Restriction Endonuclease Mapping Research Articles

14. Absence of T-Shaped Structure and Deletions of B and C Hairpins Have Minimal Effects on Essential Functions of AAV Inverted Terminal Repeats

Recent reports on severe adverse effects induced by retroviral integration into the LMO2 proto-oncogene in humans and the demonstration of preferential AAV serotype 2 (rAAV2) vector integration into genes in our previous study with a limited number of integration sites in mice1, have raised a possible concern about rAAV-mediated insertional mutagenesis. In order to further address this issue, we have expanded our previous study and performed a high-throughput analysis of rAAV2 integration sites isolated from in vivo selected hereditary tyrosinemia type I (HTI) mouse hepatocytes transduced with a human fumaryl acetoacetate hydrolase (FAH)-expressing rAAV2 shuttle vector, AAV-EF1α-hFAH.AOS. Briefly, total liver DNA was isolated from 4 HTI mice that underwent a 7-month in vivo selection of transplanted hepatocytes isolated from the donor HTI mice having received 3.0×1011 vector genomes of AAV-EF1α-hFAH.AOS via the portal vein and undergone an 8-week in vivo selection. The whole proviral rAAV2 vector genome and flanking genomic DNA sequences were isolated as a plasmid from the liver DNA by a plasmid rescue technique as previously described1. All four mice had a different donor HTI mouse, therefore, any integrations found in different mice should be considered as independent integration events. To date, we have characterized 307 independent integration events and found: 1) 191 of 307 (62%) of integrations occurred in genes; 2) there was a strong bias toward integrating into host genomes around transcription start sites, as has been observed in murine leukemia virus integrations (approximately a quarter of the total rAAV2 integrations occurred within ±1 kb from transcription start sites); 3) rAAV integration involved large genomic deletions of over 1 kb in 15% of the cases, suggesting that such large deletions may not be rare events associated with rAAV2 integration. The most striking finding was that among the 307 independent integration events, at least 4 integrations from 3 different mice (1.5 % of total integrations and 2.1 % of the genes targeted by rAAV) were found within a 30-kb region in the mouse ubiquitin C gene, and at least 4 integrations from 4 different mice fell on another sequence stretch of approximately 2.5 kb. Our preliminary analysis by restriction enzyme mapping and sequencing over a thousand base pairs has indicated that the hot spot of 2.5 kb in length likely resides in a proto-oncogene, the Evi-1 gene. It should be noted that murine leukemia found in a retroviral gene marking study was induced by insertional mutagenesis at this locus. Although the oncogenic potential of this gene in the liver is not known, overexpression of this gene can transform not only hematopoietic cells but also other cell types. Thus, the preliminary results in our high-throughput rAAV2 integration site analysis further emphasize the importance of pursuing the study on the elucidation of the mechanisms of rAAV vector integration and its consequences in the host.

A Novel Approach to Rapid Determination of βS‐Globin Haplotypes: Sequencing of the Aγ‐IVS‐II Region

β‐Globin gene cluster haplotypes were originally determined by restriction endonuclease mapping with Southern blots of polymorphic sites around the gene cluster. Over the years, haplotyping has been found to be useful, not only in population genetics but also in predicting the severity of hemoglobinopathies such as sickle cell disease. The sickle mutation occurs on five distinct haplotypes. The hitherto used methods are cumbersome and time‐consuming, making haplotype determination a tedious procedure. We report our experience with a novel, rapid approach to haplotyping based on sequence polymorphisms in the Aγ‐IVS‐II region. We provide an algorithm that allows rapid assignment of the four African haplotypes carrying the sickle mutation.

