (Camellia sinensis)

Micro RNAs（miRNAs） are endogenous non-protein-coding small RNAs that play crucial and versatile regulatory roles in plants. Using a computational identification method, we identified 55 conserved miRNAs in tea（Camellia sinensis） by aligning miRNA sequences of different plant species with the transcriptome library of tea strain 1005. We then used quantitative real-time PCR（qRT-PCR） to analyze the expression of 31 identified miRNAs in tea leaves of different ages, thereby verifying the existence of these miRNAs and confirming the reliability of the computational identification method. We predicted which miRNAs were involved in catechin synthesis using ps RNAtarget Software based on conserved miRNAs and catechin synthesis pathway-related genes. Then, we used RNA ligase-mediated rapid amplification of c DNA ends（RLM-RACE） to obtain seven miRNAs cleaving eight catechin synthesis pathway-related genes including chalcone synthase（CHS）, chalcone isomerase（CHI）, dihydroflavonol 4-reductase（DFR）, anthocyanidin reductase（ANR）, leucoanthocyanidin reductase（LAR）, and flavanone 3-hydroxylase（F3H）. An expression analysis of miRNAs and target genes revealed that miR529d and miR156 g-3 p were negatively correlated with their targets CHI and F3H, respectively. The expression of other miRNAs was not significantly related to their target genes in the catechin synthesis pathway. The RLM-RACE results suggest that catechin synthesis is regulated by miRNAs that can cleave genes involved in catechin synthesis.

Genetic Evaluation of Starch Synthesis-Related Genes and Starch Quality Traits in Special Rice Resources

The genetic diversity of 36 rice landraces and 43 breeding materials in the upper reaches of the Yangtze River in China was studied by intragenic molecular markers of 26 starch synthesis-related loci.And research on quality traits such as the amylose content(AC),gel consistency(GC)and alkali spreading value(ASV)to analyze genetic differences in quality traits.The results showed that the number of alleles,average gene diversity and polymorphism information content values of landraces were higher than those of breeding materials.The genetic similarity coefficient(GS)of 79 rice materials ranged from 0.392 to 1,with an average of 0.757.There were significant variations in the quality traits of rice landraces and breeding materials,and the high-quality compliance rates were low,only 6.3%of the varieties have an amylose content that reached grade 1.The results of cluster analysis and population structure analysis are generally consistent;that is,the two resource types are closely related and cannot be clustered independently.This study can provide a basis for genetic improvement of rice starch quality.Make full use of the quality genetic diversity of landraces in modern breeding work,further broaden the genetic base of rice and improve rice quality.

Synthesis of Codon-optimized Human Interleukin-18 Gene by Combination of Chemical and Enzymatic Method

According to the amino acid sequence and codon preference of E. coli, the human interleukin-18（IL-18） gene was optimized to avoid the rare codons. The total length of the synthesized gene is 571 bp; 18 oligonucleotides, DNA fragments were designed and synthesized by the phosphoramidite four-step chemical method. The whole DNA sequence was synthesized by a one-step total gene synthesis method, and then inserted in pUC18 vector. Five positive clones identified by blue-white colony screening were sent to Shanghai Sangon Biological Engineering Technology and Service Co., Ltd. for sequencing. The sequencing result shows that one clone contained the complete correct gene in all the five positive clones.

SYNTHESIS AND EXPRESSION OF A GENE FOR HUMAN TUMOR NECROSIS FACTOR-ALPHA (TNF-α)

TNF-α was found originally In sera of Bacillus Calmette Guerln infected mice as a macrophage derived factor. It Is cytotoxlc for tumor cell and less or not toxic to normal cells in vitor. The gene for human TNF-α with E. coli-preferred codons has been designed according to the amino acid sequence deduced from the cDNA. The gene with 504 bp was divided into 27 oligonucleotide fragments having 30. to 40 nucleotides each. The solid phase phosphotriester method was used for the synthesis of these oligonucleotides. The 27 fragments were annealed to three segments and then linked by T4 DNA ligase. The entire gene was incorporated into plasmld PDR540 with Tac promoter which was used to transform E. coli 7118. The expressed protein was estimated by SDSPAGE with a molecular weight of 1. 7×104Da. The cytotoxlc activity of the product against L-929 cell was 1. 0×107units/ml culture.

Chemical synthesis of a structural gene coding for trichosanthin

A structural gene (750 bp), which codes for a type I ribosome inactivating protein, trichosanthin, has been designed according to the codon usage of highly expressed gene in E. coli and chemically synthesized. In the synthesized gene, twenty-seven unique restriction sites were evenly dispersed with an average distance between two adjacent sites less than 50 bp to facilitate a systematic investigation on structure-functional relationship of this protein by site-directed mutagenesis. To synthesize it, the whole gene was divided into three large fragments (EP, PN and NH) which were assembled from several chemical synthetic oligonucleotides by enzymatic method. The assembly of both the fragment EP from six oligonucleotides (A-F) and the fragment PN from four oligomers (G-J) was catalyzed by T-4 DNA ligase in using the single stranded DNA method [Chen, H.-B. et al., Nucl. Acids Res., 18, 871(1990)]. And fragment NH was formed from three duplexes K, L and M by the classical double stranded DNA method. Finally, each fragment was cloned into vector pUC18 in succession to form the plasmid, pC0TCS, to complete the whole gene synthesis, The sequencing data for the synthetic gene coincides with the designed one.

Chemical synthesis of a structure gene coding for small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco

A structural gene with 385 bp, which codes for the mature small subunit (rbcS) of ribulose-1,5-bi9phosphate carboxylase/oxygenase from tobacco, has been redesigned according to the codon usage of E.coli and chemically synthesized. To facilitate the systematic investigation of structure-functional relationship of the rbcS by site-specific mutagenesis, twenty one unique restriction sites distributed throughout the synthetic gene were designed. Gene synthesis was started from chemically synthesizing sixteen oligonucleotides each with 23-66 nucleotides, and these oligonu-cleotides were annealed to form eight duplexes from which 5'- and 3'- two half molecules were formed by stepwise T4 DNA ligase reaction, and then each half molecule was cloned into plasmid pWR13, after that, two half molecules were further confirmed by DNA sequencing, finally both half molecules excised from the cloning plasmid were recombinated to form plasmid pCOTrbcS containing the whole structural gene for tobacco rbcS.