High Molecular Weight Genomic DNA Research Articles

An inexpensive and high‐throughput procedure to extract and purify total genomic DNA for population studies

AbstractWe describe here a procedure for the purification of high molecular weight genomic DNA that combines the economies of ‘do‐it‐yourself’, single‐tube protocols with the sample throughput and DNA quality of microplate‐based DNA extraction and purification kits from commercial suppliers. The procedure allows the preparation of genomic DNA of a quality suitable for polymerase chain reaction‐based studies of large populations at around one‐tenth of the cost of commercially available kits. Furthermore, 96 samples can be purified from crude tissue digests in around 30 min and are produced in microtitre plate format to allow efficient downstream processing of samples.

HAPPY mapping in a plant genome: reconstruction and analysis of a high‐resolution physical map of a 1.9 Mbp region ofArabidopsis thalianachromosome 4

HAPPY mapping is an in vitro approach for defining the order and spacing of DNA markers directly on native genomic DNA. This cloning-free technique is based on analysing the segregation of markers amplified from high molecular weight genomic DNA which has been broken randomly and 'segregated' by limiting dilution into subhaploid samples. It is a uniquely versatile tool, allowing for the construction of genome maps with flexible ranges and resolutions. Moreover, it is applicable to plant genomes, for which many of the techniques pioneered in animal genomes are inapplicable or inappropriate. We report here its demonstration in a plant genome by reconstructing the physical map of a 1.9 Mbp region around the FCA locus of Arabidopsis thaliana. The resulting map, spanning around 10% of chromosome 4, is in excellent agreement with the DNA sequence and has a mean marker spacing of 16 kbp. We argue that HAPPY maps of any required resolution can be made immediately and with relatively little effort for most plant species and, furthermore, that such maps can greatly aid the construction of regional or genome-wide physical maps.

Unique Molecular Architecture of Silk Fibroin in the Waxmoth,Galleria mellonella

Proteins of silk fibers are characterized by reiterations of amino acid repeats. Physical properties of the fiber are determined by the amino acid composition, the complexity of repetitive units, and arrangement of these units into higher order arrays. Except for very short motifs of 6-10 residues, the length of repetitive units and the number of these units concatenated in higher order assemblies vary in all spider and lepidopteran silks analyzed so far. This paper describes an exceptional silk protein represented by the 500-kDa heavy chain fibroin (H-fibroin) of the waxmoth, Galleria mellonella. Its non-repetitive N-terminal (175 residues) and C-terminal (60 residues) parts, the overall gene organization, and the nucleotide sequence around the TATA box show that it is homologous to the H-fibroins of other Lepidoptera. However, over 95% of the protein consists of highly ordered repetitive structures that are unmatched in other species. The repetitive region includes 11 assemblies AB(1)AB(1)AB(1)AB(2)(AB(2))AB(2) of remarkably conserved polypeptide repeats A (63 amino acid residues), B(1) (43 residues), and B(2) (18 residues). The repeats contain a high proportion of Gly (31.6%), Ala (23.8%), Ser (18.1%), and of residues with long hydrophobic side chains (16% for Leu, Ile, and Val combined). The presence of the GLGGLG and SSAASAA(AA) motifs suggests formation of pleated beta-sheets and their stacking into crystallites. Conspicuous conservation of the apolar sequence VIVI followed by DD or ED is interpreted as indicating the importance of hydrophobicity and electrostatic charge in H-fibroin cross-linking. The environment of G. mellonella larvae within bee cultures requires continuous production of silk that must be both strong and elastic. The spectacular arrangement of the repetitive H-fibroin region apparently evolved to meet these requirements.

A lysis, storage, and transportation buffer for long-term, room-temperature preservation of human clinical lymphoid tissue samples yielding high molecular weight genomic DNA suitable for molecular diagnosis.