Assessment of a rapid-cycle PCR assay for the identification of the recurrent c.3421C>T mutation in the ABCC6 gene in pseudoxanthoma elasticum patients

Pseudoxanthoma elasticum (PXE) is a heritable disorder of the connective tissue. Mutations in the ABCC6 gene could be linked to this disease and, just recently, the c.3421C>T mutation was also associated with a high risk of coronary artery disease. We have now developed new real-time PCR assays for the accurate and rapid determination of the c.3421C>T genotype. Using our new assay, we analyzed the presence of the c.3421C>T mutation in the largest collection of DNA samples from unrelated German PXE patients (n=64) and in a control cohort (n=910). For assay setup, two sets of samples with known genotype for the c.3421C>T mutation were analyzed over a period of 14 days. Results were confirmed by restriction endonuclease mapping, sequence-specific PCR and DNA sequencing. In order to ensure that no further mutations or deletions interfered with the c.3421C>T genotyping, we scanned the exon 24 of the ABCC6 gene by DHPLC and investigated the presence of the ABCC6del23–29 deletion in all patients. The assay has been set up on a group of patients with known genotype and validated on 64 PXE patients. In this group four PXE patients (6.3%) were found to be homozygous and 25 (39.0%) to be heterozygous carriers of the c.3421C>T mutation. The common ABCC6del23–29 deletion, possibly interfering with genotype determination, was searched and excluded. Furthermore, two novel mutations in the ABCC6 gene could be identified in two patients. The novel mutations c.3389C>T and c.3341G>A did not interfere with our new assay. Our new c.3421C>T genotyping assays can be used for the rapid identification of this frequent mutation in PXE patients and of the recently newly proposed cardiac risk factor in young patients with myocardial infarcts of unknown origin.

Identification of two novel fibrinolytic enzymes from Bacillus subtilis QK02

Two fibrinolytic enzymes (QK-1 and QK-2) purified from the supernatant of Bacillus subtilis QK02 culture broth had molecular masses of 42 000 Da and 28 000 Da, respectively. The first 20 amino acids of the N-terminal sequence are AQSVPYGISQ IKAPALHSQG. The deduced protein sequence and its restriction enzyme map of the enzyme QK-2 are different from those of other proteases. The enzyme QK-2 digested not only fibrin but also a subtilisin substrate, and PMSF inhibited its fibrinolytic and amidolytic activities completely; while QK-1 hydrolyzed fibrin and a plasmin substrate, and PMSF as well as aprotinin inhibited its fibrinolytic activity. These results indicated QK-1 was a plasmin-like serine protease and QK-2 a subtilisin family serine protease. Therefore, these enzymes were designated subtilisin QK. The sequence of a DNA fragment encoding subtilisin QK contained an open reading frame of 1149 base pairs encoding 106 amino acids for signal peptide and 257 amino acids for subtilisin QK, which is highly similar with that of a fibrinolytic enzyme, subtilisin NAT (identities 96.8%). Asp 32, His 64 and Ser 221 in the amino acid sequence deduced from the QK gene are identical to the active site of nattokinase (NK) produced by B. subtilis natto.

Homology of primate DNA fragments for estrous-associated oviductal glycoprotein.

In this study, the DNA fragments encoded for oviduct EGP were amplified by PCR method. Corresponding sequences from chimpanzee, orangutan and human were similarly amplified, but we failed to amplify the corresponding DNA sequences from: spider monkey, salmon and several different species of rodents, bandicoot, sheep and pig. Through analyzing the restriction enzyme map and the DNA sequence of the amplified fragments from primates, the data suggest that monkey and human DNA encoded for EGP are genetically more closely related to one another than each of them to other species.

Assessment of a rapid-cycle PCR assay for the identification of the recurrent c.3421C>T mutation in the ABCC6 gene in pseudoxanthoma elasticum patients.

