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PubMed1993

Exploiting structural differences among heteroduplex molecules to simplify genotyping the DQA1 and DQB1 alleles in human lymphocyte typing.

A novel approach to DNA probe hybridization and heteroduplex analysis, termed directed heteroduplex analysis (DHDA) is presented here to illustrate its utility in simplification of human lymphocyte antigen (HLA)-typing. By strategic labeling of single-stranded probe sequences, DHDA allows the identification of specific heteroduplex structures that contribute to the differentiation of DQA1 and DQB1 alleles. Because of the high degree of polymorphism among major histocompatibility complex class II second exon sequences, this analysis of 50 different heteroduplex molecules provides evidence of the importance of unpaired bases and mismatched base pairs and their effect on heteroduplex electrophoretic-mobility differences. This strategy is further used to genotype accurately a family for DQA1 which was previously analyzed by sequence specific oligonucleotide (SSO) probe hybridization. To differentiate by SSO-typing among the DQA1 and DQB1 alleles analyzed in this study requires the use of 23 different probes. Equivalent results are obtained by DHDA using only three probes. Therefore, this study suggests that accurate HLA-typing can be simplified by DHDA. Additionally, DHDA may be useful for differentiation of DNA sequence polymorphisms in other genetic systems.

Alleles↗
PubMed1997

Exon-by-exon screening for RB germline mutations using Heteroduplex-SSCP analysis.

OBJECTIVE: To disclose the nature of RB1 germline mutations in Chinese and to develop a practical and effective way for mutational screening. METHODS: Leukocyte DNA was prepared from 8 Chinese patients with hereditary retinoblastoma. PCR combined with nonisotopic heteroduplex-SSCP analysis was used to screen leukocyte DNA for RB1 germline mutations, exon-by-exon, without the use of restriction endonuclease digestion. The mutations were finally identified by sequencing. In order to testify the effectiveness of this method, the same method was used to detect other 17 samples which have been previously analyzed by other methods. RESULTS: Heterozygous germline mutations were detected in the leukocyte DNA of 6 out of 8 Chinese patients: G del/codon 46, T del/codon 131, CAGAA del/codon 257-258, GCAgta-->GCAgca/donor of exon 16, C-->T/codon 661, and C-->T/codon 787. Heteroduplex-SSCP analysis may detect RB1 germline mutations in 68% (17/25) unselected patients, which is more effective than SSCP(56%) or heteroduplex analysis(64%) alone. The corrected RB1 mutation detection rate may be 80% if the samples were previously analyzed by Southern blotting, which is much higher than those reported on literature. CONCLUSION: Mutations involving a few base pairs in RB1 gene are common in Chinese. Heteroduplex-SSCP analysis is more useful and effective than SSCP or heteroduplex analysis alone for the rapid screening for unknown mutations.

Female↗
PubMed2001

Ribosomal DNA spacer genotypes of the Anopheles bancroftii group (Diptera: Culicidae) from Australia and Papua New Guinea.

Mosquitoes of the Anopheles bancroftii group collected from Northern Australia and Papua New Guinea (PNG) were investigated for sequence variation within the ribosomal DNA ITS2. Wing fringe morphology originally used to identify members of this group was compared to genotypes identified by restriction fragment length polymorphism analysis (RFLP) and heteroduplex analysis (HDA) of the rDNA ITS2. Members of this group separated into four RFLP genotypes (A, B, C and D) with some genotypes displaying wing fringe polymorphisms. Heteroduplex analysis of the ITS2 within and between populations identified genotype A as containing two geographically separate ITS2 sequences: A1 from the Northern Territory of Australia and A2 from Queensland and the Western Province of PNG. Genotypes B and C and genotypes C and D were found sympatric and appeared to be evolving independently suggesting the possibility of cryptic species. Genotype C contained two ITS2 sequence types within the genome.

Animals↗
PubMed1994

Polymerase chain reaction heteroduplex polymorphism analysis by entangled solution capillary electrophoresis.