Molecular diagnosis of malignant lymphoma depends on the ability to extract high molecular weight genomic DNA. However, collection, storage, and transportation of frozen tissue is time consuming and expensive. We used a simple, low-cost lysis, storage, and transportation buffer (LST) to maintain clinical tissue samples at room temperature for up to 4 weeks before molecular analysis. Immersion of lymphoid tissue in LST at room temperature for 2 to 4 weeks was compared with snap-freezing in liquid nitrogen followed by storage at -75 degrees C. Southern blot analysis using an immunoglobulin heavy chain JH probe yielded identical results in 5 clonal and 6 nonclonal samples. The DNA recovered from the LST of a 12th sample was too degraded to be analyzed; however, the tissue had large zones of geographic necrosis. We also demonstrated that DNA extracted from tissue stored in LST is suitable for amplification by the polymerase chain reaction. Results from 4 of the snap-frozen and LST samples analyzed for rearrangements at the immunoglobulin heavy chain VDJ locus were identical. LST can be used in a clinical laboratory for storing tissue samples at room temperature up to 4 weeks before molecular analysis.

Isolation and Characterization of NUC70, a Cytoplasmic, Hematopoietic Apoptotic Endonuclease

Endonucleolytic DNA fragmentation is the common end point and the prevailing indicator of apoptosis. We have identified a 70-kDa endonuclease (NUC70) that is activated in drug-induced apoptosis of human hematopoietic cells. We purified NUC70 to homogeneity and generated a rabbit polyclonal antibody to distinguish it from previously identified nucleases. Biochemical characterization of isolated NUC70 demonstrates that it is Ca2+/Mg2+-dependent and active over a pH range of 6-8. When incubated with isolated HeLa nuclei, NUC70 was capable of generating internucleosomal DNA fragmentation. This endonucleolytic activity was inhibited by Zn2+, aurintricarboxylic acid, N-ethylmaleimide, spermine, and iodoacetamide. Western immunoblots using the anti-NUC70 antibody and DNA-SDS-polyacrylamide gel electrophoresis assays indicate that NUC70 expression and activity is restricted to human hematopoietic cells. No such activity was detected in human epithelial cell lines or murine hematopoietic cells. We also observed no difference in levels of NUC70 expression between apoptotic and nonapoptotic cells, suggesting that activation of NUC70 may be by posttranslational modification. We demonstrate that NUC70 activity is diminished in cells pretreated with the caspase inhibitors z-DEVD-fmk, z-VAD-fmk, and Z-CH2-Asp-DCB. Time course studies of cytoplasmic and nuclear endonuclease activities during apoptosis show that NUC70 is a cytoplasmic endonuclease that is translocated to the nucleus after the initiation of apoptosis. We confirmed this with immunostaining studies using anti-NUC70 antibody. These results demonstrate that NUC70 is an endogenous cytoplasmic endonuclease that is activated during apoptosis in a caspase-dependent mechanism.

Isolation of Genomic DNA from the Antimalarial Plant Artemisia annua

A suitable protocol is described to obtain high molecular weight, restrictable, and amplifiable genomic DNA from the antimalarial plant Artemisia annua. The method is a CTAB procedure that includes a rapid micro-column chromatography through DE-52 ion- exchange resin. The pure consistency of the template may also offer a reliability advantage for PCR and RFLP based applications. Restriction of the purified DNA with DraI and HindIII resulted in discrete bands that may have arisen due to some repeat sequences equally spaced between the restriction site(s). Perhaps this implies a scope for direct identification of some repeat sequences such as putative species-specific probes.

DNA Isolation and Amplification from Cacti

The cacti family is a morphologically heterogeneous group comprising 100 genera and about 1500 species (Hernandez and Barcenas, 1996). With the exception of one genus, all members of this family are native to America (Hernandez and Barcenas, 1996). There are three subfamilies, Opuntioideae, Cactoideae, and Pereskioideae (Gibson and Nobel, 1986). DNA isolation from cacti is notoriously difficult because they contain high amounts of polysaccharides and secondary metabolites which form insoluble complexes with nucleic acids during extraction (Guillemaut and Marechal-Drouard, 1992). Like in other groups of plants, the secondary metabolites and polysaccharides in cacti inhibit enzyme action (Porebski et al., 1997). The polysaccharides are visually evident by their viscous, glue-like texture and they make the DNA unmanageable when pipeting and hard to amplify by the polymerase chain reaction (PCR) (Poresbski et al., 1997). We report an easy and inexpensive protocol to isolate DNA from cacti. We used this method to isolate DNA from 85 species (170 individuals) of 39 genera of the subfamilies Pereskioideae, Opuntioidea, and Cactoideae. This procedure is a modification of a protocol described by De la Cruz et al. (1995) for the Cacti family. It requires only a few grams of tissue and does not require destruction of the whole plant to produce high molecular weight genomic DNA. The DNA from this procedure can be amplified consistently by PCR and used for RAPD analysis.

