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PubMed1999

p53 immunoreactivity and single-strand conformational polymorphism analysis often fail to predict p53 mutational status.

The intent of this study was to investigate the ability of p53 expression and single-strand conformational polymorphism analysis (SSCP) to predict p53 mutational status in archival, paraffin-embedded tissues of gastric cancer. We evaluated paraffin-embedded tissues from 78 patients with advanced gastric cancer. The mutational status of the p53 gene (exons 5-9) was examined by SSCP analysis and by direct sequencing. These results were compared with p53 expression as assessed by immunohistochemical analysis (IHC). We graded p53 expression on a scale from 0 to 8 on the basis of both the intensity and the number of cells staining. Overall, we detected p53 immunoreactivity in 75.6% of the gastric cases; 19 (32.2%) of these cases scored from 1 to 4, and 40 (67.8%) cases scored from 5 to 8. p53 gene mutations were detected in 18 cases (23.1%) by SSCP and in 28 cases (36%) by direct sequencing. Thus, SSCP failed to detect 38% of the mutations found by sequencing. The majority of missed mutations involved exons 7 and 8. The concordance between IHC and SSCP was 37%, and the concordance between IHC and direct sequencing was 50%. Forty-five percent of cases positive by IHC failed to show mutations in exons 5 through 9. Five percent of cases negative by IHC (4 cases) contained mutations. One had a 1-base pair insertion; one had a mutation that resulted in a stop codon; the third had a mutation in exon 8; and the fourth had a mutation in both exons 5 and 8. Our findings indicate that p53 immunoreactivity correlates with the presence or absence of gene mutations in 50% of advanced gastric cancers when exons 5 through 9 are examined and that IHC cannot be reproducibly used as a marker of mutation in the most commonly mutated exons of the p53 gene. Furthermore, the sensitivity of SSCP for detecting mutations is only 62%. Thus, SSCP analysis cannot be used reliably to screen for p53 mutations.

Base Sequence↗
PubMed2006

Allelic losses of chromosome 10 in glioma tissues detected by quantitative single-strand conformation polymorphism analysis.

BACKGROUND: Detection of loss of heterozygosity (LOH) in clinical tissue samples is frequently difficult because samples are usually contaminated with noncancerous cells or because tumor cells in single tissues have genetic heterogeneity, and the precision of available techniques is insufficient for reliable analysis in such materials. We hypothesized that single-strand conformation polymorphism (SSCP) analysis can precisely quantify the gene dosage in mixed samples and is suitable for detection of LOH in clinical tissue samples. METHODS: We assessed the accuracy of a fluorescent SSCP method for the quantification of single-nucleotide polymorphism (SNP) alleles, using DNAs that were composed of cancerous DNA mixed with noncancerous DNA at various ratios. We applied this method to precisely characterize LOH in glioma tissue samples, using 96 SNPs that were evenly distributed throughout chromosome 10. RESULTS: LOH could be detected even in the cancerous DNA heavily contaminated (up to 80%) with noncancerous DNA. Using this method, we obtained LOH profiles of 56 gliomas with resolution at the SNP level (i.e., 1.5-Mbp interval). Anaplastic astrocytomas exhibited both 10p and 10q LOH, whereas diffuse astrocytomas frequently (63% of the cases) exhibited loss of 10p alone. We also found a possible new LOH region (around 10p13) in gliomas. CONCLUSIONS: The present method is effective for precise mapping of LOH region in surgically obtained tumor tissues and could be applicable to the genetic diagnosis of cancers other than gliomas.

Alleles↗
PubMed1994

Rapid detection of phenylketonuria mutations by non-radioactive single-strand conformation polymorphism analysis.

