Showing papers on "genomic DNA published in 1991"

Distribution of repetitive DNA sequences in eubacteria and application to finerpriting of bacterial enomes

Abstract: Dispersed repetitive DNA sequences have been described recently in eubacteria. To assess the distribution and evolutionary conservation of two distinct prokaryotic repetitive elements, consensus oligonucleotides were used in polymerase chain reaction [PCR] amplification and slot blot hybridization experiments with genomic DNA from diverse eubacterial species. Oligonucleotides matching Repetitive Extragenic Palindromic [REP] elements and Enterobacterial Repetitive Intergenic Consensus [ERIC] sequences were synthesized and tested as opposing PCR primers in the amplification of eubacterial genomic DNA. REP and ERIC consensus oligonucleotides produced clearly resolvable bands by agarose gel electrophoresis following PCR amplification. These band patterns provided unambiguous DNA fingerprints of different eubacterial species and strains. Both REP and ERIC probes hybridized preferentially to genomic DNA from Gram-negative enteric bacteria and related species. Widespread distribution of these repetitive DNA elements in the genomes of various microorganisms should enable rapid identification of bacterial species and strains, and be useful for the analysis of prokaryotic genomes.

A simple and rapid method for the preparation of plant genomic DNA for PCR analysis.

Abstract: The polymerase chain reaction (PCR) has revolutionised the rapid analysis of mammalian genomic DNA (1). However, PCR is less useful in the analysis of plant DNA due to the difficulties in extracting nucleic acids from limited amounts of plant tissue. We have developed a method for the rapid extraction of small amounts of plant genomic DNA suitable for PCR analysis. The method is applicable to a variety of plant species and has the added advantage of not requiring any phenol or chloroform extraction. Thus it is possible to complete an extraction within 15 minutes without handling any hazardous organic solvents. Samples for PCR analysis (usually leaf tissue) are collected using the lid of a sterile Eppendorf tube to pinch out a disc of material into the tube. This ensures uniform sample size and also reduces the possibilities of contamination arising from handling the tissue. DNA is extracted as follows: The tissue is macerated (using disposable grinders from Bel-art Products: Scienceware, Pequannock, NJ, 07440 USA. catalog no 992) in the original Eppendorf tube at room temperature, without buffer, for 15 seconds. 400 yl of extraction buffer (200 mM Tris HC1 pH 7.5, 250 mM NaCl, 25 mM EDTA, 0.5% SDS) is added and the sample vortexed for 5 seconds. This mixture can then be left at room temperature until all the samples have been extracted (> 1 hour). The extracts are centrifuged at 13,000 rpm for 1 minute and 300 y\\ of the supernatant transferred to a fresh Eppendorf tube. This supernatant is mixed with 300 /il isopropanol and left at room temperature for 2 minutes. Following centrifugation at 13,000 rpm for 5 minutes, the pellet is vacuum dried and dissolved in 100 /xl 1XTE. This DNA is stable at 4°C for greater than one year. 2.5 yX of this sample is sufficient for a standard 50 y\\ PCR (Figure 1). When older tissue is used this may be increased to 25 /xl without any deleterious effect on the PCR. Using this protocol we have found it possible to process hundreds of individual samples in a single working day.

Activating mutations of the stimulatory G protein in the McCune-Albright syndrome.

Abstract: Background. The McCune-Albright syndrome is a sporadic disease characterized by polyostotic fibrous dysplasia, cafe au lait spots, sexual precocity, and hyperfunction of multiple endocrine glands. These manifestations may be explained by a somatic mutation in affected tissues that results in activation of the signal-transduction pathway generating cyclic AMP (cAMP). We analyzed DNA from tissues of patients with the McCune-Albright syndrome for the presence of activating mutations of the gene for the a subunit of the G protein (Gsα) that stimulates cAMP formation. Methods. Genomic DNA fragments encompassing regions (exons 8 and 9) previously found to contain activating missense mutations of the Gsα gene (gsp mutations) in sporadically occurring pituitary tumors were amplified in tissues from four patients with the McCune-Albright syndrome by the polymerase chain reaction. The amplified DNA was analyzed for mutations by denaturing gradient gel electrophoresis and allele-specific oligonucleotide hyb...

