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At least 1,261 records · Page 70Linked to original sources
PubMed1992

Detection of a Ha-ras point mutation by polymerase chain reaction-single strand conformation polymorphism analysis in 2-amino-3,4-dimethylimidazo[4,5-f]quinoline-induced mouse forestomach tumors.

Ha-ras activation in forestomach squamous cell carcinomas of CDF1 mice induced by 2-amino-3,4-dimethylimidazo[4,5-f]quinoline (MeIQ), one of the heterocyclic amines isolated from broiled sardine was analyzed. Mutations were detected in two of three primary original carcinomas and two of four cell lines derived from other independent carcinomas by the polymerase chain reaction followed by analysis of single strand conformation polymorphism and direct sequencing. All the mutations detected were G----T transversions at the second letter of codon 13 resulting in an amino acid change from Gly to Val. This finding together with the previous reports on squamous cell carcinomas of the rat Zymbal gland suggest that MeIQ induces a specific type of mutation at a specific site of the Ha-ras gene during squamous cell carcinogenesis, in a species-independent manner.

Animals↗
PubMed1983

Theoretical conformational studies on some dopamine antagonistic benzamide drugs: 3-pyrrolidyl- and 4-piperidyl derivatives.

Model derivatives of 3-pyrrolidyl- and 4-piperidyl-o-methoxybenzamides, as representatives of neuroleptic substituted benzamide drugs, have been investigated by theoretical conformational analysis. Folded conformers of 2-methoxy-N-(1-methyl-3-pyrrolidyl)benzamide have the lowest energy, but extended conformers are only a few kilocalories per mole less stable. As regards to piperidyl derivative, it has been found that folded conformers are of much higher energy than extended ones. These and previous results are discussed in terms of the pharmacologically active conformers of substituted benzamide drugs and of possible modes of interaction with the dopamine receptor.

Animals↗
PubMed2002

Leucamide A: a new cytotoxic heptapeptide from the Australian sponge Leucetta microraphis.

Leucamide A (1), a bioactive cyclic heptapeptide containing a unique mixed 4,2-bisheterocycle tandem pair consisting of a methyloxazole and thiazole subunit was isolated together with the known compound BRS1 (2), from the dichloromethane extract of the Australian marine sponge Leucetta microraphis. The planar structure of leucamide A (1) was elucidated by employing spectroscopic techniques (NMR, MS, UV, and IR). Its absolute stereochemistry was established by chemical degradation, derivatization, and chiral GC[bond]MS analysis. A conformational analysis of 1 was made using MMFF. Leucamide A (1) was found to be moderately cytotoxic toward several tumor cell lines.

Amino Acids↗
PubMedDate not supplied

[Conformation of a triple collagen spiral as a function of primary structure].

It has been shown by the method of conformational analysis that conformation of the polypeptide chain of a collagen molecule varies from one type of sequence to another, but in all the sequences the only two types of conformations can be characterized by minimal conformational energy. The collagen molecule as a whole is a combination of the single-bond Rich and Crick model and new double-bonded structure. Rigorous comparison with "thick" conformations obtained by Scheraga and coworkers was undertaken using precise calculations with flexible proline.

Amino Acid Sequence↗
PubMed1997

High resolution single strand conformation polymorphism analysis using formamide and ethidium bromide staining.

Single strand conformation polymorphism (SSCP) analysis using ethidium bromide can be improved by adding formamide as the denaturant. This gives higher resolution than previous SSCP methods; it had 100% sensitivity in the discrimination of 14 PCR samples from two different genes, even for a long fragment close to the upper limit of 250 base pairs. This modified procedure is a rapid, simple, safe, and yet highly sensitive method for detecting structural differences in DNA fragments.

Catechol O-Methyltransferase↗
PubMed1993

Two new mutations detected by single-strand conformation polymorphism analysis in cystic fibrosis from Russia.