Pseudoxanthoma elasticum (PXE) is a heritable disorder of the connective tissue. Mutations in the ABCC6 gene could be linked to this disease and, just recently, the c.3421C>T mutation was also associated with a high risk of coronary artery disease. We have now developed new real-time PCR assays for the accurate and rapid determination of the c.3421C>T genotype. Using our new assay, we analyzed the presence of the c.3421C>T mutation in the largest collection of DNA samples from unrelated German PXE patients (n=64) and in a control cohort (n=910). For assay setup, two sets of samples with known genotype for the c.3421C>T mutation were analyzed over a period of 14 days. Results were confirmed by restriction endonuclease mapping, sequence-specific PCR and DNA sequencing. In order to ensure that no further mutations or deletions interfered with the c.3421C>T genotyping, we scanned the exon 24 of the ABCC6 gene by DHPLC and investigated the presence of the ABCC6del23-29 deletion in all patients. The assay has been set up on a group of patients with known genotype and validated on 64 PXE patients. In this group four PXE patients (6.3%) were found to be homozygous and 25 (39.0%) to be heterozygous carriers of the c.3421C>T mutation. The common ABCC6del23-29 deletion, possibly interfering with genotype determination, was searched and excluded. Furthermore, two novel mutations in the ABCC6 gene could be identified in two patients. The novel mutations c.3389C>T and c.3341G>A did not interfere with our new assay. Our new c.3421C>T genotyping assays can be used for the rapid identification of this frequent mutation in PXE patients and of the recently newly proposed cardiac risk factor in young patients with myocardial infarcts of unknown origin.

A new 9-lipoxygenase cDNA from developing rice seeds.

We isolated a novel C9 position specific lipoxygenase (r9-LOX1) cDNA from developing rice seeds. The enzymatic features of r9-LOX1 resembled those of rice LOX-L3 known to be contained in rice germ and to have C9-specific LOX activity. However, the expression level of the r9-LOX1 gene was higher in imbibed seeds rather than developing seeds. A homology search against the rice nucleotide database revealed the r9-LOX1 gene to be on rice chromosome 3 (accession number AC093017). The restriction enzyme map of the reported genomic sequence agreed with the result of the Southern blot analysis for the r9-LOX1. The enzyme could be useful for in vitro synthesis of 9,10-ketol-octadecadienoic acid.

NEBcutter: A program to cleave DNA with restriction enzymes.

NEBcutter, version 1.0, is a program available via a web server (http://tools.neb.com/NEBcutter) that will accept an input DNA sequence and produce a comprehensive report of the restriction enzymes that will cleave the sequence. It produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://www.neb.com/rebase). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.

Association between hemochromatosis (HFE) gene mutation carrier status and the risk of colon cancer.

Iron is a pro-oxidant that may promote carcinogenesis. Mutations in the hemochromatosis (HFE) gene are associated with increased total body iron stores in some individuals. We assessed the risk of colon cancer among individuals with and without HFE gene mutations. We performed a population-based, case-control study in North Carolina. Case patients with colon cancer and control subjects provided information on multiple environmental exposures, including total iron intake and nonsteroidal anti-inflammatory drug (NSAID) use. They also provided a venous blood sample, from which DNA was extracted, amplified, and subjected to diagnostic restriction enzyme mapping to detect two major HFE gene mutations, C282Y and H63D. Data were analyzed with Fisher's exact test and logistic regression. All statistical tests were two-sided. Thirteen hundred and eight subjects participated (475 case patients, 833 control subjects). The allele frequencies of the H63D and C282Y mutations were greater among case patients (0.11 and 0.046, respectively) than among control subjects (0.09 and 0.044, respectively; P =.14 and P =.85, respectively). When we controlled for age, race, sex, red meat consumption, NSAID use, and total iron intake, subjects with any HFE gene mutation were more likely to have colon cancer than subjects with no HFE gene mutations (adjusted odds ratio [OR] = 1.40, 95% confidence interval [CI] = 1.07 to 1.87). The magnitude of the effect was similar for both the H63D (adjusted OR = 1.44, 95% CI = 1.04 to 1.98) and C282Y mutations (adjusted OR = 1.39, 95% CI = 0.88 to 2.19). The risk of colon cancer associated with an HFE gene mutation was similar for those who did and did not have a family history of colon cancer. Among those with HFE mutations, cancer risk increased with increasing age and total iron intake. HFE gene mutations are associated with an increased risk of colon cancer. Cancer risk is greatest in mutation carriers who are older or consume high quantities of iron.