DNA amplification fingerprinting using very short arbitrary oligonucleotide primers.

Abstract: The surprising finding that amplification of genomic DNA can be directed by only one oligonucleotide primer of arbitrary sequence to produce a characteristic spectrum of short DNA products of varying complexity, was applied as a strategy to detect genetic differences between organisms. This approach, DNA amplification fingerprinting (DAF), does not depend on cloning or DNA sequence information and can generate fingerprints from DNA of viral, bacterial, fungal, plant and animal origins. Primers as short as 5 nucleotides in length can produce complex banding patterns that are resolved by polyacrylamide gel electrophoresis and silver staining. Amplification fragment length polymorphisms (AFLPs) were detected between different human individuals as well as between soybean cultivars. It is anticipated that DAF will have wide application for DNA analysis.

A fast method for high-quality genomic DNA extraction from whole human blood.

Abstract: A simple and fast protocol is described for the purification of genomic DNA from 0.3 ml of whole human blood. The recovery of DNA is quantitative and reproducible; the quality is such that it can be used for all relevant molecular biology techniques.

Method of sequencing of genomes by hybridization of oligonucleotide probes

Abstract: The conditions under which oligonucleotides hybridize only with entirely homologous sequences are recognized. The sequence of a given DNA fragment is read by the hybridization and assembly of positively hybridizing probes through overlapping portions. By simultaneous hybridization of DNA molecules applied as dots and bound onto a filter, representing single-stranded phage vector with the cloned insert, with about 50,000 to 100,000 groups of probes, the main type of which is (A,T,C,G)(A,T,C,G)N8(A,T,C,G), information for computer determination of a sequence of DNA having the complexity of a mammalian genome are obtained in one step. To obtain a maximally completed sequence, three libraries are cloned into the phage vector, M13, bacteriophage are used: with the 0.5 kb and 7 kbp insert consisting of two sequences, with the average distance in genomic DNA of 100 kbp. For a million bp of genomic DNA, 25,000 subclones of the 0.5 kbp are required as well as 700 subclones 7 kb long and 170 jumping subclones. Subclones of 0.5 kb are applied on a filter in groups of 20 each, so that the total number of samples is 2,120 per million bp. The process can be easily and entirely robotized for factory reading of complex genomic fragments or DNA molecules.

Rapid identification of markers linked to a Pseudomonas resistance gene in tomato by using random primers and near-isogenic lines.

Abstract: An approach to isolating DNA sequences that are linked to important plant genes is described. The strategy is based upon a recent modification of the polymerase chain reaction in which synthetic primers are used to amplify random sequences from genomic DNA. This technique, used in conjunction with near-isogenic lines (which differ only by the presence or absence of the target gene and a small region of surrounding DNA), leads to the rapid identification of sequences linked to the gene of interest. The feasibility of this method has been demonstrated by analyzing a pair of tomato near-isogenic lines that differ for a region on chromosome 5 that contains a gene (Pto) conferring resistance to Pseudomonas syringae pv. tomato. One hundred forty-four random primers were screened on these lines, and seven amplified products were identified that were present in one but not the other line. Of four products that were further investigated, three were confirmed by segregation analysis to be tightly linked to the Pto gene. Linked sequences identified by this method are useful for detecting the presence of the target gene in plant populations (e.g., in plant breeding) and, if very tightly linked, as starting points for a chromosome walk to isolate the gene. Since near-isogenic lines are a typical product of plant breeding and classical genetic studies, this method is applicable to a wide variety of species.

Exon amplification: a strategy to isolate mammalian genes based on RNA splicing.