A non-radioactive single-strand conformation polymorphism (SSCP) method was used to detect various phenylketonuria (PKU) mutations in Japanese and Chinese patients. Arginine413-to-proline (R413P) mutation in exon 12 of the phenylalanine hydroxylase gene was identified in a Japanese patient by this method. The segregation of the R413P mutation in the proband's family was clearly demonstrated and the carrier status of each family member was determined. Analysis of DNA fragments containing exon 7 originated from Chinese patients revealed two mutations, arginine243-to-glutamine (R243Q) and arginine261-to-glutamine (R261Q), and a polymorphism, valine245-to-valine (V245V). Although R261Q has been identified previously among Caucasian subjects, this report is the first to describe this mutation among Orientals. Since the non-radioactive SSCP method employs pre-cast acrylamide gels and pre-made gel buffer strips combined with semi-automated temperature-controlled electrophoresis, it can be performed without much expertise in molecular biological techniques. The ability of this method to detect various mutations as demonstrated in this study and its ease of use make it feasible to detect PKU mutations in a routine DNA diagnostic laboratory.

Asian People↗
PubMed2000

Single strand conformation polymorphism analysis of ras oncogene by capillary electrophoresis with laser-induced fluorescence detector.

Single strand conformation polymorphism (SSCP) analysis of the N-ras oncogene was achieved by capillary electrophoresis with a laser-induced fluorescence detector (CE-LIF) using methylcellulose as a molecular sieving agent. The PCR-amplified N-ras oncogene, which is known to have a point mutation at codon 61 in the neuroblastoma, was investigated by CE-LIF combined with SSCP (SSCP-CE-LIF). A mixture of wild- and mutant-type single strand DNA fragments (103 bp) of the N-ras oncogene was separated by buffer solution containing 1.0% methylcellulose and 0.2 microM fluorescent dye (YO-PRO-1) at 25 degrees C. The SSCP-CE-LIF technique gave good resolution for wild- and mutant-type single strand DNA fragments with separation completed within 7 min. SSCP analysis using a CE system with a LIF detector was successfully applied to the detection of the one point mutation on the N-ras oncogene.

Base Sequence↗
PubMed1996

Relative ratios of mRNA molecules encoded by genes with homologous sequences using fluorescence-based single-strand conformation polymorphism analysis.

The combination of reverse transcribed (RT)-PCR and fluorescence-based single-strand conformation polymorphism (SSCP) analysis is proposed for the quantitative determination of the ratio of mRNA molecules with homologous sequences. We applied this procedure to lactate dehydrogenase (LDH) subunits A and B. We designed fluorescence labeled common PCR primers in the sequences highly homologous between LDH-A and LDH-B cDNAs and performed RT-PCR-SSCP analysis. When PCR efficiency was almost the same between the different target sequences, analysis of mixtures of known amounts of LDH-A and LDH-B revealed linear and precise proportions of LDH-A mRNA. Template concentrations and PCR cycles did not affect the determination of proportions of LDH-A to total LDH. The present procedure could be easily applied to investigation of expression levels of genes encoding mRNAs with homologous sequences.

Amino Acid Sequence↗
PubMed1993

Methods in laboratory investigation. Rapid and simple detection of c-Ki-ras2 gene codon 12 mutations by nonradioisotopic single-strand conformation polymorphism analysis.

BACKGROUND: To achieve simple and rapid detection of codon 12 mutations of the c-Ki-ras2 gene, we developed a nonradioisotopic single-strand conformation polymorphism analysis using silver stain. EXPERIMENTAL DESIGN: After a conventional polymerase chain reaction, amplified DNA fragments were mixed with formamide, heated and subjected to electrophoresis for 1.5 hours using minigels of polyacrylamide. The gels were then silver stained and single-strand DNA fragments were visualized directly. RESULTS: Electrophoresis and subsequent silver staining were completed within 2.5 hours. Plasmids carrying various codon 12 mutations of the c-Ki-ras2 gene were used as controls of Nonradioisotopic single-strand confirmation polymorphism analysis, and all six mutations were successfully separated from the normal allele in a single electrophoretic run. In the analysis of tumor cell lines and tumor samples, the results were identical with those of conventional dot blot hybridization using 32P-labeled oligonucleotide probes. Of 10 colorectal carcinoma tissues examined, 4 tumors were shown to carry codon 12 mutations of the c-Ki-ras2 gene. CONCLUSIONS: We conclude that this novel technique is a rapid, simple and useful method that may replace conventional methods.