Genetic Distinction of Radix Adenophorae From Its Adulterants by the DNA Sequence of 5S-rRNA Spacer Domains

Radix Adenophorae (Shashen), a traditional Chinese medicine commonly used as an antitussive and expectorant, is derived from roots of Adenophora stricta Miq. and Adenophora tetraphylla (Thunb.) Fisch. Twelve species and varieties of Adenophora and Glehnia, however, could act as substitutes or adulterants of Radix Adenophorae on the commercial markets in South East Asia, and roots of Adenophora hunanensis Nannf. and Glihnia littoralis F. Schmidt ex Miq. are the most common examples. The authentic identification of dried roots of A. stricta and A. tetraphylla, however, is difficult on the basis of appearance and morphology. A molecular genetic approach was developed here to identify the species of Radix Adenophorae. The 5S-rRNA spacer domains (approximately 250 bp) were amplified by the polymerase chain reaction (PCR) from genomic DNAs isolated from A. stricta, A. tetraphylla, A. hunanensis and G. littoralis, and subsequently, the nucleotide sequences were determined. Diversity in DNA sequence and restriction enzyme mapping among various species were found in their 5S-rRNA spacer domains, which could serve as markers for authentic identification of Radix Adenophorae.

Strain variation in Mycobacterium marinum fish isolates.

A molecular characterization of two Mycobacterium marinum genes, 16S rRNA and hsp65, was carried out with a total of 21 isolates from various species of fish from both marine and freshwater environments of Israel, Europe, and the Far East. The nucleotide sequences of both genes revealed that all M. marinum isolates from fish in Israel belonged to two different strains, one infecting marine (cultured and wild) fish and the other infecting freshwater (cultured) fish. A restriction enzyme map based on the nucleotide sequences of both genes confirmed the divergence of the Israeli marine isolates from the freshwater isolates and differentiated the Israeli isolates from the foreign isolates, with the exception of one of three Greek isolates from marine fish which was identical to the Israeli marine isolates. The second isolate from Greece exhibited a single base alteration in the 16S rRNA sequence, whereas the third isolate was most likely a new Mycobacterium species. Isolates from Denmark and Thailand shared high sequence homology to complete identity with reference strain ATCC 927. Combined analysis of the two gene sequences increased the detection of intraspecific variations and was thus of importance in studying the taxonomy and epidemiology of this aquatic pathogen. Whether the Israeli M. marinum strain infecting marine fish is endemic to the Red Sea and found extremely susceptible hosts in the exotic species imported for aquaculture or rather was accidentally introduced with occasional imports of fingerlings from the Mediterranean Sea could not be determined.

Comparison of amylase mRNAs from rat parotid gland, pancreas and liver using reverse transcriptase–polymerase chain reaction

The expression of mRNA for amylase was examined using the reverse transcriptase–polymerase chain reaction (RT–PCR). An amylase product was strongly detected in parotid and pancreas, but less strongly in liver. The degree of identity between the PCR products was assessed by restriction-enzyme mapping using two restriction enzymes, EcoRI and ScaI, and DNA sequencing. The PCR product from pancreas was cut by both EcoRI and ScaI, while the products from parotid and liver were cut by EcoRI but not by ScaI. The sequence of the parotid product was 90.4% homologous to that of the pancreas, and 100% homologous to that of the liver. These results indicate that the same amylase mRNA may be expressed in parotid and liver. In addition, the expression of amylase mRNAs in other rat tissues was investigated using RT–PCR, and the sensitivity of each PCR product to ScaI was tested. A weak single band was detected in submandibular gland, sublingual gland and stomach. ScaI digestion cut the stomach product into two fragments, but had no effect on the submandibular and sublingual products. Thus, it may be possible to classify amylase isoenzymes into pancreatic and parotid types based on the sensitivity of their PCR products to ScaI.

Construction of BAC libraries from two apomictic grasses to study the microcolinearity of their apospory-specific genomic regions.