Heteroduplex DNA polymorphism analysis (HPA) makes use of conformational polymorphisms to alter electrophoretic mobility of fragments and can be used to detect non-restrictable loci. We have developed a novel application of entangled solution capillary electrophoresis (ESCE) to separate heteroduplex and homoduplex DNA molecules. The addition of ethidium bromide and glycerol to the free solution sieving buffer resulted in the improved peak resolution and good reproducibility. Reannealed polymerase chain reaction products could be used directly for mutation screening and with fully automated ESCE the entire HPA may be completed in less than 30 min including sample handling. This technology could provide a rapid and highly efficient way for screening rare mutations among large numbers of individuals.

Base Sequence↗
PubMed1983

Heterology of mitochondrial DNA from mammals detected by electron microscopic heteroduplex analyses.

Heteroduplex analysis of mitochondrial DNA (mtDNA) from evolutionary closely related mammals (rat vs. mouse, man vs. monkey) are analyzed and compared to heteroduplex analysis of mt-DNA from more distantly related mammals (rat vs. man, rat vs. monkey, mouse vs. man, mouse vs. monkey and man vs. cow). Each analysis is transformed into a heteroduplex map and all maps are aligned to restriction enzyme maps and to genetic maps and where possible compared with the known sequence. We show that early evolutionary changes are seen mainly in URF2, URFA6L, URF6 and the D-loop region. The regions of rRNA, URF1, COI and COIII are generally very conserved regions but areas with some evolutionary activity can be localized. Heteroduplex analysis between distantly related species show much more heterology than do closely related species and the heteroduplex maps between all the distantly related species show a common pattern of heterology. Comparisons between the DNA sequence of mtDNA from man, cow and mouse and the equivalent heteroduplex maps show that base pair homologies higher than 73% are displayed as homologous regions. In the heteroduplex analysis of mtDNA's from more closely related species very few heterologies are displayed at 50% formamide but an increase in formamide concentration to 65-70% demonstrate also in these instances general heterologous regions.

Animals↗
PubMed2001

Point mutation and polymorphism in Duchenne/Becker muscular dystrophy (D/BMD) patients.

Duchenne and Becker muscular dystrophies (D/BMD) are caused by mutations in the dystrophin gene. Two-thirds of patients have large intragenic deletions or duplications and the remaining one-third have point mutations, small deletions or insertions. Point mutations are more difficult to detect due to the enormous size (2.4 Mb) of the gene and its large transcript (14 kb). In the present study, a total of 50 DNA samples from unrelated D/BMD (38 DMD and 12 BMD) patients who did not show intragenic deletions by multiplex PCR, were analyzed for detection of point mutations. Single stranded conformation analysis and heteroduplex analysis observed electrophoretic mobility shifts in one (BMD) and two (DMD and BMD) patients, respectively. The mobility shift and heteroduplexes were observed in exon 17 in all of the three patients. Sequencing of the amplified PCR products revealed a nucleotide change (-37 g to t) in the intronic region in two of the patients while a C2268T substitution in the exonic region in one. Mutation database search for D/BMD mutations showed the nucleotide substitution in the exonic region as a novel change in the human dystrophin gene, which was not reported earlier. It resulted in an amino acid transition from threonine to methionine in the 687th position of the dystrophin protein. This novel substitution has been included in the mutation database of Leiden muscular dystrophy pages (http://www.dmd.nl) in the rare polymorphism/mutation category. The substituted nucleotide segregated with the disease phenotype in the family suggesting that it can be directly used for carrier detection and prenatal diagnosis without identification of disease causing mutation.

Amino Acid Sequence↗
PubMed2005

Human enterovirus isolates from an outbreak typed using heteroduplex mobility analysis.