Alleles↗
PubMed1997

Characterization of colominic acid by circular dichroism and viscosity analysis.

Conformations of oligo- and poly-(alpha (2-->8)-D-Neu pNAc) (colominic acid) and its derivatives were studied by circular dichroism (CD) spectroscopy and viscometry to understand the molecular basis of their unusual antigenic properties. No temperature-dependent conformational transition between 5 and 70 degrees C or divalent salt effect of Ca2+ or Mg2+ was observed in colominic acid or its N-deacetylated form by CD spectroscopy. However, CD spectroscopy indicated that the distribution of conformers in oligocolominic acid changes continuously from n = 2 to octamer, and there was no further change of the conformer distribution for n > 9. Colominic acid exhibited a much lower intrinsic viscosity compared with the values for other polyelectrolytes of similar linear charge density, such as polynucleic acids. The apparent absence of induced conformational transition by salt or temperature, and the high flexibility indicated that the binding of colominic acid to its antibodies may not contain a significant amount of specific conformationally controlled determinant. Instead, our data suggest that more than nine saccharide units are needed for a cooperative binding process.

Calcium↗
PubMed1991

Detection of frequent p53 gene mutations in primary gastric cancer by cell sorting and polymerase chain reaction single-strand conformation polymorphism analysis.

Mutations of the p53 gene were investigated after tumor cell enrichment by cell sorting based on differences in DNA content and polymerase chain reaction single-strand conformation polymorphism analysis in 24 surgical specimens of primary gastric cancer. p53 mutations were detected in exons 4-8 in 64% (9 of 14) of aneuploid tumors but in none of 10 diploid tumors examined. Four of five tumors containing two or three aneuploid subpopulations showed the presence of p53 gene mutations. No correlation was found between the presence of p53 mutations and the degree of histological differentiation of tumors. These findings suggest that p53 gene mutations are related to DNA ploidy alterations as relatively late events of carcinogenesis in gastric cancer. The present method is highly sensitive for detection of genetic abnormalities and is applicable even when various kinds of nontumorous cells are present in tumor samples.

Base Sequence↗
PubMed2003

Single-stranded conformational polymorphism analysis using automated capillary array electrophoresis apparatuses.

We describe a new environment of a single-stranded conformational polymorphism (SSCP) analysis using automated capillary array sequencers (e.g., ABI Prism 3100 and 3700). In this environment, electrophoretic conditions, settings for instrument management, and software for data analysis are adjusted for SSCP analysis. Highly reproducible results are obtained with this new system, and fragments with mutations and/or polymorphisms in different capillaries or different runs can be reliably detected. The relative peak heights between alleles are quantitative and reproducible between runs, and so allele frequencies of single nucleotide polymorphisms can be accurately estimated by a pooled DNA strategy. The method allows unattended, low-cost, and quantitative SSCP analysis using instruments that are widely accessible.

Alleles↗
PubMed1995

Studies in patients with corticosteroid contact allergy. Understanding cross-reactivity among different steroids.

