Cloning of large genomic sequences is an enabling technology in synthetic biology. To obtain large gene fragments, traditional cloning methods are faced with various defects, for instance, random library cloning relies always on high-throughput screening. It is difficult to get gene fragments more than 10 kb by PCR amplification. Assembly of small fragments is labor intensive with high mutation rates. It is difficult to find suitable cleavage sites on the fragment ends by restriction endonuclease. Recently genome-wide editing creates a new high-performance large fragments cloning methods. For example, CRISPR/cas9 system can identify and cut 20 bp nucleic acid sequences recognition sites used to obtain any desired gene fragments; if combined with Gibson or transformation associated recombination (TAR) assembly technology, these methods can efficiently clone large fragments. This article introduces large fragments cloning technology by classification, then proposes the choice criteria of methods for cloning gene fragments of different sizes.
CRISPR-Cas Systems ; Cloning, Molecular ; DNA Restriction Enzymes ; Multigene Family ; Polymerase Chain Reaction ; Synthetic Biology

PURPOSE: Helicobacter pylori is a widely distributed gram-negative bacterium that infects the human stomach and duodenum. HpaA is a H. pylori-specific lipoprotein that has been shown to be an effective protective antigen against H. pylori infection. HpaA of H. pylori as a vaccine antigen is fully competent for stimulation of immune responses. The aim of this project is cloning, expression, and purification flagellar sheath adhesion of H. pylori in Escherichia coli host by fast protein liquid chromatography (FPLC) as a vaccination target. MATERIALS AND METHODS: The hpaA gene was inserted into pET28a (+) as cloning and expression vectors respectively. The recombinant plasmid (pET-hpaA) was subjected to sequencing other than polymerase chain reaction (PCR) and digestion analysis. Protein expression was induced by adding 1 mM isopropyl-beta-D-thiogalactoside to cultures of E. coli strain BL21 transformed with pET-hpaA. Protein expression assessed with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. Protein purification of flagellar sheath adhesion was by FPLC. RESULTS: The restriction endonuclease digestion, PCR amplification analysis showed that the hpaA gene of 730 bp was amplified from H. pylori DNA and sequencing analysis of the pET-hpaA confirmed the cloning accuracy and in frame insertion of hpaA fragment. SDS-PAGE analysis showed the expression of an approximately 29,000 Da protein. CONCLUSION: Sequencing results along with SDS-PAGE analysis confirms the expression of recombinant hpaA in the heterologous E. coli BL21. Conclusion A prokaryotic expression system for hpaA gene was successfully constructed. These results indicate that production of a specific recombinant protein is an alternative and potentially more expeditious strategy for development of H. pylori vaccine.
Chromatography, Liquid ; Clone Cells* ; Cloning, Organism* ; Digestion ; DNA ; DNA Restriction Enzymes ; Duodenum ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli* ; Escherichia* ; Helicobacter pylori* ; Helicobacter* ; Humans ; Lipoproteins ; Plasmids ; Polymerase Chain Reaction ; Sodium Dodecyl Sulfate ; Stomach ; Vaccination*

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.
Bacteria ; Binding Sites ; Cholera ; Computer Simulation* ; Developing Countries ; DNA ; DNA Restriction Enzymes ; Drug Discovery ; Drug Resistance, Microbial ; Genome ; Humans ; Integrases ; Sewage ; Solubility ; Vibrio cholerae ; Vibrio cholerae O139* ; Water Purification

Gene cloning is one of the most important and widely used technologies in molecular biology research. Generally, DNA fragment is cut with restriction enzyme, and then the product is ligated to a linearized vector with complementary sticky end or blunt end by DNA-ligase. This traditional DNA cloning method requires compatible enzyme recognition sites existing in both PCR fragment and targeted vector. Several ligase-free methods have been established to avoid the using of restriction enzyme. However, those methods are time-consuming, labor-intensive and expensive. To overcome these shortcomings, we developed an Exonuclease III based DNA cloning method that takes only 30 minutes with high cloning efficiency and significant economic advantage. Therefore, this method is suitable for large-scale gene cloning.
Cloning, Molecular ; methods ; DNA ; chemistry ; DNA Restriction Enzymes ; Exodeoxyribonucleases ; chemistry ; Genetic Vectors ; Polymerase Chain Reaction

Single nucleotide polymorphisms (SNP) is an important molecular marker in traditional Chinese medicine research, and it is widely used in TCM authentication. The present study created a new genotyping method by combining restriction endonuclease digesting with melting curve analysis, which is a stable, rapid and easy doing SNP genotyping method. The new method analyzed SNP genotyping of two chloroplast SNP which was located in or out of the endonuclease recognition site, the results showed that when attaching a 14 bp GC-clamp (cggcgggagggcgg) to 5' end of the primer and selecting suited endonuclease to digest the amplification products, the melting curve of Lonicera japonica and Atractylodes macrocephala were all of double peaks and the adulterants Shan-yin-hua and A. lancea were of single peaks. The results indicated that the method had good stability and reproducibility for identifying authentic medicines from its adulterants. It is a potential SNP genotyping method and named restriction endonuclease digest - melting curve analysis.
Atractylodes ; classification ; genetics ; DNA Restriction Enzymes ; metabolism ; DNA, Plant ; genetics ; Drug Contamination ; Genotype ; Lonicera ; classification ; genetics ; Plants, Medicinal ; classification ; genetics ; Polymorphism, Single Nucleotide