The ectomycorrhizal basidiomycete Hebeloma circinans harbors a linear plasmid encoding a DNA- and RNA polymerase.

Bulk DNA isolated from the ectomycorrhizal basidiomycete Hebeloma circinans was treated with proteinase K and submitted to agarose gel electrophoresis. In addition to high molecular weight genomic DNA, three minor bands were detected. The band with the highest electrophoretic mobility (2.2 kbp) corresponds to double-stranded RNA. The two other bands, termed pHC1 and pHC2, were shown to be dsDNA molecules of 10.3 and 9.1 kbp, respectively. Treatment of the pHC elements with 3'- and 5'-specific exonucleases revealed a linear structure and proved that the 5' ends are protected from digestion; for pHC2, linearity was confirmed by restriction mapping. A 3.2 kbp HindIII fragment of pHC2 was cloned and sequenced; it contains two open reading frames encoding putative viral B type DNA and RNA polymerases. Thus, the fungus harbors a typical linear plasmid, up to now, rarely described for basidiomycetes and hitherto unknown for mycorrhizal species.

Protein-DNA Interactions at a Drug-responsive Element of the Human Apolipoprotein A-I Gene

Previously, we demonstrated that when two human hepatoma cell lines, Hep3B and HepG2, were exposed to gemfibrozil, a hypolipidemic drug, a 2-fold induction in apolipoprotein A-I (apoA-I) mRNA levels resulted. To determine if mRNA stabilization was responsible for the changes in apoA-I mRNA levels, the half-lives for apoA-I mRNA were measured in the presence of actinomycin D with and without gemfibrozil. These experiments revealed no differences in stability. However, nuclear run-off assays indicated that the transcription rate of the apoA-I gene was increased 2-fold in gemfibrozil-treated cells. Transient transfection experiments also indicated that the induction of apoA-I mRNA level in response to gemfibrozil is mediated at the transcriptional level. We have identified two copies of the "drug-responsive element" (DRE) in the apoA-I promoter region that may be responsible for the increase in apoA-I transcriptional activity by gemfibrozil. Using gel mobility shift assays with a synthetic DRE oligonucleotide, we have demonstrated that exposure of Hep3B and HepG2 cells to gemfibrozil resulted in strong induction of a protein-DNA complex. The formation of this complex is highly sequence-specific as indicated by the DNA competition experiments. The drug-inducible nuclear proteins bind to the DRE of the human apoA-I gene with an apparent Kd of 4.1 nM. Methylation interference experiments have localized the contact sites of nuclear factors to the DRE region. Southwestern blot analyses have identified two groups of drug-inducible nuclear proteins with molecular masses of approximately 30 and 15 kDa. When a copy of synthetic DRE oligonucleotide was inserted upstream of the thymidine kinase promoter and luciferase reporter construct, a significant 2-fold induction in luciferase activity was observed in the presence of gemfibrozil following transient transfection of two human hepatoma cell lines, HepG2 and Hep3B. However, a plasmid containing one copy of mutated apoA-I-DRE oligomer did not confer responsiveness to gemfibrozil treatment. Furthermore, pGL2 (apoA-I -250 mutant DRE), which carried an internal mutation of the DRE in the human apoA-I proximal promoter region, showed no increase in luciferase activity in response to gemfibrozil. These results implicate protein-DNA interactions at the DRE region in the transcriptional induction of human apoA-I gene expression by gemfibrozil.

Molecular genetic analysis of the ripening-inhibitor and non-ripening loci of tomato: a first step in genetic map-based cloning of fruit ripening genes.