We have constructed bacterial artificial chromosome (BAC) libraries from two grass species that reproduce by apospory, a form of gametophytic apomixis. The library of an apomictic polyhaploid genotype (line MS228-20, with a 2C genome size of approximately 4,500 Mbp) derived from a cross between the obligate apomict, Pennisetum squamulatum, and pearl millet ( P. glaucum) comprises 118,272 clones with an average insert size of 82 kb. The library of buffelgrass ( Cenchrus ciliaris, apomictic line B-12-9, with a 2C genome size of approximately 3,000 Mbp) contains 68,736 clones with an average insert size of 109 kb. Based on the genome sizes of these two lines and correcting for the number for false-positive and organellar clones, library coverages were found to be 3.7 and 4.8 haploid genome equivalents for MS 228-20 and B12-9, respectively. Both libraries were screened by hybridization with six SCARs (sequence-characterized amplified regions), whose tight linkage in a single apospory-specific genomic region had been previously demonstrated in both species. Analysis of these BAC clones indicated that some of the SCAR markers are actually amplifying duplicated regions linked in coupling in both genomes and that restriction enzyme mapping will be necessary to sort out the duplications.

Characterisation and molecular cloning of an erythromycin resistance plasmid of Lactococcus lactis isolated from chicken cecum.

An erythromycin resistance plasmid, pAJ01 was isolated from Loctococcus lactis isolate C5 that was isolated from a healthy two-week-old chicken cecum. A 4 kb plasmid was transformed into plasmidless L. lactis MG1363 before a restriction endonuclease map was constructed. It was then fused with pUC19 to form pAJ02, which can replicate in Escherichia coli XLI-Blue as well as L. lactis MG1363. The plasmid was stably maintained in Lactococcus for more than 100 generations.

Integrating internet assignments into a biochemistry/molecular biology laboratory course

AbstractA main challenge in educating undergraduate students is to introduce them to the Internet and to teach them how to effectively use it in research. To this end, an Internet assignment was developed that introduces students to websites related to biomedical research at the beginning of a biochemistry/molecular biology laboratory course. The basic sites introduced cover many subjects, include searching for specific DNA sequences, restriction enzyme mapping, RNA folding, analyzing three‐dimensional protein images, and literature searches. These newly learned Internet skills are incorporated into other aspects of the laboratory course. In the example illustrated here, students sequence DNA inserts from randomly chosen bacterial colonies prepared from a human cDNA plasmid library. The obtained DNA sequence is used to search on‐line data bases introduced in the initial Internet assignment to determine whether the cDNAs have already been identified. The sequencing “wet‐lab” module, coupled with the Internet assignment, gives students experience in four areas. 1) purifying plasmid DNA, 2) performing restriction endonuclease digests on the plasmid DNA, 3) sequencing double‐stranded DNA, and 4) comparison of obtained sequence data to known DNA sequences in the human genome data base in a way that simulates a research experience.

Tacg – a grep for DNA

BackgroundPattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple motifs with IUPAC degeneracies, regular expressions, patterns allowing mismatches, and probability matrices.ResultsI describe a small application which allows searching for all the above pattern types individually, which further allows these atomic motifs to be assembled into logical rules for more sophisticated analysis.Conclusiontacg is small, portable, faster and more capable than most alternatives, relatively easy to modify, and freely available in source code.

Isolation of Plasmid DNA by Adsorption on Glass Fibers

ABSTRACTSimple, fast and low cost method for isolation of plasmid DNA, affordable for any laboratory is presented. The method is based on the specific adsorption of double stranded (ds) DNA on glass fibers in the presence of high concentration of guanidine hydrochloride (GnHCl) and elution of the retained DNA with ordinary buffers. Among the various types of glass filters and other silicate materials tested, the most appropriate for isolation of plasmid DNA was found to be the Schleicher & Schuell glass filters GF92. The best retention of dsDNA on these filters was achieved in 1.5 M GnHCl, pH 4.0. The plasmid DNA preparations obtained by this method contained mainly supercoiled plasmid DNA endowed with a high transformation activity. Besides for transformation, this DNA can be used also for restriction endonuclease mapping and sequencing.

The expression of human alpha -like globin genes in transgenic mice mediated by bacterial artificial chromosome.