Genotyping and serotyping of enteroviruses is important for epidemiological, prognostic, and therapeutic reasons. In this study clinical isolates of enterovirus 71 during an outbreak of childhood meningoencephalitis in Sydney, Australia were identified using heteroduplex mobility analysis (HMA) of products from RT-PCR amplification of the 5' untranslated region. Five enterovirus 71 isolates shared identical heteroduplex patterns and nucleotide sequences in the 5' untranslated region. A sixth isolate exhibited minor differences in heteroduplex pattern and sequencing confirmed the isolate varied by 1% at the nucleotide level. The use of multiple reference strains and the analysis of heteroduplex patterns increased the confidence of isolate identification, and allowed identification of strain variation which could be subsequently further analyzed using sequencing. HMA can be used to accurately distinguish identical and variant isolates derived from sporadic cases and clustered infections with enteroviruses, including those causing serious infections.

5' Untranslated Regions↗
PubMed1995

Susceptibility mutations in the mitochondrial small ribosomal RNA gene in aminoglycoside induced deafness.

Aminoglycoside induced deafness has been linked recently to a predisposing homoplasmic mutation in the 3' end of the small ribosomal RNA (rRNA) gene of the human mitochondria (1555 A-->G) that makes the mitochondrial rRNA structurally more similar to its bacterial counterpart. This mitochondrial DNA mutation was consistently found in families in which the susceptibility to develop ototoxic deafness was inherited through the maternal lineage. However, the 1555 A-->G mutation was rarely found in sporadic patients in China, where a significant proportion of the population has been exposed to aminoglycosides. To further characterize the mutations predisposing to aminoglycoside ototoxicity, we analysed the 12S rRNA gene in 35 Chinese sporadic patients without the 1555 A-->G mutation. Using single stranded conformational polymorphism (SSCP) analysis, heteroduplex (HD) analysis, sequencing, and allele specific oligonucleotide hybridization, we found three out of 35 sporadic patients with unique sequence changes in the 12S rRNA gene. Two of the patients had homoplasmic mutations. One patient displayed localized heteroplasmy around nt 961, with an absence of the thymidine at this position and different populations of mitochondrial DNA with varying numbers of inserted cytosines. The description of these putative susceptibility mutations, in particular the heteroplasmic mutation around nt 961, provides further support for the important role of the mitochondrial 12S rRNA in genetic predisposition to aminoglycoside induced ototoxic deafness.

Aminoglycosides↗
PubMed1997

NF1 mutation analysis using a combined heteroduplex/SSCP approach.

Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder characterized predominantly by neurofibromas, café-au-lait spots, and Lisch nodules. The disease is caused by disruptive mutations of the large NF1 gene, with half of cases caused by new mutation. Less than 100 constitutional mutations have thus far been published, ranging from very large deletions to point mutations. We have pursued NF1 mutation analysis by heteroduplex analysis (HDA) and single-strand conformational polymorphism analysis (SSCP) of individual exons. We streamlined these techniques to eliminate the use of radioactivity, to apply both methods to the same PCR product, and to multiplex samples in gels. Applied simultaneously to a set of 67 unrelated NF1 patients, HDA and SSCP have thus far identified 26 mutations and/or variants in 45 of the 59 exons tested. Disease-causing mutations were found in 19% (13/67) of cases studied. Both techniques detected a variety of mutations including splice mutations, insertions, deletions, and point changes, with some overlap in the ability of each method to detect variants.

Base Sequence↗
PubMed1983

DNA restriction--modification genes of phage P1 and plasmid p15B. Structure and in vitro transcription.

The EcoP1 and EcoP15 DNA restriction-modification systems are coded by the related P1 prophage and p15B plasmid. We have examined the organization of the genes for these systems using P1 itself, "P1-P15" hybrid phages expressing the EcoP15 restriction specificity of p15B and cloned restriction fragments derived from these phage DNAs. The results of transposon mutagenesis, restriction cleavage analysis. DNA heteroduplex analysis and in vitro transcription mapping allow the following conclusions to be drawn concerning the structural genes. (1) All of the genetic information necessary to specify either system is contained within a contiguous DNA segment of 5 x 10(3) bases which encodes two genes. One of them, necessary for both restriction and modification, we call mod and the other, required only for restriction (together with mod), we call res. (2) The res gene is about 2.8 x 10(3) bases long and at the heteroduplex level is largely identical for P1 and P15: it shows a small region of partial nonhomology and some restriction cleavage site differences. The mod gene is about 2.2 x 10(3) bases long and contains a 1.2 x 10(3) base long region of non-homology between P1 and P15 toward the N-terminus of the gene. The rest of the gene at this level of analysis is identical for the two systems. (3) Each of the genes is transcribed in vitro from its own promoter. It is possible that the res gene is also transcribed by readthrough from the mod promoter.