BACKGROUND AND DESIGN: Most corticosteroid-allergic patients react to several corticosteroids. Irrefutable proof for the existence of cross-reactions is provided by reactions to substances to which the patient has never been exposed. Four groups of cross-reactions have been proposed, and our own observations support this. However, we have found that budesonide, in particular, tends to be involved not only in cross-reactions with corticosteroids of its own group (group B) but also with those of the ester group (group D). To test clinical observations on patients sensitive to corticosteroids and to establish a molecular basis for cross-reactivity patterns, a statistical analysis of our cases and a conformational study of major corticosteroids were performed. RESULTS: Statistically highly significant positive or negative correlations were found for the combination of tixocortol pivalate plus hydrocortisone and hydrocortisone plus budesonide, respectively. This indicates that budesonide and hydrocortisone or tixocortol pivalate detect different groups of corticosteroid-sensitive patients. Moreover, significant positive correlations were found between budesonide and amcinonide, both molecules belonging to the acetonide group C, and also between budesonide and some esters of group D such as hydrocortisone-17 butyrate and alclometasone dipropionate. These clinical observations were fully supported by a conformational analysis of the electronic shape of corticosteroids involved in this study. Groups A, B, and D were found to be highly homogeneous within each group in terms of molecular structures, while significant differences were observed among the groups. The special behavior of budesonide can be fully explained on the base of its unique molecular structure. Finally, molecular characteristics have been defined for each group. This could be useful for the prediction of potential cross-reactions to new corticosteroid molecules. CONCLUSIONS: The statistical analysis confirms that tixocortol pivalate and hydrocortisone contact allergies are definitely associated, while reactions to budesonide are strongly correlated with the reactions to both the acetonide group and the ester group. These clinical observations are fully supported by the conformational analysis of the molecules involved in this study. Tixocortol pivalate and budesonide should certainly be added to the standard series for the detection of patients sensitized to corticosteroids.

Adrenal Cortex Hormones↗
PubMed1972

A molecular theory of ion-conductng channels: a field-dependent transition between conducting and nonconducting conformations.

Structural and conformational requirements for an electric field-dependent transition between conducting and nonconducting macromolecular systems are: two kinetically interconvertible and energetically similar conformations, one conducting and the other nonconducting, which have axes spanning the lipid layer of biological membranes, but which have different net dipole moments along those axes. Two examples are described. A previously defined helix, the pi(6)LD-helix now termed the beta(6) (3,3)-helix, is proposed as the conducting species, and the linear peptide correlate of the cyclic hexapeptide conformation containing two beta-turns and an inversion element of symmetry is proposed as a nonconducting species. The latter is termed an anti-beta(6) (2)-spiral and contains little or no net dipole moment per turn, whereas the beta(6) (3,3)-helix contains a net dipole moment along the helix axis of about 0.5 Debye per dipeptide unit. A related conducting and nonconducting pair with large net dipole moments of opposite sign, termed syn-beta(6) (2)-spiral and beta(6) (2,4)-helix, are also described. The spiral conformations are stabilized in a lipid layer by intermolecular hydrogen bonds, leading to a linear association of transmembrane structures. A conformational transition in one member of the array could lead to destabilization of an adjacent member of the array. The conformational analysis uses a concept of cyclic conformations with linear conformational correlates. The anti-beta(6) (2)-spiral and beta(6) (3,3)-helix are derivable from the conformations of the cyclic structure [unk], whereas the syn-beta(2)-spiral and beta(6) (2,4)-helix may be derived from the cyclic structure [unk].The conformational analysis leads to the expectation that N-formyl-(L-Ala-L-Ala-Gly)(n) would form conducting channels.

Amino Acid Sequence↗
PubMed1998

Rapid detection of K-ras gene mutations in canine lung cancer using single-strand conformational polymorphism analysis.

A total of 126 spontaneous lung tumors from pet dogs were examined for K-ras mutations within exon 1 and exon 2 using a non-radioisotope single-strand conformational polymorphism analysis (SSCP) detection method on PCR products. Mutations were confirmed by direct DNA sequencing. Tumors were classified as adenomas (9), bronchioloalveolar carcinomas (59), adenocarcinomas (30), adenosquamous carcinomas (16), squamous cell carcinomas (3) and anaplastic carcinomas (9). Nineteen mutations were detected in the malignant tumors: 18 occurred in exon 1 codon 12 and one in exon 2 codon 61. No mutations were present in the adenomas. The most common mutation was a G-->A transition (11/19) in the second position of codon 12. Based on this study, K-ras mutations occur in canine non-small cell lung carcinomas. The frequency and type of mutation more closely matches tumors from human non-smokers with K-ras mutations than smokers. With the application of screening techniques such as SSCP, large numbers of dog tumors can be examined to provide a large animal model for comparative studies of carcinogenesis.