After screening a bacterial artificial chromosome of human genomic DNA library with human HS-40, zeta-, alpha-, and theta-globin probes, a 110-kb clone bearing the whole human alpha-globin gene cluster was obtained and rare restriction endonuclease mapping was performed. The bacterial artificial chromosome DNA was isolated, and transgenic mice were generated. Three founders were detected from 35 newborn mice. The copy numbers were 1, 2, and 2, and the expression of human alpha-globin genes in various tissues at different developmental stages in the transgenic mice was assayed. The human alpha-globin mRNA can be detected in bone marrow, kidney, liver, brain, but not in muscle, testis, or thymus. The human zeta-globin genes were switched off, and the alpha-globin genes were switched at day 11.5 in mouse embryo, indicating that developmental stage-specific expression of the alpha-like globin genes was properly regulated. The human alpha-globin mRNA ranged between 17-68% of the endogenous mouse alpha-globin, suggesting that the expression of human alpha-globin genes is integration site-dependent in transgenic mice. The ratio of human alpha(2)- and alpha(1)-globin gene expression in adult transgenic mouse is about 2.5:1 similar to the expression in human.

Innovation and discovery: The application of nucleic acid-based technology to avian virus detection and characterization

Polymerase chain reaction (PCR)-based approaches to the detection, differentiation and characterization of avian pathogens continue to be developed and refined. The PCRs, or reverse transcriptase-PCRs, may be general, designed to detect all or most variants of a pathogen, or to be serotype, genotype or pathotype specific. Progress is being made with respect to making nucleic acid approaches more suitable for use in diagnostic laboratories. Robotic workstations are now available for extraction of nucleic acid from many samples in a short time, for routine diagnosis. Following general PCR, the DNA products are commonly analyzed by restriction endonuclease mapping (restriction fragment length polymorphism), using a small number of restriction endonucleases, based on a large body of sequence data. Increasingly, however, nucleotide sequencing is being used to analyze the DNA product, in part due to the expanding use of non-radioactive sequencing methods that are safe and enable high throughout. In this review, I highlight some recent developments with many avian viruses: Newcastle disease virus; circoviruses in canary and pigeon; infectious bursal disease virus (Gumboro disease virus); avian adenoviruses, including Angara disease/infectious hydropericardium virus, haemorrhagic enteritis virus of turkeys, and egg drop syndrome virus; avian herpesviruses, including infectious laryngotracheitis virus, duck plague virus, psittacine herpesvirus (Pacheco's parrot disease virus), Marek's disease virus and herpesvirus of turkeys; avian leukosis virus (associated with lymphoid leukosis or myeloid leukosis, and egg transmission); avian pneumoviruses (turkey rhinotracheitis virus); avian coronaviruses, including infectious bronchitis virus, turkey coronavirus and pheasant coronavirus; astrovirus, in the context of poult enteritis and mortality syndrome, and avian nephritis virus; and avian encephalomyelitis virus, a picornavirus related to hepatitis A virus.

Apolipoprotein E genotyping: a comparative study between restriction endonuclease mapping and allelic discrimination with the LightCycler

Background: The apolipoprotein E (apo E) polymorphism is associated with the risk of developing cardiovascular disease and the risk and the time of onset of Alzheimer's disease. Therefore, the interest in apo E genotyping is high, both for epidemiological research and for the purpose of diagnosing dyslipidemia or dementia. The aim of our study was to compare and evaluate two different methods for apo E genotyping, both on the basis of polymerase chain reaction (PCR). Methods: Genomic DNA of 197 subjects was extracted from whole blood. The first method involved DNA amplification performing a PCR using specific primers and endonuclease restriction mapping. The second one was a DNA assay that used real-time PCR on the LightCycler™ instrument (Roche). Results: We obtained a 100% concordance between the two methods and we found a relative allelic frequency distribution typical for an Italian population. Conclusions: The LightCycler (LC) allelic discrimination method for apo E genotyping seems to be rapid, simple and accurate, suggesting a possible successful use of this method for diagnostic purposes.