Zinc finger nuclease (ZFN), which is a chimeric fusion structure between a Cys2-His2 zinc-finger protein (ZFP) and the cleavage domain of Fok I endonuclease, can be used to introduce targeted double-stranded breaks (DSBs). ZFN-mediated cleavage leads to mutations when double-stranded breaks are repaired by homologous recombination (HR) or nonhomologous end joining (NHEJ). In recent years, ZFNs are widely used in the fields of genetic research. In this review, the methodology and technical advantages of ZFNs were briefly discussed.
Animals ; Deoxyribonucleases, Type II Site-Specific ; chemistry ; genetics ; metabolism ; Humans ; Zinc Fingers

OBJECTIVETo construct a reverse transcriptase-polymerase chain reaction (RT-PCR)approach that can improve the specificity of primers while dropping down the nonspecific amplification.

METHODSIn the recent study we reported a new RT-PCR assay which improved markedly the specificity. However its efficiency of regressing nonspecific amplification remains to be accurately checked and further documented. In primer design, we looked over again some sequences that showed differences at 5' or 3' ends between human CAV1 and mouse Cav1 genes. cDNAs and the diluted plasmids which harbored the sequence of human CAV1 or mouse Cav1 gene were chosen as the templates. The ordinary PCR compared with one, of which primers modified by phosphorothioate and combined with proofreading polymerase, for their efficiencies of nonspecific amplification inhibited.

RESULTSTaq DNA polymerase without proofreading activity could efficiently catalyze the extension of primers with a single or multiple mismatched base pairs at the 3' terminus, but the kind of primer extension can be effectively blocked by phosphorothioate modified primers combined with proofreading polymerase. Compared with ordinary PCR reaction, this new PCR method can effectively regress the primer mismatched amplification of 50 ng DNA almost equaling to 2 x 10(4) unmatched template copies in a final volume of 50 microL.

CONCLUSIONCompared with the first generation of polymerases with or without proofreading activities mediating RT-PCR reaction, the introduction of nuclease-resistant 3' modified primers (3' phosphorothioate primer extension) can offer more simplicity, accuracy, and also decrease cost.

Animals ; Caveolin 1 ; genetics ; Deoxyribonucleases ; metabolism ; Gene Amplification ; Humans ; Mice ; Reverse Transcriptase Polymerase Chain Reaction ; methods ; Thionucleotides ; metabolism

UNLABELLEDTo identify differentially expressed genes between fetal mesenchymal stem cell (MSC) and adult MSC, especially specified genes expressed in fetal MSC, a cDNA subtractive library of fetal MSC was constructed using suppression subtractive hybridization (SSH) technique. At first, total RNA was isolated from fetal and adult MSC. Using SMART PCR synthesis method, single-strand and double-strand cDNAs were synthesized. After Rsa I digestion, fetal MSC cDNAs were divided into two groups and ligated to adaptor 1 and adaptor 2 respectively. Results showed that the amplified library contains 890 clones. Analysis of 890 clones with PCR demonstrated that 768 clones were positive. The positive rate is 86.3%. The size of inserted fragments in these positive clones was between 0.2 - 1 kb, with an average of 400 - 600 bp.

CONCLUSIONSSH is a convenient and effective method for screening differentially expressed genes. The constructed cDNA subtractive library of fetal MSC cDNA lays solid foundation for screening and cloning new and specific function related genes of fetal MSC.

Cloning, Molecular ; DNA, Complementary ; genetics ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Fetus ; Gene Library ; Humans ; Mesoderm ; cytology ; metabolism ; Polymerase Chain Reaction ; Stem Cells ; cytology ; metabolism

OBJECTIVETo determine the relationship between vitamin D receptor (VDR) gene polymorphism and osteoporosis in postmenopausal women.

METHODSThe polymerase chain reaction-restriction fragment length polymorphism was used to detect VDR genotype in 40 patients with osteoporosis and 21 healthy postmenopausal women.