Abstract: We have developed a method, exon amplification, for fast and efficient isolation of coding sequences from complex mammalian genomic DNA. This method is based on the selection of RNA sequences, exons, which are flanked by functional 5' and 3' splice sites. Fragments of cloned genomic DNA are inserted into an intron, which is flanked by 5' and 3' splice sites of the human immunodeficiency virus 1 tat gene contained within the plasmid pSPL1. COS-7 cells are transfected with these constructs, and the resulting RNA transcripts are processed in vivo. Splice sites of exons contained within the inserted genomic fragment are paired with splice sites of the flanking tat intron. The resulting mature RNA contains the previously unidentified exons, which can then be amplified via RNA-based PCR and cloned. Using this method, we have isolated exon sequences from cloned genomic fragments of the murine Na,K-ATPase alpha 1-subunit gene. We have also screened randomly selected genomic clones known to be derived from a segment of human chromosome 19 and have isolated exon sequences of the DNA repair gene ERCC1. The sensitivity and ease of the exon amplification method permit screening of 20-40 kilobase pairs of genomic DNA in a single transfection. This approach will be extremely useful for rapid identification of mammalian exons and the genes from which they are derived as well as for the generation of chromosomal transcription maps.

A rapid procedure for extracting genomic DNA from leukocytes

Abstract: 1. Collect 5 ml of blood in a vacutainer tube (Becton Dickinson) containing EDTA and mix. 2. Make volume up to 10 ml with solution 1 (10 mM Tris pH 7.6; 10 mM KC1; 10 mM MgCy. 3. Add 120 /il Nonidet P40 (BDH) to lyse the cells. Mix well by inverting several times. 4. Spin down the nuclear pellet at 2000 rpm for 10 mins. 5. Pour off the supernatant without dislodging the pellet. The pellets can be stored frozen. 6. Gently resuspend pellet well in 800 /il of solution 2 (10 mM Tris pH 7.6; 10 mM KC1; 10 mM MgCl2; 0.5 M NaCl; 0.5% SDS; 2 mM EDTA). Solution 2 will lyse the nuclei so be careful not to shear the DNA. Transfer to a 1.5 ml microcentrifuge tube. 7. Add 400 /il of distilled phenol (saturated with 1 M Tris pH 8.0) and mix well. 8. Microfuge for 1 min at 12000 rpm. Transfer upper phase to a clean microfuge tube. Do not worry about transferring a little of the interface. 9. Add 200 /tl of phenol and 200 /il of chloroform :isoamyl alcohol (24:1). Mix well by inverting. 10. Spin for 1 min at 12000 rpm. Transfer upper phase to a clean microfuge tube. 11. Add 700 /tl of chloroform:isoamyl alcohol and extract as above. 12. Transfer upper aqueous phase to a small clean container. Avoid removing the interface. Add 2 volumes of ice cold ethanol and mix to precipitate the DNA*. 13. With the sealed tip of a pasture pipette, transfer the DNA fibres to a microcentrifuge tube containing 1 ml of 70% ethanol. Mix well to wash the DNA. 14. Spin for 5 mins at full speed. Discard the ethanol and dry pellet in a speed vac. Resuspend DNA in sterile water at 65°C. Do not over-dry genomic DNA or it will be difficult to resuspend. SIZE A / /Kb Hindll l

Identification of a second human nm23 gene, nm23-H2.

Abstract: Reduced RNA and/or protein levels corresponding to the murine nm23-1 and human nm23-H1 complementary DNA clones have been correlated with high tumor metastatic potential in several rodent model systems and human breast carcinomas. We report the identification of a second human nm23 gene, designated nm23-H2. The pNM23-H2S complementary DNA clone predicted a Mr 17,000 protein 88% identical to nm23-H1. nm23-H2 also shared a significant homology with nucleoside diphosphate kinases and a Drosophila developmental gene. Southern blots containing BglII-restricted genomic DNA, which exhibited an allelic restriction fragment length polymorphism for nm23-H1, contained nonallelic bands upon rehybridization to the nm23-H2 probe. Thus, nm23-H1 and nm23-H2 are distinct genes. Northern blot hybridization of nm23-H1- and nm23-H2-specific probes to breast tumors and cell lines indicated that nm23-H1 expression was reduced in high metastatic potential tumor cells to a greater extent than nm23-H2. The data indicate the existence of a family of independently regulated nm23 genes.

A genomic scanning method for higher organisms using restriction sites as landmarks.