Single-strand conformation polymorphism (SSCP) analysis followed by direct sequencing of exons containing ATP-binding domains of the cystic fibrosis transmembrane conductance regulator (CFTR) gene was performed on 80 Russian DNA samples. Two new alterations--S1196X (exon 19) and W1282R (exon 20)--and two novel polymorphisms--1525-61 (intron 9) and 1716+12 T-C (intron 10)--were identified. Mutation S1196X changes a TCA codon to TGA and destroys an EcoRI site. Alteration W1282R results from a T-to-C change at position 3976. It was found in one Russian patient and creates an AciI site; however, it is unclear whether this is a disease-causing mutation or a polymorphism. Polymorphism 1525-61 results from an A-to-G change. Alteration 1716+12 T-C was found in a Moldovian patient and creates a new MaeII site. It is not known whether this alteration affects the splicing of the mRNA. The previously described A4002G polymorphism was encountered in approximately 9% of Russian CF chromosomes. In addition, we have found the previously described 3732delA mutation in 7 CF chromosomes, making it the second (after delta F508) most frequent mutation in the Russian population.

Cystic Fibrosis↗
PubMed2004

Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing.

The diversity of Archaea in anaerobic digesters was characterized by strand conformation polymorphism (SSCP) analysis and the sequencing of 16S rDNA genes. The 44 digesters sampled, located in eight different countries, treated effluents from agriculture, the food processing and petro-chemical industries, pulp and paper plant, breweries, slaughterhouses and municipal waste. All the existing processes were represented among the samples (fixed-film, fluidized bed, stirred-tank, UASB, sequential batch reactor, lagoon). Single strand conformation polymorphism analysis targeting the V3 region of 16S rDNA revealed between four to six distinct archaeal peaks per digester. The diversity of dominant Archaea in the 44 digesters was estimated as 23 different 16S rDNA sequences. Cloning of archaeal 16S rRNA genes from 11 distinct total genomic DNA, screening of clones by SSCP and the sequencing of 170 of them made it possible to characterize these SSCP peaks. All the sequences retrieved were members of the Euryarchaeaota subdomain. Furthermore, most of the sequences retrieved were very close to already known and cultivated strains or to environmental clones. The most frequent archaeal sequences were close to Methanosaeta concilii and to a 16S rDNA clone vadinDC06 located in the Methanobacterium clade (84% and 73% of digesters respectively). The other sequences were members of the Methanobacteriales and the Methanomicrobiales families. Only one sequence was far from any sequence of the database and it could be grouped with several sequences of environmental clones. Each digester harboured between two to nine archaeal sequences with only one of them corresponding to a putative acetate-utilizing species. Furthermore, the process in the digesters appeared to play a part in the distribution of archaeal diversity.

Acetates↗
PubMed1994

Single-strand conformation polymorphism analysis of human decorin, biglycan and fibromodulin cDNAs.

The coding regions of the human decorin, biglycan and fibromodulin cDNAs have been examined utilizing the method of single-strand conformation polymorphism analysis. Analysis of total RNA from a group of eight human skin fibroblast cell lines did not detect any sequence variations in the decorin cDNA. In contrast, the analysis detected three sequence variations in the biglycan cDNA and one in the fibromodulin cDNA from the same group of cell lines. For the biglycan cDNA, one variation involved a position in the 5'-untranslated region, while the other two affected the wobble bases of triples encoding serine residues 10 and 143 of the mature core protein. For the fibromodulin cDNA, the variation involved the wobble position of the codon for glutamic acid residue 61 of the putative mature core protein. Single-strand conformation polymorphism analysis of these proteoglycan cDNAs was also applied to study patients exhibiting a variety of connective tissue pathologies, including chondrodysplasia punctata, Desbuquois syndrome, Dyggve-Melchior-Clausen syndrome, dyssegmental dysplasia, Ehlers-Danlos syndrome types I and III, Ellis van Creveld syndrome and thanatophoric dysplasia, though no additional sequence variations were detected.

Base Sequence↗
PubMed1995

Intracranial germ cell tumors: detection of p53 gene mutations by single-strand conformation polymorphism analysis.

Using polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis, p53 gene mutation was examined in 12 intracranial germ cell tumors (5 yolk sac carcinomas and 7 germinomas), many of which were derived from young patients in the first to the second decade. A total of 10 mutations were detected in 4 of the 12 cases and, in 3 of them, the mutations were multiple or tandem. Among the 10 mutations, 7 were missense, 1 was splicing and 2 were silent. The 7 missense mutations were located at previously proposed hot spot codons or in their vicinity or, when outside the hot spots, at a codon encoding an amino acid conserved in most vertebrates. These findings suggested that all 7 missense mutations may actually give rise to functional alteration of the p53 protein. The splicing mutation was considered to be a germ-line mutation, though its biological effect was equivocal, since the neoplastic tissue contained an additional mutation. The pattern of the mutations was predominancy of G:C-A:T transition with frequent involvement of the CpG site. These mutations were more frequently detected in yolk sac carcinomas (60%; 3/5 cases) than in germinomas (14%; 1/7 cases), suggesting that the contribution of the p53 mutation to carcinogenesis differed with the histological type of the intracranial germ cell tumor.