RESULTSIn the patients with osteoporosis, the bb, Bb, and BB genotype accounted for 82.5%, 17.5% and 0, respectively; in healthy groups, they were 85.71%, 14.29% and 0, respectively (P>0.05).

CONCLUSIONSignificant association between VDR genotype and osteoporosis in Chinese women was observed in this study.

DNA ; genetics ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Female ; Gene Frequency ; Genotype ; Humans ; Middle Aged ; Osteoporosis, Postmenopausal ; genetics ; Polymorphism, Genetic ; Receptors, Calcitriol ; genetics

The purpose of this study is to investigate the Sal I, Nru I and Mse I restriction fragment length polymorphisms (RFLPs) of factor IX gene in Chinese Han people. The frequencies of FIX-192 and FIX-793 for A and G, and FIX-698 for T and C were analyzed by polymerase chain reaction (PCR) in unrelated normal Chinese Han people. A sample of 214, 210 and 206 unrelated X chromosomes were analyzed for FIX-192 and FIX-793 and FIX-698, respectively. The results showed that the frequencies for FIX-192 were 0.878 for A and 0.122 for G, with a heterozygosity rate of 0.213, and the frequencies for FIX-793 were 0.552 for A and 0.448 for G, with a heterozygosity rate of 0.494, the frequencies for FIX-698 were 0.311 for T and 0.689 for C, with a heterozygosity rate of 0.429. It was concluded that the SalIand NruI and MseI RFLPs of FIX gene may be useful markers for carrier detection and prenatal diagnosis in Chinese families with hemophilia B patients.
China ; DNA ; genetics ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Factor IX ; genetics ; Female ; Gene Frequency ; Heterozygote ; Humans ; Male ; Polymorphism, Restriction Fragment Length

Adrenal Hyperplasia, Congenital ; genetics ; Chromatography, High Pressure Liquid ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Female ; Humans ; Point Mutation ; genetics ; Polymerase Chain Reaction ; methods ; Pregnancy

OBJECTIVETo develop a simple method for genotyping of hepatitis E virus (HEV) and to investigate HEV genotype distribution in Nanjing area.

METHODSTwenty-seven full HEV sequences currently-available in GenBank were analyzed with MegAlign and MapDraw programs of DNA STAR software. Degenerate primers were designed and applied to amplify a fragment in HEV ORF1 region. HEV genotypes were determined by the size of the PCR products and by single restriction endonuclease analysis.

RESULTSThe PCR products of HEV genotype 1 and 2 were 275 bp and 269 bp in size. Distinctively, the PCR products of genotype 3 and 4 were 317 bp and 314 bp in size. Moreover, the PCR products of genotype 1 could be digested by Nae 1, but the products of genotype 2 could not. Distinctively, the PCR products of HEV genotype 3 could be digested by Not 1, but the products of genotype 4 could not. Six HEV reference strains standing for different HEV genotypes were clustered into their own types as predicted. Within 43 HEV IgM-positive clinical specimens collected in Nanjing, 19 were HEV PCR-positive and identified as genotype 4.

CONCLUSIONA simple method of PCR combined with single restriction endonuclease analysis is developed for HEV genotyping. This assay allows rapid identification of a large number of HEV isolates directly from clinical specimens. Among patients with hepatitis E in Nanjing, most were infected with HEV genotype 4.

DNA Restriction Enzymes ; metabolism ; DNA, Complementary ; genetics ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Genotype ; Hepatitis E ; blood ; genetics ; immunology ; Hepatitis E virus ; genetics ; Humans ; Polymerase Chain Reaction ; methods ; RNA, Viral ; genetics ; Reverse Transcriptase Polymerase Chain Reaction

OBJECTIVETo optimize the performance of Pulsed-Field Gel Electrophoresis (PFGE) for the comparison of inter-laboratory results and information exchange of Borrelia burgdorferi subtyping.

METHODSA panel of 34 strains of B. burgdorferi were used to optimize PFGE for subtyping. In order to optimize the electrophoretic parameters (EPs), all 34 strains of B. burgdorferi were analyzed using four EPs, yielding different Simpson diversity index (D) values and the epidemiological concordance was also evaluated.