Abstract: We have developed a powerful genomic scanning method, termed "restriction landmark genomic scanning," that is useful for analysis of the genomic DNA of higher organisms using restriction sites as landmarks. Genomic DNA is radioactively labeled at cleavage sites specific for a rare cleaving restriction enzyme and then size-fractionated in one dimension. The fractionated DNA is further digested with another more frequently occurring enzyme and separated in the second dimension. This procedure gives a two-dimensional pattern with thousands of scattered spots corresponding to sites for the first enzyme, indicating that the genome of mammals can be scanned at approximately 1-megabase intervals. The position and intensity of a spot reflect its locus and the copy number of the corresponding restriction site, respectively, based on the nature of the end-labeling system. Therefore, this method is widely applicable to genome mapping or detection of alterations in a genome.

Analysis of Interstrain Variation in Cytomegalovirus Glycoprotein B Sequences Encoding Neutralization-Related Epitopes

Abstract: Nucleotide sequences of a part of the envelope glycoprotein B (gB) gene of human cytomegalovirus (CMV), encoding epitopes recognized by virus-neutralizing monoclonal antibodies, were determined for 12 distinct clinical strains of CMV after amplification of suitable templates using the polymerase chain reaction. Sequence analysis of this region (codons 384-717) revealed that the clinical strains and previously sequenced laboratory strains Towne and AD169 belong to one of four variant groups, each with a characteristic nucleotide and peptide sequence. Peptide homology was greater than 99% for strains within a group, and varied from 91% to 98% for strains in different groups. Variation was most frequent between codons 448 and 480. The gB group of a CMV strain could be determined by restriction analysis of a small target sequence amplified from viral genomic DNA, and an additional 28 clinical strains were grouped in this manner. The existence of a limited number of variants of gB among clinical strains facilitates analysis of biologic function and cross-reactivity of immune responses.

Complete Structure of the Human Gene for 92-kDa Type IV Collagenase

Abstract: The complete structure of the human gene for 92kDa type IV collagenase was determined. Two overlapping genomic clones spanning 26 kilobases (kb) of genomic DNA were shown to contain the entire 7.7-kb structural gene together with 15 and 3.5 kb of 5’-end and 3’-end flanking regions, respectively. The 92-kDa type IV collagenase gene contains 13 exons as does the 72-kDa type IV collagenase gene. All intron locations of the 92-kDa enzyme gene coincided with intron locations in the 72-kDa enzyme gene. Exons 5,6, and 7 which were 174, 174, and 177 base pairs long, respectively, each encoded one complete internal repeat which resembles the collagen-binding domains of fibronectin. The sequence coding for a unique 48-residue segment in the 92-kDa type IV collagenase that has no counterpart in other metalloproteinases was not present in a separate exon, but was contained in exon 9 which also codes for sequences with homology to the

Human monoamine oxidase A gene determines levels of enzyme activity.

Abstract: Monoamine oxidase (MAO) is a critical enzyme in the degradative deamination of biogenic amines throughout the body. Two biochemically distinct forms of the enzyme, A and B, are encoded in separate genes on the human X chromosome. In these studies we investigated the role of the structural gene for MAO-A in determining levels of activity in humans, as measured in cultured skin fibroblasts. The coding sequence of the mRNA for MAO-A was determined by first-strand cDNA synthesis, PCR amplification, and direct dideoxy sequencing. Two single-basepair substitutions were observed in cDNAs from cells with a 30-fold difference in activity levels. These two substitutions were in the third base of a triplet codon and hence did not affect the deduced amino acid sequence but did affect the presence or absence of restriction-enzyme sites for EcoRV and Fnu4HI, which could be elucidated on PCR fragments derived from genomic DNA or cDNAs. A third polymorphism for MspI in the noncoding region of the MAOA gene was also evaluated by Southern blot analysis using genomic DNA. Statistically significant associations were observed between the alleles for MAOA and levels of MAO activity in human male fibroblast lines. This association indicates that the MAOA gene itself is a major determinant of activity levels, apparently, in part, through noncoding, regulatory elements.

p53 is frequently mutated in Burkitt's lymphoma cell lines.

Abstract: A panel of 12 Burkitt's lymphoma cell lines and four other B cell lines were tested for the presence of mutations in p53. Protein analysis using a mutant-specific antibody and sequencing of both cDNA and genomic DNA revealed changes relative to the standard p53 protein sequence in 12 of the 16 lines studied, including 10 of the BL lines. Mutation of p53 in the BL lines was usually accompanied by loss of the other allele of p53. Testing of the mutated p53 cDNAs for gain of transforming activity or loss of growth suppression activity showed that several of the BL mutants were functionally altered from wild-type p53.