Adolescent↗
PubMed1992

Detection of mutations in the p53 gene in human head and neck carcinomas by single strand conformation polymorphism analysis.

Using the polymerase chain reaction (PCR)-based single strand conformation polymorphism (SSCP) analysis, we have examined the highly conserved regions of the p53 gene in 58 biopsy samples of head and neck tumors. Mutations were found in 13/58 (23%) tumor specimens, but not in 6 normal tissues. Ten of 13 mutations were due to single base changes and the remaining 3 were 1- or 8-base deletion mutants. These mutations were clustered in exons 5 and 7 and resulted in amino acid changes. Our results seem to indicate that mutations in the p53 gene contribute to a significant number of cases of the head and neck tumors including 20% of nasopharyngeal carcinoma biopsies. The relationship of Epstein-Barr virus or human papillomavirus and p53 gene mutations in this group of cancers was also analyzed and discussed.

Base Sequence↗
PubMed1993

The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions.

Single-strand conformation polymorphism (SSCP) analysis has proven to be a simple and effective technique for the detection of single base substitutions. We have used SSCP to analyze 29 mouse globin mutations, 27 p53 mutations, and 8 rhodopsin mutations contained within different size PCR products. Our results indicate that the type of mutation (transition versus transversion) did not play a major role in determining whether a mutation was detected by SSCP analysis. The position of the base substitution was more important than the precise base substitution in determining whether a mutation was detected. We report that SSCP sensitivity varies dramatically with the size of the DNA fragment being analyzed. The optimal size fragment for sensitive base substitution detection by SSCP is approximately 150 bp. Our results illustrate the need to keep the size of the PCR fragment small when performing SSCP to detect mutations. Larger fragments can be analyzed when screening for polymorphisms when the need to detect every sequence variation is not as critical.

Animals↗
PubMed1985

The study of conformational states of proteins by nuclear magnetic resonance.

By the use of examples, mainly of rather rigid proteins, we hope to have shown that conformational analysis of proteins is a problem that is not simply related to the conformational analysis of small molecules. The primary difficulties with proteins are (1) the multitude of possible conformers, (2) the complex dynamical behaviour and (3) the degree of co-operativity within the molecules. Any experimentally derived structural description of a protein is an attempt to represent some average of a complex time dependence. N.m.r. techniques have now reached the point where it is possible to use them to describe many detailed structural features of small globular proteins in solution and to detect and to describe conformational changes in such proteins. In addition, analysis is becoming possible of much less ordered regions of polypeptides, such as are found in less compact proteins, of for example myosin, histones and virus coat proteins, or in denatured states. The limits to the detailed conformational analysis of such proteins are likely to be ones of reality rather than method but the description of the properties shown in Table 1 is by its very nature an extremely important problem in conformational analysis of dynamic macromolecules.

Cytochrome c Group↗
PubMed1997

Optimization of single-strand conformation polymorphism analysis in the presence of polyethylene glycol.

We report optimization of single-strand conformation polymorphism (SSCP) analysis in the presence of polyethylene glycol. The protocol developed separates single-strand conformers in a much shorter time (1-3 h) than conventional SSCP protocols and broadens the applicability of SSCP analysis from 150 to as much as 500 bp of DNA by different percentages of GC content present. We conclude that addition of polyethylene glycol helps improve the differential separation of conformers and, in combination with high-resolution polyacrylamide gel electrophoresis, offers an alternative to previous SSCP analysis protocols. This protocol should be very useful for clinical applications in routine detection of mutations as well as for research purposes.

Cystic Fibrosis Transmembrane Conductance Regulato↗
PubMed1998

Gene mapping in zebrafish using single-strand conformation polymorphism analysis.