Animals↗
PubMed2000

Fluorescence-based single-strand conformation polymorphism analysis of mutations by capillary electrophoresis.

Capillary electrophoresis in combination with fluorescence-based single-strand conformation polymorphism (SSCP) analysis was used to screen for known mutations as well as for unknown mutations. The mutations causing hemochromatosis and thrombogenetic diseases (factor V Leiden mutation and prothrombin mutation) are well defined. Familial hypercholesterolemia is caused by mutations in the low density lipoprotein (LDL) receptor gene. Because the mutations are heterogeneously localized in all 18 exons of the LDL receptor gene, effective screening procedures are necessary. The three well known mutations and 59 of 61 previously characterized mutations in the LDL receptor gene were detected by a distinct abnormal fragment pattern in capillary electrophoresis. The remaining two mutations in the LDL receptor gene showed only slight abnormalities under standard electrophoresis conditions (13 kV, 30 degrees C, 30 min). However, the abnormal pattern could be amplified by increasing the electrophoresis temperature. In all cases, heterozygous and homozygous mutations could clearly be differentiated from wild-type alleles. Because of the high efficiency of mutation detection, capillary electrophoresis in combination with fluorescence-based SSCP analysis would be attractive for the detection of well-defined mutations as well as for the screening of unknown mutations. The accuracy and the degree of automation make this technique well suited for routine genetic diagnosis.

Animals↗
PubMed1996

Single-strand conformation polymorphism analysis of RT-PCR products of UK isolates of barley yellow mosaic virus.

Single-strand conformation polymorphism (SSCP) analysis of the bipartite genomes of several UK isolates of barley yellow mosaic virus (Ba YMV) was done using fragments of cDNA amplified by RT-PCR. Isolates differed in their SSCP patterns in several regions, but in no case was the pattern able to distinguish between common and resistance-breaking strains. In regions where the nucleotide sequences of UK isolates had been determined, there was no simple relationship between numbers of nucleotide differences and SSCP patterns: differences of only 2 or 3 nucleotides (nt) gave different SSCP patterns, whereas differences of as many as 29 nt did not. Although SSCP analysis has some potential as a rapid and sensitive tool for distinguishing virus isolates, differences detected do not necessarily relate to biological properties and the results are highly dependent on gel conditions.

Acrylic Resins↗
PubMed1994

Detection of point mutations in the androgen receptor gene using non-isotopic single strand conformation polymorphism analysis. German Collaborative Intersex Study Group.

Point mutations in the androgen receptor gene cause androgen insensitivity syndromes, clinically characterized by masculinization defects in karyotypic males due to endorgan resistance to androgenic steroids. Characterization of these mutations with single strand conformation polymorphism analysis utilizing radioactive PCR can serve as a diagnostic tool for molecular subclassification of these syndromes. It is the basis for genetic counseling and for therapeutic decisions. Here we report an improved non-radioactive single strand polymorphism analysis for rapid detection of androgen receptor gene mutations in affected individuals. In addition to previously reported mutations, 10 patients with clinical features of androgen resistance were studied. DNA was isolated from peripheral blood leucocytes and exons 1 to 8 of the coding region of the androgen receptor gene amplified by PCR. Amplification products were denatured and run on non-denaturing gels. These were subjected to fixation and silver staining. Variations were directly sequenced. In all patients a different point mutation in one of the exons was detected. While one insertion mutation was found in a patient with complete androgen insensitivity, all other mutations cause amino acid substitutions. These data suggest that the described non-radioactive single strand polymorphism analysis is a useful tool for the characterization of androgen receptor gene mutations. The omission of radioisotopes is advantageous in a clinical setting. The mutations described emphasize the clinical and molecular heterogeneity of this disease.

Amino Acid Sequence↗
PubMed1993

Mutations in the p53 gene in human astrocytomas: detection by single-strand conformation polymorphism analysis and direct DNA sequencing.