Abundance and DNA sequence of two-base repeat regions in tropical tree genomes.

Abstract: Tandem DNA repeats of two-base pairs are potentially important tools for population genetic studies because of their abundance and length variation. As part of our research into the ecology of tropical forest plants, we began a study of dinucleotide repeat regions in several genera of tropical trees. Genomic libraries in bacteriophage lambda were screened with the oligonucleotide probes poly(GT) and poly(AG). Both types of repeat regions were abundant in the genomes of all six plant species examined. Using the size of inserts in the phage libraries and number of phage screened, we estimated that there were 5 x 10(3) to 3 x 10(5) poly(AC) sites per genome, with slightly more AG than AC sites. When libraries were made from smaller fragments of genomic DNA, abundance estimates were higher, suggesting that two-base repeat sites were clustered in the genome. Poly(AC) sites were 16-22 bp in length, and four of the five sequenced were adjacent to either poly(AG)or poly(AT) sites. Other repeat region s appeared in DNA flanking the AC sites. This further demonstrated that two-base repeats and other repetitive DNA were clustered in the genome. Two-base repeats are abundant in plant genomes and could provide a large number of polymorphic markers for studies of plant population genetics.

Genomic DNA fingerprinting by pulsed-field gel electrophoresis as an epidemiological marker for study of nosocomial infections caused by methicillin-resistant Staphylococcus aureus.

Abstract: In this study, we have compared genomic DNA fingerprintings among isolates of methicillin-resistant Staphylococcus aureus (MRSA) by using pulsed-field gel electrophoresis (PFGE). Chromosomal fragments digested with SmaI were most suitable for the PFGE separation. SmaI cut genomic DNA into 15 to 20 fragments whose sizes ranged from about 30 to 1,500 kb. Thirty-one distinctive fragment patterns were identified in 111 infecting and colonizing MRSA isolates from six different hospitals in Japan. On the basis of the genomic typing by PFGE, we performed an epidemiological investigation of an outbreak of nosocomial MRSA infections among inpatients in Nagoya University Hospital. Ten types of chromosomal digestion were identified in the 20 strains isolated from 18 infected patients and 1 from colonized hospital personnel. According to the restriction patterns, we found that four types of these strains had caused epidemic infections among 13 patients in the outbreak. Two types (types 1 and 4) of the strains were involved in the death of five patients. The other infections were sporadic. The clarity and polymorphism of the chromosomal digestion patterns enabled us to discriminate between isolates which could not be differentiated by antibiogram or plasmid analysis. Classification of the genomic DNA fingerprinting patterns by PFGE is therefore proposed as a useful method for investigating the source, transmission, and spread of nosocomial MRSA infections.

Cloning genes by complementation in yeast.

Abstract: Publisher Summary This chapter describes the use of genomic and cDNA banks to isolate specific genes by complementation in Saccharomyces cerevisiae. The most straightforward approach to cloning genes from plasmidborne banks is complementation of a recessive marker. A recipient strain is constructed that carries a recessive mutation in the gene of interest as well as a nonreverting null allele of the chromosomal cognate of the selectable marker carried on the plasmid vector, This strain is then transformed with pools of plasmids from a bank constructed from wild-type genomic DNA. Transformants are recovered by selecting for eomplementation by the vector-borne selectable marker. Cloning genes that are defined by dominant alleles is a straightforward extension of cloning by complementation of recessive alleles. The only difference is that the clone bank has to be constructed de novo from genomic or cDNA prepared from the strain carrying the dominant mutation. In the absence of any direct information about the identity of a gene or its gene product, one recourse is to isolate a set of genes whose regulation fulfills some interesting set of criteria. One approach to achieving this end has been to clone random genomic fragments into a plasmid carrying an enhancerless promoter that drives expression of a readily scored gene, such as lacZ. Random transformants are then examined for conditional expression of lacZ in response to the desired signal.

cDNA selection: efficient PCR approach for the selection of cDNAs encoded in large chromosomal DNA fragments.

