Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Conformational analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,243 records · Page 69Linked to original sources
PubMed2004

Genotyping of enteric adenoviruses by using single-stranded conformation polymorphism analysis and heteroduplex mobility assay.

Single-stranded conformation polymorphism (SSCP) analysis and heteroduplex mobility assays (HMAs) were used to identify and genotype enteric adenoviruses (EAd). The results were compared to those of restriction endonuclease assays, species-specific PCRs, and direct nucleotide sequence analyses. Of the 31 stool samples tested, 15 isolates were identified as EAd and 7 were identified as nonenteric Ad by all methods. An agreement of 100% was found between the SSCP and HMA results.

Adenovirus Infections, Human↗
PubMed1991

Detection of p53 gene mutations in human brain tumors by single-strand conformation polymorphism analysis of polymerase chain reaction products.

Single-strand conformation polymorphism analysis of polymerase chain reaction products (PCR-SSCP analysis) was used for detection of mutations of the p53 gene in surgical specimens of human brain tumors. Six of 45 brain tumors showed mobility shifts in the analyses. These six tumors also showed loss of a normal allele. The samples were examined further by direct sequencing. Results showed that four of them had single-base substitutions and the other two had deletions of one and eight base pairs. Five of the six mutations detected were clustered in highly conserved regions of the p53 gene. The frequency of p53 gene mutations in primary brain tumors examined was 9.8%. We also found two new polymorphic markers in the p53 gene, one in intron 7 and the other in an Alu repeat in exon 11. Both markers could be detected by SSCP analysis. Using these two markers, we found two cases of loss of heterozygosity in other brain tumor specimens. Results suggested that aberrations of the p53 gene were not correlated with the malignancy of some types of brain tumors such as anaplastic astrocytoma and glioblastoma, contrary to previous observations on colorectal cancers.

Astrocytoma↗
PubMed1995

Analysis of N-ras mutations in human cutaneous melanoma: tumor heterogeneity detected by polymerase chain reaction/single-stranded conformation polymorphism analysis.

Determination of the activation state of oncogenes as well as tumor suppressor genes is a main subject of interest in the analysis of the mechanism of tumor initiation. In human melanoma, the c-myc and N-ras oncogenes have been found to be activated in approximately 50% and 15% of the analyzed material, respectively. These studies have mostly been done on fresh tumor material or cell lines. Only in a few cases has an attempt been made to look at tumor heterogeneity or clonality with respect to the activation of oncogenes. We have adjusted the polymerase chain reaction (PCR)/single-stranded conformation polymorphism analysis (SSCP) technique to screen paraffin-embedded melanoma material for the presence of N-ras mutations and found genetic defects at particular progression stages. In one melanoma of the skin, we were able to sublocalize an N-ras mutation in the intraepidermal tumor part, that was absent in the part deeply invading the dermal layer. We conclude that a thorough investigation of N-ras activation in human melanoma should include analysis of histologically different parts of the tumor.

Base Sequence↗
PubMed2005

beta-Tubulin mutations in ovarian cancer using single strand conformation analysis-risk of false positive results from paraffin embedded tissues.

Mutations in the beta-tubulin gene have been proposed as a resistance mechanism to paclitaxel. We therefore investigated the presence of mutations in the beta-tubulin M40 gene in 40 ovarian tumours (16 paraffin-embedded and 24 freshly frozen) selected for good or poor response to chemotherapy with paclitaxel or non-tubulin-affecting regimens. The presence of mutations was investigated using single strand conformation analysis followed by sequencing of the products with altered mobility. No sequence variants in the exons of the beta-tubulin M40 gene were detected. Non-reproducible shifts were identified, in eight out of 16 paraffin embedded samples. This may explain some of the previously published discrepancies. In conclusion, sequence variants in the beta-tubulin M40 gene are rare and are unlikely to be a clinically relevant explanation of resistance to paclitaxel.

Antineoplastic Agents, Phytogenic↗
PubMed2000

A CoMFA analysis with conformational propensity: an attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method.