Ripening represents a complex developmental process unique to plants. We are using tomato fruit ripening mutants as tools to understand the regulatory components that control and coordinate the physiological and biochemical changes which collectively confer the ripe phenotype. We have genetically characterized two loci which result in significant inhibition of the ripening process in tomato, ripening-inhibitor (rin), and non-ripening (nor), as a first step toward isolating genes likely to encode key regulators of this developmental process. A combination of pooled-sample mapping as well as classical restriction fragment length polymorphism (RFLP) analysis has permitted the construction of high-density genetic maps for the regions of chromosomes 5 and 10 spanning the rin and nor loci, respectively. To assess the feasibility of initiating a chromosome walk, physical mapping of high molecular weight genomic DNA has been employed to estimate the relationship between physical distance (in kb) and genetic distance (in cM) around the targeted loci. Based on this analysis, the relationship in the region spanning the rin locus is estimated to be 200-300 kb/cM, while the nor locus region ratio is approximately 200 kb/1 cM. Using RFLP markers tightly linked to rin and nor, chromosome walks have been initiated to both loci in a yeast artificial chromosome (YAC) library of tomato genomic DNA. We have isolated and characterized several YAC clones linked to each of the targeted ripening loci and present genetic evidence that at least one YAC clone contains the nor locus.

In male mouse germ cells, copper-zinc superoxide dismutase utilizes alternative promoters that produce multiple transcripts with different translation potential.

Copper-zinc superoxide dismutase (SOD-1) is an enzyme that is widely expressed in eukaryotic cells and performs a vital role in protecting cells against free radical damage. In mouse testis, three different sizes of SOD-1 mRNAs of about 0.73, 0.80, and 0.93 kilobases (kb) are detected. The 0.73-kb mRNA is found in early stages of male germ cells and in all somatic tissues. The mRNAs of 0.80 and 0.93 kb are exclusively detected in post-meiotic germ cells. RNase H digestions and Northern blot analyses reveal that the three SOD-1 mRNAs are derived from two transcripts, a ubiquitously expressed transcript and a post-meiotic transcript, which differ by 114-120 nucleotides. RNase protection assays demonstrate that the additional nucleotides present in the post-meiotic mRNA are solely in the 5'-untranslated region. Using a probe derived from the 5'-untranslated region of the 0.93-kb SOD-1 mRNA, we have established that it originates from an alternative upstream promoter contiguous with the somatic SOD-1 promoter. Polysomal gradient analysis of the three mouse testis SOD-1 mRNAs reveals that the 0.93-kb SOD-1 mRNA is primarily non-polysomal, while the 0.80- and 0.73-kb SOD-1 mRNAs are mostly polysome associated. A faster migrating form of the 0.93-kb SOD-1 mRNA is present on polysomes as a result of partial deadenylation. In a cell-free translation system, the 0.73-kb SOD-1 mRNA translates about 2-fold more efficiently than the 0.93-kb SOD-1 mRNA. These data demonstrate that male germ cells transcribe two size classes of SOD-1 mRNAs with different translation potential by utilizing two different promoters, post-meiotic SOD-1 mRNAs undergo adenylation changes, and one of the post-meiotic SOD-1 mRNAs is transcribed during mid-spermiogenesis and translated days later in a partially deadenylated form.

Mutants of downy mildew resistance in Lactuca sativa (lettuce).

As part of our investigation of disease resistance in lettuce, we generated mutants that have lost resistance to Bremia lactucae, the casual fungus of downy mildew. Using a rapid and reliable screen, we identified 16 distinct mutants of Latuca sativa that have lost activity of one of four different downy mildew resistance genes (Dm). In all mutants, only a single Dm specificity was affected. Genetic analysis indicated that the lesions segregated as single, recessive mutations at the Dm loci. Dm3 was inactivated in nine of the mutants. One of five Dm 1 mutants was selected from a population of untreated seeds and therefore carried a spontaneous mutation. All other Dm1, Dm3, Dm5/8 and Dm7 mutants were derived from gamma- or fast neutron-irradiated seed. In two separate Dm 1 mutants and in each of the eight Dm3 mutants analyzed, at least one closely linked molecular marker was absent. Also, high molecular weight genomic DNA fragments that hybridized to a tightly linked molecular marker in wild type were either missing entirely or were truncated in two of the Dm3 mutants, providing additional evidence that deletions had occurred in these mutants. Absence of mutations at loci epistatic to the Dm genes suggested that such loci were either members of multigene families, were critical for plant survival, or encoded components of duplicated pathways for resistance; alternatively, the genes determining downy mildew resistance might be limited to the Dm loci.