In our screening for photosensitizers from natural resources, four alkaloids were isolated from Glycosmis pentaphylla by various chromatography techniques. Their structures were identified as glycoborinine (1), glybomine B (2), carbalexin A (3) and N-p-coumaroyltyramine (4) by spectral analysis. Their photoactivated antimicrobial activities were evaluated by thin-layer chromatography (TLC) agar overlay assay against Staphylococcus aureus and Bacillus subtilis. It was found that compounds 1 and 4 showed photo-activated antimicrobial activities. Meantime, photo-activated DNA binding activities of these compounds were also assessed by using a specially prepared 1.8 kb DNA fragment and restriction enzymes. Under UVA irradiation, compound 1 showed moderate inhibition on Nde I, Xba I, Nco I and Bcl I which have either 5'-TpA or 5'-ApT and trace or no inhibition on other restriction enzymes. It showed a similar inhibition pattern with the reference 8-methoxypsoralen. However, compounds 2-4 showed no inhibition against any of the restriction enzymes.
Anti-Bacterial Agents ; chemistry ; isolation & purification ; pharmacology ; Bacillus subtilis ; drug effects ; Carbazoles ; chemistry ; isolation & purification ; pharmacology ; Chromatography, Thin Layer ; Coumaric Acids ; chemistry ; isolation & purification ; pharmacology ; DNA Fragmentation ; DNA Restriction Enzymes ; metabolism ; Light ; Molecular Structure ; Photosensitizing Agents ; pharmacology ; Plants, Medicinal ; chemistry ; Protein Binding ; Rutaceae ; chemistry ; Staphylococcus aureus ; drug effects ; Ultraviolet Rays

STUDY DESIGN: Genetic screening of the estrogen receptor 2 (ESR2) genes in patients with ossification of the posterior longitudinal ligament (OPLL). OBJECTIVE: We studied the relationships between ESR2 gene polymorphisms and OPLL to understand the pathophysiology of OPLL. SUMMARY OF LITERATURE REVIEW: The OPLL has a strong genetic component. Several familial surveys and human leukocyte antigen (HLA) haplotype studies reveal that genetic background is an important component in the occurrence of OPLL and a large number of gene analysis studies were utilized to clarify the susceptible gene for OPLL, including COL11A2, BMP-2, TNF-alpha, NPPS, leptin receptor, transforming growth factor (TGF)-beta, Retinoic X receptor, ER, IL-1, PTH, and VDR have been performed. MATERIALS AND METHOD: Genomic deoxyribonucleic acid (DNA) samples obtained from 164 patients (93 men and 71 women) with OPLL and 219 control subjects, without the disease (105 men and 114 women) were amplified by polymerase chain reaction, and polymorphism genotypes were determined by the restriction endonuclease digestion. The distribution of genotypes was compared between the patients with the disease and the control subjects. RESULTS: The polymorphism of ESR2 [rs1256049, exon6, Val328Val, p=0.018, odd ratio (OR)=2.41, 95 confidence interval (CI)=1.15-5.02 in the recessive model] only showed statistically significant association between the control and the OPLL groups. The rest SNPs of ESR2 did not show any significant differences between the control and the OPLL groups. CONCLUSIONS: Estrogen receptor 2 (ESR2) gene polymorphisms (rs 1256049) was associated with OPLL. In future studies, we will perform target SNP chip between OPLL and candidate gene.
Digestion ; DNA ; DNA Restriction Enzymes ; Estrogen Receptor beta ; Estrogens ; Genetic Testing ; Genotype ; Haplotypes ; Humans ; Interleukin-1 ; Leukocytes ; Longitudinal Ligaments ; Male ; Ossification of Posterior Longitudinal Ligament ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Receptors, Leptin ; Spine ; Succinimides ; Transforming Growth Factors ; Tumor Necrosis Factor-alpha