Abstract: Identification of coding segments in large fragments of genomic DNA is a recurrent problem in genome mapping and positional cloning studies. We have developed a rapid and efficient protocol to achieve this goal, based on hybridization of cDNA fragments to immobilized DNA and recovery of the selected cDNAs by the PCR. The procedure permits rapid cloning of cDNA fragments encoded by large genomic DNA fragments, groups of yeast artificial chromosomes, or cosmids and has the potential to directly enrich cDNAs encoded in chromosome segments. By this approach we have been able to identify several non-major histocompatibility complex class I clones from a yeast artificial chromosome that includes the HLA-A locus.

Characterization of anastomosis groups of binucleate Rhizoctonia species using restriction analysis of an amplified ribosomal RNA gene.

Abstract: Seven U.S. and 16 Japanese binucleate Rhizoctonia anastomosis tester isolates, representing 21 different anastomosis groups, were characterized by restriction analysis of a ribosomal RNA (rRNA) gene. Genomic DNA was extracted from each isolate and a region of DNA coding for a portion of the 25S rRNA (rDNA) was amplified using the polymerase chain reaction. Five tester isolates (CAG1, AGF, AGI, AGJ, and AGK) produced either two or three bands ranging from 1.4 to 1.8 kilobases (kb), whereas five other tester isolates (CAG5, AGBa, AGC, AGD, and AGH) produced a single, 1.8-kb fragment (...)

Platelet-derived growth factor receptor alpha-subunit gene (Pdgfra) is deleted in the mouse patch (Ph) mutation

Abstract: Platelet-derived growth factor receptors are composed of two subunits (alpha and beta) that associate with one another to form three functionally active dimeric receptor species. The two subunits are encoded by separate loci in humans and other species. In this study, we used conventional interspecific backcross mapping and an analysis of a deletional mutation to establish close linkage between the alpha-subunit gene (Pdgfra) and the dominant spotting (W) locus on mouse chromosome 5. Further, by analyzing the restriction fragment length polymorphisms in interspecific F1 hybrids, we were able to demonstrate that the closely associated patch (Ph) locus carries a deletion in Pdgfra. This observation was confirmed by both DNA and RNA analysis of 10.5-day fetuses produced from crosses between Ph heterozygotes. Out of 16 fetuses analyzed, Pdgfra genomic sequences were absent and no mRNA for the receptor was detected in 6 fetuses that were developmentally abnormal (the presumptive Ph homozygotes). We also determined that the deletion associated with the Ph mutation does not extend into the coding sequences of the adjacent Kit gene, by analysis of the genomic DNA from both the interspecific F1 hybrids and the presumptive Ph homozygotes. The absence of Pdgfra genomic sequences and the lack of detectable message associated with the Ph mutation should make this mutant a valuable asset for understanding the role of the receptor alpha subunit during mammalian development.

Molecular analysis of a human interferon-inducible gene family.

Abstract: Three functional members of the 1–8 gene family have been isolated on a single human genomic DNA fragment of less than 18 kb. The 1–8U and 1–8D genes are extremely similar: each is contained within a 90% identity over 70% of the coding sequence. For the 1–8U and D genes the high similarity extends into the 5′ non-coding and flanking regions. The open reading frames encode polypeptides that are likely to be of very similar structure. Antiserum to a conserved peptide detects a polypeptide(s) of about 14 kDa on PAGE which separates into three components on isoelectric focussing. The 9–27 and 1–8U genes are highly interferon-inducible, the 1–8D gene is much less so. These differences are mimicked by the activities of the corresponding ISREs placed 5′ of a marker gene in expression constructs. They presumably reflect differences in the interaction of the ISREs with the various interferon-inducible and constitutive factors that govern the interferon response.

Transformation of the oomycete pathogen, Phytophthora infestans.