Preparation and screening of an arrayed human genomic library generated with the P1 cloning system.

We describe here the construction and initial characterization of a 3-fold coverage genomic library of the human haploid genome that was prepared using the bacteriophage P1 cloning system. The cloned DNA inserts were produced by size fractionation of a Sau3AI partial digest of high molecular weight genomic DNA isolated from primary cells of human foreskin fibroblasts. The inserts were cloned into the pAd10sacBII vector and packaged in vitro into P1 phage. These were used to generate recombinant bacterial clones, each of which was picked robotically from an agar plate into a well of a 96-well microtiter dish, grown overnight, and stored at -70 degrees C. The resulting library, designated DMPC-HFF#1 series A, consists of approximately 130,000-140,000 recombinant clones that were stored in 1500 microtiter dishes. To screen the library, clones were combined in a pooling strategy and specific loci were identified by PCR analysis. On average, the library contains two or three different clones for each locus screened. To date we have identified a total of 17 clones containing the hypoxanthine-guanine phosphoribosyltransferase, human serum albumin-human alpha-fetoprotein, p53, cyclooxygenase I, human apurinic endonuclease, beta-polymerase, and DNA ligase I genes. The cloned inserts average 80 kb in size and range from 70 to 95 kb, with one 49-kb insert and one 62-kb insert.

Comparison of different procedures for the extraction of DNA from small blood samples of non-human primates

In this study three different techniques suitable to recover high molecular weight genomic DNA from small blood samples of different species of malagasy primates are compared: we suggest the use of a very simple phenol-chlorophorm DNA extraction for badly stored or coagulated blood as for samples collected under difficult field conditions.Furthermore we briefly describe the use of this DNA in determining RLFP patterns and DNA fingerprints.

Isolation of dna and rna from Streptococcus sobrinus OMZ176 using CsTFA gradients

1.1. A simple procedure for isolation of high molecular weight genomic DNA, and RNA, from Streptococcus sobrinus OMZ176 is described.2.2. Cell cultures were grown aerobically for 10 hr.3.3. Spheroplast formation and lysis was achieved by mutanolysin/lysozyme-dependent digestion of the cell wall, followed by N-lauroylsarcosinate-mediated lysis.4.4. Nucleic acids were isolated directly from cell-lysates using cesium-trifluoroacetate (CsTFA) densitygradient centrifugation.5.5. Three different centrifugation regimes were tested: self-generated density gradients in a fixed angle rotor; self-generated density-gradients in a swinging-bucket rotor; pre-formed density-gradients in a swinging-bucket rotor.6.6. Genomic DNA isolated by the CsTFA-procedure was found to have higher purity as compared to genomic DNA isolated in a conventional CsCl gradient.7.7. Isolated DNA was shown to be of a quality suitable for applications in molecular biology.

Comparison of different procedures for the extraction of DNA from small blood samples of non-human primates

In this study three different techniques suitable to recover high molecular weight genomic DNA from small blood samples of different species of malagasy primates are compared: we suggest the use of a very simple phenol-chlorophorm DNA extraction for badly stored or coagulated blood as for samples collected under difficult field conditions. Furthermore we briefly describe the use of this DNA in determining RLFP patterns and DNA fingerprints.