Coliphages↗
PubMed1999

A recurrent frameshift mutation in exon 19 of the type VII collagen gene (COL7A1) in Mexican patients with recessive dystrophic epidermolysis bullosa.

Dystrophic epidermolysis bullosa (DEB) is an inherited blistering skin disorder caused by mutations in the type VII collagen gene (COL7A1). In this study, we determined the molecular basis of autosomal recessive DEB in a 19-year-old Hispanic Mexican woman by PCR amplification of genomic DNA, heteroduplex analysis, and automated sequencing of heteroduplex bandshifts. This approach revealed a homozygous frameshift mutation, 2470insG, in exon 19 of COL7A1 and resulted in attenuated basement membrane zone expression of type VII collagen, a reduced number of anchoring fibrils at the dermal-epidermal junction, and a sub-lamina densa level of blister formation. Clinically, the patient had widespread trauma-induced skin fragility and complete loss of the nails, but had less pseudosyndactyly of the fingers and toes and milder mucosal involvement compared to most patients with the generalized form of this genodermatosis. We also screened 7 other Hispanic-Mexican patients with recessive DEB, none of whom were known to be related to this individual, for the mutation 2470insG using heteroduplex analysis and direct sequencing and detected this mutation on 7/14 alleles. Haplotype analysis using intragenic COL7A1 and flanking polymorphisms and microsatellite markers revealed that all the mutant alleles had arisen on similar allelic backgrounds, consistent with propagation of a common Hispanic Mexican ancestral haplotype. In view of the high allelic frequency of the mutation 2470insG in the patients studied, we recommend initial screening for this mutation when attempting to identify the molecular pathology of recessive DEB in Hispanic Mexican patients.

Adult↗
PubMed2001

Ullrich scleroatonic muscular dystrophy is caused by recessive mutations in collagen type VI.

Ullrich syndrome is a recessive congenital muscular dystrophy affecting connective tissue and muscle. The molecular basis is unknown. Reverse transcription-PCR amplification performed on RNA extracted from fibroblasts or muscle of three Ullrich patients followed by heteroduplex analysis displayed heteroduplexes in one of the three genes coding for collagen type VI (COL6). In patient A, we detected a homozygous insertion of a C leading to a premature termination codon in the triple-helical domain of COL6A2 mRNA. Both healthy consanguineous parents were carriers. In patient B, we found a deletion of 28 nucleotides because of an A --> G substitution at nucleotide -2 of intron 17 causing the activation of a cryptic acceptor site inside exon 18. The second mutation was an exon skipping because of a G --> A substitution at nucleotide -1 of intron 23. Both mutations are present in an affected brother. The first mutation is also present in the healthy mother, whereas the second mutation is carried by their healthy father. In patient C, we found only one mutation so far-the same deletion of 28 nucleotides found in patient B. In this case, it was a de novo mutation, as it is absent in her parents. mRNA and protein analysis of patient B showed very low amounts of COL6A2 mRNA and of COL6. A near total absence of COL6 was demonstrated by immunofluorescence in fibroblasts and muscle. Our results demonstrate that Ullrich syndrome is caused by recessive mutations leading to a severe reduction of COL6.

Base Sequence↗
PubMed1985

An electron microscopic heteroduplex study of the sequence relations between the bacteriophages LP52 and theta.