Abstract: A stable transformation procedure has been developed for Phytophthora infestans, an oomycete fungus that causes the late blight diseases of potato and tomato. This is the first description of reliable methods for transformation in an oomycete pathogen. Drug-resistant transformants were obtained by using vectors that contained bacterial genes for resistance to hygromycin B or G418 fused to promoters and terminators from the Hsp70 and Ham34 genes of the oomycete, Bremia lactucae. Using polyethylene glycol and CaCl2, vector DNA was introduced into protoplasts as a complex with cationic liposomes or with carrier DNA only. Transformants were obtained at similar frequencies with each combination of promoter and selectable marker and were confirmed by DNA and RNA hybridization and phosphotransferase assays. Transformation occurred through the integration of single or tandemly repeated copies of the plasmids into genomic DNA, conferring mitotically stable drug-resistant phenotypes. The sizes of the marker gene mRNAs in each transformant and the results of transcript mapping studies were consistent with the function of the B. lactucae regulatory sequences in P. infestans. A hygromycin-resistant transformant was tested and found to maintain pathogenicity, indicating that the gene transfer procedure will be useful for the molecular analysis of genes relevant to disease.

A frameshift mutation destabilizes androgen receptor messenger RNA in the Tfm mouse.

Abstract: A composite mouse androgen receptor DNA sequence was obtained by amplifying genomic DNA or cDNA using the polymerase chain reaction. The open reading frame was 2,697 basepairs, encoding a polypeptide of 899 amino acids (98,204 mol wt). Amino acid sequence comparisons indicated that the mouse androgen receptor (AR) is 97% homologous with rat AR and 83% with human AR. The amino acid sequences of the three receptors are identical within the DNA- and steroid-binding domains. Northern blot analysis revealed the predominant mouse AR mRNA to be 10 kilobases (kb). A 1.7-kb mRNA species was detected in mouse kidney using a cDNA probe containing only 5′ untranslated AR sequence. Lack of hybridization with AR-coding sequence probes suggested that the 1.7-kb mRNA was not a truncated form of AR mRNA. Sequencing of genomic DNA isolated from testicular feminized (Tfm) mice revealed a single base deletion in the N-terminal domain, resulting in a frameshift mutation. Cycloheximide treatment caused a dramatic increase in A...

Mutations in the p53 gene in primary human breast cancers.

Abstract: Twenty-six primary breast tumors were examined for mutations in the p53 tumor suppressor gene by an RNase protection assay and nucleotide sequence analysis of PCR-amplified p53 complementary DNAs. Each method detected p53 mutations in the same three tumors (12%). One tumor contained two mutations in the same allele. Single strand conformation polymorphism analysis of genomic DNA and complementary DNA proved more sensitive in the detection of mutations. Combining this technique with the other two a total of 12 mutations in the p53 gene were demonstrated in 11 tumors (46%), and a polymorphism at codon 213 was detected in another tumor. Loss of heterozygosity on chromosome 17p was detected by Southern blot analysis in 30% of the tumor DNAs. Not all of the tumors containing a point mutation in p53 also had loss of heterozygosity of the remaining allele, suggesting that loss of heterozygosity may represent a later event.

In vivo mapping of a DNA adduct at nucleotide resolution: detection of pyrimidine (6-4) pyrimidone photoproducts by ligation-mediated polymerase chain reaction.

Abstract: DNA adducts in unique sequences along the mammalian genome are mapped in vivo at single-nucleotide resolution. Pyrimidine (6-4) pyrimidone photoproducts [(6-4) photoproducts] represent one of the two major adduct classes found after UV irradiation of DNA and were shown to play an important role in UV-induced mutagenesis. After UV light treatment of cells, DNA is prepared and chemically cleaved at (6-4) photoproducts with piperidine. Gene-specific fragments are then amplified from total genomic DNA by use of a ligation-mediated polymerase chain reaction. Analysis of the human chromosome X-linked phosphoglycerate kinase (PGK1) gene's promoter has shown that the frequency of (6-4) photoproducts expressed as piperidine-labile sites is (i) high at TpC and CpC dinucleotides, (ii) dependent on the nearest-neighbor bases, (iii) inhibited by the binding of a transcription factor, and (iv) different for DNA derived from the active and inactive X chromosome. This latter difference is mainly a consequence of the presence of 5-methylcytosine (m5C) in CpG dinucleotides on the inactive X chromosome. 5-Methylcytosine in the sequences Tm5CG and Cm5CG inhibits the formation of (6-4) photoproducts. Thus, in addition to in vivo mapping of a DNA adduct at nucleotide resolution, we also report another method for methylation analysis and photofootprinting.