To exploit fully the power of the zebrafish system as a model for vertebrate development, it will be necessary to develop efficient tools for genomic analysis. In this report we have tested whether single-strand conformation polymorphism analysis (SSCP) can be utilized for gene mapping in zebrafish. Over 100 primer pairs derived from noncoding regions of known genes and partially characterized cDNAs were analyzed, and a polymorphism frequency of approximately 50% was detected in zebrafish strains used for genetic mapping studies. A subset of these polymorphic cDNAs was localized on the zebrafish map. SSCP thus represents an efficient strategy for mapping transcribed sequences with a high resolution in the zebrafish genome, which will facilitate the integration of existing zebrafish framework maps, the generation of a zebrafish EST map, and the application of alternative gene localization strategies such as comparative mapping.

3' Untranslated Regions↗
PubMed1997

Pancreatic lymph nodal and plexus micrometastases detected by enriched polymerase chain reaction and nonradioisotopic single-strand conformation polymorphism analysis: a new predictive factor for recurrent pancreatic carcinoma.

K-ras point mutations have been observed in approximately 90% of pancreatic carcinomas. We genetically analyzed cases of pancreatic regional lymph nodal and plexus micrometastases in invasive ductal carcinoma of the pancreas who were node negative or had metastases limited histopathologically to pancreaticoduodenal lymph nodes. These cases underwent curative resection in our institute. The utility of genetic analysis was compared with that of histopathological study, in terms of postoperative clinical outcome, as a predictive factor for recurrent pancreatic carcinoma. Samples for DNA extraction were obtained from formalin-fixed, paraffin-embedded specimens. A 0.5-microg quantity of DNA was subjected to enriched PCR and nonradioisotopic single-strand conformation polymorphism analysis. K-ras codon 12 mutations were detected in 83% (10 of 12) of invasive ductal carcinomas. In four cases, the genetic analysis of regional lymph nodal metastases and pancreatic plexus invasion of the pancreatic carcinoma yielded results concordant with those of histopathological analysis. In six cases, however, the metastases detected by genetic analysis were more advanced than was indicated by the histopathological examination. The survival rate of cases with metastases beyond the pancreaticoduodenal lymph nodes was significantly lower than that of cases with metastases limited to the pancreaticoduodenal lymph nodes or with no nodal involvement based on genetic analysis (P < 0.05). Intraoperative analysis of point mutations at K-ras codon 12 in the regional lymph nodes and the pancreatic plexus by enriched PCR/nonradioisotopic single-strand conformation polymorphism analysis is a highly accurate predictive factor for recurrent pancreatic carcinoma.

Adult↗
PubMed1994

Simple and rapid detection of cholesteryl ester transfer protein deficiency by using nonradioisotopic single-strand conformation polymorphism analysis.

We developed a polymerase chain reaction (PCR)-single-strand conformation polymorphism (SSCP) analysis technique by using silver staining to detect the G-->A point mutation of intron 14 of the cholesteryl ester transfer protein (CETP) gene, which is a common mutation in CETP deficiency. After conventional PCR, amplified DNA was heated and subjected to electrophoresis in polyacrylamide gel containing glycerol. The gel was then stained with silver to identify DNA bands. With this technique, we examined 40 subjects with high concentrations of high-density lipoprotein cholesterol (> or = 1 g/L) and found one homozygote and eight heterozygotes. The procedure is suitable for screening because it is quick and does not require radioactive materials or restriction enzymes.

Base Sequence↗
PubMed1996

Sensitive detection of loss of heterozygosity in the TP53 gene in pancreatic adenocarcinoma by fluorescence-based single-strand conformation polymorphism analysis using blunt-end DNA fragments.

We have developed a fluorescence-based single-strand conformation polymorphism analysis to detect Haelil-sensitive polymorphic sites in intron 1 of the TP53 gene. It is important to treat the PCR products with Klenow fragment to remove a 3'-protruding nucleotide from the amplified DNA fragments added during the reaction in order to obtain a single peak for each allele. A comparison of the signal profiles of two alleles with those of normal heterozygotes by data processing using computer software has enabled sensitive detection of loss of heterozygosity (LOH) from clinical materials with a fraction of tumor cells below 10%. In analysis of 14 pancreatic carcinomas in which the proportion of the tumor cells is usually low due to the abundance of the stromal component, 7 samples (50%) were informative and 5 of the 7 (71.4 %) were positive for LOH at the TP53 locus. This approach would be useful for allelotyping tumors with low cellularity, as well as other clinical samples such as biopsied specimens and paraffin embedded tissues.

Adenocarcinoma↗