PURPOSE: We applied a simplified method using polymerase chain reaction (PCR)-based enzymatic digestion for the detection of epidermal growth factor receptor (EGFR) mutation. MATERIALS AND METHODS: We selected 74 samples of adenocarcinoma of the lung with EGFR exons 19 and 21 that had been previously sequenced. We designed PCR primers and chose a DNA restriction enzyme. Seventy four additional lung cancer samples were tested as a test set. For test sets, the PCR-based method was performed first, followed by validation of the result by DNA sequencing. RESULTS: In the first sample group, we found 15 (20.3%) mutations in exon 19, and 9 (12.2%) mutations in exon 21 using the sequencing method. By using the PCR-based method, we were able to identify all of the mutated samples detected by the sequencing method. The PCR-based method also detected mutations in exon 19 in three additional samples and in exon 21 in one additional sample. In the second sample group, by performing the PCR-based method, we found 10 (13.5%) and 7 (9.5%) mutations in exons 19 and 21, respectively. Additional mutations in exon 19 were identified in 2 samples by the sequencing method. However, the sequencing method failed to identify a mutation in exon 21 in one sample. CONCLUSION: The sensitivity of the PCR-based enzymatic digestion method seems to be comparable to that of the traditional sequencing method for detecting EGFR mutations. Our method can be widely used as a screening test to select patients who may benefit from EGFR targeted therapy.
Adenocarcinoma ; Carcinoma, Non-Small-Cell Lung ; Digestion ; DNA ; DNA Restriction Enzymes ; Epidermal Growth Factor ; Exons ; Genes, erbB-1 ; Humans ; Lung ; Lung Neoplasms ; Mass Screening ; Polymerase Chain Reaction ; Receptor, Epidermal Growth Factor ; Restriction Mapping

OBJECTIVETo establish the BGC-823/WTX-EGFP gastric cancer cell line with stable expression of Wilms tumor gene on the X chromosome (MTX) for functional analysis of WTX gene.

METHODSThe full-length WTX cDNA was amplified from human embryonic kidney 293FT cells and cloned into the pEGFP-N1 vector containing the reporter gene of green fluorescence protein. The recombinant pEGFP-WTX expression vector, after digestion by restriction enzyme to identify the size of target gene fragment, was transfected into 293FT cells and the expression of fluorescent reporter gene was observed under fluorescence microscope. pEGFP-WTX vector was transfected into human gastric cancer BGC-823 cell line to establish BGC-823/WTX-EGFP cell line stably expressing WTX. Quantitative RT-PCR and immunocytochemical staining were used to detect the expression of WTX in both BGC-823/WTX-EGFP and control BGC-823 cells.

RESULTSThe recombinant pEGFP-WTX plasmid was successfully constructed and verified by PCR and sequencing. The mRNA and protein expressions of MTX were significantly increased in BGC-823/WTX-EGFP cells as compared with those in the control cells.

CONCLUSIONThe full-length WTX expression vector (pEGFP-WTX) and BGC-823/WTX-EGFP gastric cancer cell line have been successfully established to facilitate further functional study of WTX gene.

Cell Line ; Cell Line, Tumor ; Chromosomes, Human, X ; genetics ; DNA Restriction Enzymes ; DNA, Complementary ; Genes, Wilms Tumor ; Genetic Vectors ; Green Fluorescent Proteins ; genetics ; Humans ; Plasmids ; Stomach Neoplasms ; genetics ; Transfection

OBJECTIVETo identify the F VIII gene mutations of patients and suspected female carriers in 10 Hemophilia A (HA) families, and to guide the prenatal diagnosis.

METHODSPCR, denaturinghigh performance liquid chromatogramphy (DHPLC) and DNA sequencing technologies were applied to screen the F VIII gene of 8 HA patients and 12 suspected female carriers in the 10 families. Linkage analysis was performed by using St 14(DXS 52), intron 13 (CA)n and EX18/Bcl I of the F VIII gene in the HA families. In prenatal diagnosis, we screened the same mutation found in the patients. PCR-restriction fragment length polymorphism was applied to detect the new missense mutations of F VIII gene in 100 unrelated healthy individuals to exclude the possibility of polymorphism.

RESULTSFive missense mutations, 3 frameshift mutations, 2 nonsense mutations and 2 single nucleotide polymorphism (SNP) were identified in 10 the HA families. Among them, c.878A to G, c.1015A to G, c.6870G to T, c.1282delA, c.3072_3073insT, c.4880_4881insA and c.5000G to A were novel mutations or polymorphism. No missense mutations c.878A G, c.1015A to G and c.6870G to T, were found in the 100 healthy unrelated controls. (2) Nine suspected female carriers were confirmed at the gene level. (3) X risk chromosome could be determined to in 4 HA families by genetic linkage analysis. (4) Among the four fetuses for prenatal diagnosis, 2 were normal, 1 was carrier and the remaining 1 was a patient.

CONCLUSIONSix novel mutations, i.e., c.878A to G, c.1015A to G, c.6870G to T, c.1282delA, c.3072_3073insT and c.4880_4881insA, were identified in this study. PCR, DHPLC and DNA sequencing could be used to screen the gene mutations of HA patients, to carry out carrier detection and prenatal diagnosis of HA families efficiently, by combining with restriction endonuclease analysis and genetic linkage analysis.

Chromosomes, Human, X ; DNA Mutational Analysis ; methods ; DNA Restriction Enzymes ; genetics ; Factor VIII ; genetics ; Female ; Genetic Testing ; methods ; Hemophilia A ; diagnosis ; genetics ; Heterozygote ; Humans ; Male ; Mutation ; Pedigree ; Polymorphism, Single Nucleotide ; Prenatal Diagnosis ; methods ; Sequence Analysis, DNA ; methods