The genomes of the phylogenetically related but morphologically distinct bacteriophages LP52 and theta (theta) were compared by electron microscopic heteroduplex analysis. The heteroduplex maps were aligned with known restriction maps. In the heteroduplices of LP52 DNA (63.8 kb) with the DNA of the lytic phage theta c (65.9 kb) the tracts of homologous DNA cover about 50% of the genome length and are interspaced by four large and ten smaller non-base-paired regions. The largest block of non-homologous DNA (18.9 kb), represents the right-hand end and there is an unmatched piece of DNA at the left-hand end as well. Most of the heterology is due to substitution resulting in the conservation of the total length of DNA; the three insertions/deletions amount to less than 3.2% of the genome length. Heteroduplices between the DNAs of phage LP52 and the temperate phage theta 1 (65.0 kb) resembled those of LP52:theta c except for the absence of minor loops. Heteroduplex theta c:theta 1 displayed about 9% heterology in seven separate loops which coincided with sections of diversity on the restriction maps; 4.8% of theta 1 DNA did not hybridize with either theta c or LP52 DNA.

Bacillus↗
PubMed1982

Restriction fragment maps of the genome of Bacillus subtilis bacteriophage SP beta.

Six different restriction endonucleases were used to generate restriction fragment maps of the genome of the temperate Bacillus subtilis phage SP beta. AvaI and SalI each had six target sites in the phage DNA, AvaII had three, BamHI had seven, PstI had twenty, and SacI had sixteen. Restriction analysis and heteroduplex analysis were used to locate a 10-kb region of DNA that is deleted in the clear-plaque mutant, SP beta cl. The deletion lay approx. 50 kb from the left end of the 126-kb phage genome.

Bacillus subtilis↗
PubMed1995

Mucopolysaccharidosis IVA: screening and identification of mutations of the N-acetylgalactosamine-6-sulfate sulfatase gene.

Mutations causing mucopolysaccharidosis IVA in 15 Japanese and one Caucasian patient were characterized. To screen these mutations, we used a combination of single strand conformation polymorphism analysis and heteroduplex analysis for PCR products of targeted cDNA or genomic DNA. Various small mutations were identified in 23 of 26 alleles, while the other six alleles had large rearrangements. Cycle sequencing of PCR products revealed 15 different mutations, including 12 missense, one nonsense, one frame shift (2 bp deletion) and one splice site mutation, in accord with the broad range of clinical phenotypes. Two alleles have different mutations in the same nucleotide position of exon 3 (R94C, CGC-->TGC; R94G, CGC-->GGC), diagnosed by sequencing and by allelic-specific oligohybridization (ASO). One allele had two amino acid changes, E450V in exon 12 and V488M in exon 13, thereby indicating a double point mutation. All 16 mutations reported were confirmed by restriction enzyme assay or by allelic-specific oligohybridization. Transfection of mutagenized cDNAs into patients' fibroblasts showed that all mutations caused completely deficient or markedly decreased N-acetylgalactosamine-6-sulfate sulfatase (GALNS) activity, thereby indicating that these mutations were responsible for the enzyme deficiency.

Alleles↗
PubMed1999

Comparison of prophylactic oophorectomy specimens from carriers and noncarriers of a BRCA1 or BRCA2 gene mutation. United Kingdom Coordinating Committee on Cancer Research (UKCCCR) Familial Ovarian Cancer Study Group.