RESULTSThe EP of a switch time of 1 s to 25 s for 13 h and 1 s to 10 s for 6 h produced the highest D value and was declared to be optimal for MluI and SmaI PFGE of B. burgdorferi. MluI and SmaI were selected as the first and second restriction enzymes for PFGE subtyping of B. burgdorferi according to discrimination and consistency with epidemiological data.

CONCLUSIONPFGE can be used as a valuable test for routine genospecies identification of B. burgdorferi.

Animals ; Bacterial Proteins ; metabolism ; Bacterial Typing Techniques ; Borrelia burgdorferi ; classification ; genetics ; isolation & purification ; DNA, Bacterial ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Electrophoresis, Gel, Pulsed-Field ; Humans ; Ixodes ; Rats

OBJECTIVETo study the clonality of uterine leiomyomas, especially the relationship between different nodules in multinodular cases.

METHODSGenomic DNA was extracted from fresh tissue samples and digested through incubation with Hpa II and amplified through nested polymerase chain reaction for phosphoglycerate kinase (PGK) gene. The products were treated with Bst XI and resolved on agarose gels.

RESULTSAmong the 103 cases examined, 32 (31%) carried the polymorphic Bst XI site at the PGK locus. Eighty-nine tumors from the 29 cases were subjected to the cloning assay. Loss of polymorphism at the PGK locus was found in all tumor nodules, indicating the monoclonality of the tumor. The relationship between multiple tumors was also assessed by comparing their inactivated alleles. Seven nodules from a leiomyosarcoma were found to have originated from a single cell. However, the relationship was found to be more complicated, as demonstrated in 15 cases of multiple leiomyomas. The same inactivated allele was found in all nodules of 8 cases and in most nodules in 2 cases, while totally different inactivation patterns were observed in 5 cases. The difference was not associated with cell proliferation.

CONCLUSIONSClonality analysis can be applied to define the clonality of focal or nodular lesions. Uterine leiomyomas are of clonal origin. Multiple uterine leiomyomas may be subtyped into fully independent and aggressive types as well as a mixed type of both.

Base Sequence ; Clone Cells ; DNA, Neoplasm ; genetics ; metabolism ; Deoxyribonuclease HpaII ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Female ; Humans ; Leiomyoma ; genetics ; pathology ; Neoplasms, Multiple Primary ; genetics ; pathology ; Uterine Neoplasms ; genetics ; pathology

OBJECTIVETo study the imprinting status and expression level of insulin-like growth factor 2 (IGF2) gene in colorectal cancer and to provide a clue for the mechanism of carcinogenesis of colorectal cancer.

METHODSThe expression levels of IGF2 in the paired colorectal cancer and adjacent normal tissue were examined and compared by use of semi-quantitative reverse transcription-polymerase chain reaction. The imprinting status of IGF2 was detected by restriction fragment length polymorphism. The relationships between the expression level of IGF2, its imprinting status, and the carcinogenesis of colorectal cancer were analyzed.

RESULTSIGF2 was overexpressed in 82.4% (28/34) of colorectal cancer tissues which was significantly higher than those of the matched normal tissues (P<0.01, t=3.01). 87.5% (14/16) of colorectal cancer showed loss of imprinting(LOI), while 71.4%(10/14) of normal tissues also displayed LOI of IGF2.

CONCLUSIONOverexpression of IGF2 was found to play an important role in carcinogenesis of colorectal cancer. LOI of IGF2 may be a prophase manifestation of colorectal cancer.

Colorectal Neoplasms ; genetics ; pathology ; DNA, Neoplasm ; genetics ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Female ; Gene Expression Regulation, Neoplastic ; Genomic Imprinting ; Humans ; Insulin-Like Growth Factor II ; genetics ; Male ; Middle Aged ; RNA, Neoplasm ; genetics ; metabolism ; Reverse Transcriptase Polymerase Chain Reaction