Procedural Protocol, Survival to Hatching and Plasmid DNA Fate After Microinjection into Tilapia Zygotes

The plasmid vector, pBRd-AK1-BGH4.6.10 (pBGH), containing the bovine growth hormone sequence driven by an avian retroviral long terminal repeat (LTR) was microinjected at 0.1, 0.5, 1 or 5 ng of pDNA/20 nl of physiological saline into tilapia, Oreochromis mossambicus × O. niloticus embryos. In 24 replicates, normally 60 zygotes were microinjected with either the entire linear 8.5 kb pBGH/ClaI vector or a 3.8 kb pBGH/SalI restriction fragment. Overall mean survival to fry hatching was 7.6% in plasmid DNA-microinjected, 15.6% in sham-microinjected and 48.1% in uninjected control embryos. There were no significant (P > 0.05) differences in survival to hatching between those embryos microinjected with the 3.8 or the 8.5 kb restriction fragment, nor was there a trend toward decreasing survival as the plasmid DNA concentration increased from 0.1 to 5 ng. The significant (P < 0.05) increase in survival among uninjected control embryos to hatching indicates that microinjection trauma was the major cause of mortality. Large quantities of plasmid DNA were recovered from pooled-embryo samples. Multiple bands (positive signals) were detected usually in the high molecular weight (HMW) genomic DNA regions. Position shifting of these HMW bands upon digesting with various restriction endonucleases provided evidence for plasmid DNA integration into tilapia embryo chromosomal DNA. Otherwise, these positive signah may have been end-twnd ligations of increasingly longer plasmid DNA constructs. Putative transgenic O. mossmbicus × O. niloticus were found among eight of 27 surviving adults.

Cloning high molecular weight DNA fragments by the bacteriophage P1 system

The cloning of high molecular weight genomic DNA promises to provide the means of mapping chromosomes, isolating genes, and understanding long-range effects on gene expression. This review describes the background and some recent advances in cloning of high molecular weight DNA using the bacteriophage P1 system

The use of genomic DMA fingerprinting in studies of the epidemiology of bacteria in periodontitis

Recent studies of microbial epidemiology emphasizing the genetic organization and distribution of organisms associated with orofacial infections have led to new insights into the possible origins of pathogenicity. Studies into genetic heterogeneity, acquisition and transmission of these organisms have been markedly advanced by the utilization of the powerful technique of genomic DNA fingerprinting. Characteristic fingerprints for each bacterial isolate can be produced by cleavage of high molecular weight genomic DNA by restriction endonucleases. It is assumed that each DNA fingerprint represents a clonal type. In this report, we review and analyze studies of the epidemiology of bacteria associated with orofacial infections with an emphasis on periodontal disease. Studies of nontypable (NT) Haemophilus influenzae associated with recurrent otitis media illustrate the utility of this technique. DNA fingerprinting clearly demonstrates genetic heterogeneity of NT H. influenzae isolates, and clonality of infection of any individual. Furthermore, DNA fingerprinting has shown that the same clonal type is seen in siblings concurrently suffering from otitis media, suggesting horizontal transmission within the family. Studies of mutans Streptococci also show extensive genetic heterogeneity and show vertical transmission of a predominant clonal type only from mother to infant, but not from father to infant. Studies of Actinobacillus actinomycetemcomitans show considerable genetic heterogeneity among monkey isolates. Thus far, three clonal types have been reported with DNA fingerprinting among isolates from periodontal patients, but additional genetic heterogeneity can be found using specific DNA fragments as probes in hybridization experiments. Intrafamilial transmission of A. actinomycetemcomitans has been demonstrated. Porphyromonas (Bacteroides) gingivalis shows extensive genetic heterogeneity and case reports suggest clonal infection of any one individual. In contrast, results with DNA fingerprinting of Eikenella corrodens, Fusobacterium nucleatum, and Bacteroides intermedius show that individuals may be infected with 2 or more clonal types. These studies point to the great potential of DNA fingerprinting for investigating the epidemiology of putative orofacial pathogens. Such studies with periodontal microorganisms will likely reveal steps in the acquisition, intraoral and person-to-person transmission, which then could possibly be inhibited or interfered with to prevent periodontal disease or its recurrence.

Rapid isolation of genomic DNA from animal tissues

A simple technique for the isolation of very high molecular weight genomic DNA from animal tissues and cells is described. The method involves rapid isolation of nuclei and their embedding in agarose beads followed by extraction of lipids and proteins with SDS. The protocol does not require proteolytic digestion and the whole procedure can be completed in 1 day. The isolated DNA is digestible by restriction enzymes and free of ligase inhibitors.