The p53 gene was examined in a series of formalin-fixed paraffin-embedded astrocytic neoplasms of various types by polymerase chain reaction (PCR), single-strand conformation polymorphism analysis (SSCP), and direct sequencing of amplified DNA. PCR primers were designed to amplify three DNA fragments encompassing exons 5, 7, and 8 with splice sites, including all four mutational "hot spots" within this gene. SSCP was performed in a polyacrylamide gel containing 10% glycerol. Two mutations were found among the 20 high and intermediate grade adult astrocytomas studied by this sensitive screening technique and confirmed by sequencing of the PCR product. (1) An anaplastic astrocytoma disclosed a T-A transversion in Codon 246 giving rise to a methionine to lysine amino acid substitution. (2) A giant cell glioblastoma disclosed a G to A transition in Codon 285 resulting in a glutamic acid to lysine substitution. Both mutations were associated with loss of the normal allele. Twenty-three DNA fragments that disclosed no mutation by SSCP analysis were confirmed to be negative by direct sequencing of amplified DNA. No mutations were detected in a series of eight juvenile cerebellar astrocytomas, a biologically distinct form of low-grade astrocytoma. Mutations of the p53 gene may play an important pathogenetic role in a subset of human astrocytomas.

Adult↗
PubMed2003

Molecular epidemiological investigation of Ascaris genotypes in China based on single-strand conformation polymorphism analysis of ribosomal DNA.

Using a single-strand conformation polymorphism-based approach, we investigated nucleotide variation in part of the first internal transcribed spacer (pITS-1) of nuclear ribosomal DNA within and among a large number of Ascaris individuals from humans and pigs from six endemic regions in China, and examined the frequency of the different genotypes of Ascaris in relation to host species and geographical origin. Five different SSCP genotypes (G1-G5) were recorded for human Ascaris (n = 486), of which three (genotypes G1-G3) were detected for pig Ascaris (n = 329). Of the five Ascaris genotypes detected, genotype G1 predominantly infected humans (approximately 63-74%) whereas genotype G3 infected mainly pigs (approximately 79-86%), indicating that each of these genotypes has a particular host affiliation. In contrast, the frequencies of the other three genotypes was substantially lower for each of the two host species. The findings also suggested that the rate of cross infection of Ascaris between humans and pigs is relatively low and that gene flow between the predominant genotypes is limited, consistent with previous proposals for endemic regions in other countries. While the nature and extent of nucleotide variation in the pITS-1 (and the proposal of host affiliated Ascaris populations) may relate to "introgression" or "lineage sorting and retention of ancentral polymorphism", other explanations are possible. Evidence of multiple pITS-1 sequence types in some Ascaris individuals representing particular genotypes (e.g., G2 and G5) may suggest hybridization between human- and pig-affiliated Ascaris. This aspect and the species status of Ascaris (from each host species) warrant future experimental testing, employing the pig/Ascaris model and the present electrophoretic approach.*

Animals↗
PubMed2003

Simultaneous genotyping of alcohol dehydrogenase 2 and aldehyde dehydrogenase 2 by single-strand conformation polymorphism analysis.

Alcohol dehydrogenase (ADH; EC 1.1.1.1) and aldehyde dehydrogenase (ALDH; EC 1.2.1.3) have important roles in the elimination of ingested ethanol. These enzymes have polymorphisms resulting from single-point mutations that cause kinetic differences in their respective enzyme activities. Simultaneous observation of these enzymes would be useful in investigating the association between these enzyme polymorphisms and alcohol-related problems. In this study amplified genomic DNA was amplified from nail clippings with two sets of primers for ADH2 and ALDH2 genes, respectively, in a micro test tube and the accuracy of the amplification was verified by direct sequencing. The PCR products were separated into four distinct bands by single-strand conformation polymorphism analysis. This genotyping method is fast, accurate. reliable and inexpensive, and requires the same amount of template DNA as non-simultaneous methods. In other words, the required amount of template DNA for this method is only half that required for the separate genotyping of ADH2 and ALDH2.

Alcohol Dehydrogenase↗