BACKGROUND: The natural history of ovarian cancer is not well understood and, to date, there is conflicting evidence as to whether or not there is a demonstrable precursor lesion. Some women at high risk of developing ovarian cancer because of their family history elect to have a prophylactic oophorectomy. To determine whether or not a recognizable premalignant lesion could be defined in familial ovarian carcinogenesis, we reviewed ovarian tissue specimens from women whose ovaries were removed prophylactically before gene testing became available and who were tested subsequently for BRCA1 or BRCA2 gene mutations. METHODS: We analyzed ovarian tissue specimens from 37 women. The specimens were examined for the presence of the following four features: inclusion cysts, clefts and fissures, ovarian epithelial metaplasia, and the presence of papillae on the ovarian surface epithelium. The specimens were also examined closely for the presence of dysplasia and occult neoplasia. Furthermore, the occurrence of endometriosis and benign ovarian tumors was documented in these women. The protein truncation test, nonradioactive single-stranded conformation polymorphism analysis, and heteroduplex analysis, followed by DNA sequencing, were used to identify BRCA1 or BRCA2 mutations in either blood samples or ovarian tissue specimens. RESULTS: Eleven women had inherited a mutated BRCA1 or BRCA2 gene; 26 women had not. There was no difference between these groups for any of the features studied. CONCLUSIONS: Our data suggest that many of the histologic "abnormalities" described in "normal" ovaries are, in fact, variations of the normal and are not associated with the development of cancer.

Adult↗
PubMed1999

Mutation screening of the CHRNA4 and CHRNB2 nicotinic cholinergic receptor genes in Alzheimer's disease.

Potential genomic changes leading to decreased nicotine binding, crucial for cognitive dysfunction in Alzheimer's disease (AD), have not yet been studied. A search for mutations of the genes coding for the most widely distributed nicotinic receptor subtype alpha4beta2 (CHRNA4/CHRNB2) has been performed in AD patients by screening the coding regions of both genes by single strand conformation analysis and heteroduplex analysis of fibroblast-derived genomic DNA. Polymorphisms in CHRNA4, none of which led to amino acid changes in the predicted sequence, were found in three patients. Although the other receptor subunits have yet to be screened, it appears likely that the reduction of nicotine binding sites in AD is not due to genomic changes.

Aged↗
PubMed1984

Physical state and transcription of the cottontail rabbit papillomavirus genome in warts and transplantable VX2 and VX7 carcinomas of domestic rabbits.

The physical state and the transcription of the genome of cottontail rabbit papillomavirus (CRPV) in non-virus-producing warts and in the VX2 and VX7 transplantable carcinomas of domestic rabbits were compared. The CRPV DNA present in VX2 and VX7 carcinomas (10 to 20 and 100 to 200 genome equivalents per diploid cell, respectively) was found to be entirely integrated into the cellular DNA, most probably as head-to-tail tandem repeats, in contrast to warts, in which viral DNA (10 to 100 copies per diploid cell) was found only as free, mainly monomeric, molecules. In the VX7 tumor, ca. 50% of the viral DNA molecules were found to be longer than one genome length, indicating that viral DNA rearrangements had occurred. A major viral transcript of 1,250 bases was detected in warts and in VX2 and VX7 carcinomas. Complementary sequences were localized within the E region, the putative transforming region inferred from the nucleotide sequence of the CRPV genome (I. Giri, O. Danos, and M. Yaniv, manuscript in preparation). Analysis of heteroduplexes formed between single-stranded CRPV DNA and polyadenylated RNAs from the VX2 tumor showed that the 1,250-base RNA resulted from the splicing of the sequences corresponding to the open reading frame E6 to those corresponding to the 3' third of E2. A second viral transcript, measuring 2,000 bases, was detected in warts and, in lesser amounts than the 1,250-base species, in VX2 carcinoma, and a 2,100-base RNA was found in VX7 carcinoma. Complementary sequences to these messengers were localized to the same part of the genome as the 1,250-base species and to a contiguous fragment situated upstream. Heteroduplex analysis showed that the 2,000-base species from VX2 carcinoma resulted from the splicing of the sequences corresponding to E6 and E7 to those corresponding to the 3' third of E2. The sequences spliced out upon the maturation of the two messengers of VX2 carcinoma correspond to E1, the two-thirds of E2, and most of E4. Additional transcripts were found in VX7 carcinoma, a major 3,100-base species transcribed from the E region, and several minor species, measuring from 2,400 bases, which all hybridize with a subgenomic fragment contained in the L region encoding the viral capsid polypeptides. This could account for the antiviral antibodies found in animals bearing the VX7 carcinoma.

Animals↗