CoMFA analysis, a widely used 3D-QSAR method, has limitations to handle a set of SAR data containing diverse conformational flexibility since it does not explicitly include the conformational entropic effects into the analysis. Here, we present an attempt to incorporate the conformational entropy effects of a molecule into a 3D-QSAR analysis. Our attempt is based on the assumption that the conformational entropic loss of a ligand upon making a ligand-receptor complex is small if the ligand in an unbound state has a conformational propensity to adopt an active conformation in a complex state. For a QSAR analysis, this assumption was interpreted as follows: a potent ligand should have a higher conformational propensity to adopt an 'active-conformation'-like structure in an unbound state than an inactive one. The conformational propensity value was defined as the populational ratio, Nactive/Nstable, of the number of energetically stable conformers, Nstable, to the number of 'active-conformation'-like structures, Nactive. The latter number was calculated by counting the number of conformers that satisfied the structural parameters deduced from the active conformation. A set of SAR data of imidazoleglycerol phosphate dehydratase inhibitors containing 20 molecules with different conformational flexibility was used as a training set for developing a 3D structure-activity relationship by a CoMFA analysis with the conformational propensity value. This resulted in a cross-validated squared correlation coefficient of the CoMFA model with the conformational propensity value (Rcross2 = 0.640) higher than that of the standard CoMFA model (Rcross2 = 0.431). Then we evaluated the quality of the CoMFA models by predicting the inhibitory activity for a new molecule.

Models, Molecular↗
PubMed1997

Use of a single-strand conformation polymorphism analysis to perform a simple genotyping of bovine kappa-casein A and B variants.

We propose an alternative method for casein genotyping, generally carried out using polymerase chain reaction followed by restriction fragment length polymorphism analysis. Application of the single-strand conformation polymorphism technique detects nucleotide changes in the fragment amplified by means of polymerase chain reaction and thus avoids the use of restriction enzymes. A 453 bp fragment from exon IV of kappa-casein has been amplified. The two variants (A and B), found with the highest frequencies in most bovine breeds and included in some dairy cattle selection schemes, can be discriminated using single-strand conformation polymorphism analysis of heat denatured fragments in acrylamide-bis-acrylamide (100:1) gels followed by silver staining. kappa-Casein genotyping is therefore simplified, although variants A and E on the one hand, and B and C on the other, are not distinguishable with this technique.

Animals↗
PubMed1994

A 3D QSAR approach to the search for geometrical similarity in a series of nonpeptide angiotensin II receptor antagonists.

A 3D QSAR methodology based on the combined use of conformational analysis and chemometrics was applied to perform a comparative analysis of the 3D conformational features of 13 nonpeptide angiotensin II receptor antagonists showing different levels of binding affinity. Conformational analysis by using a molecular mechanics MM2 method was carried out for each of these structures to obtain conformational minima. These minima were described by ten interatomic distances which define the relative spatial disposition of five significant atoms belonging to relevant functional groups present in all the 13 molecules. The structure-activity relationship between the interatomic distances and the biological activity was then assessed by using chemometric methods (cluster analysis, principal component analysis, classification methods). With our indirect approach based on the search for geometrical similarity it was possible, even though structural information on the receptor active site was lacking, to identify the 3D geometrical requirements for the binding affinity of nonpeptide angiotensin II receptor inhibitors.

Amino Acid Sequence↗
PubMed2005

Analysis of sequence variation in Gnathostoma spinigerum mitochondrial DNA by single-strand conformation polymorphism analysis and DNA sequence.

Morphological variations were observed in the advance third stage larvae of Gnathostoma spinigerum collected from swamp eel (Fluta alba), the second intermediate host. Larvae with typical and three atypical types were chosen for partial cytochrome c oxidase subunit I (COI) gene sequence analysis. A 450 bp polymerase chain reaction product of the COI gene was amplified from mitochondrial DNA. The variations were analyzed by single-strand conformation polymorphism and DNA sequencing. The nucleotide variations of the COI gene in the four types of larvae indicated the presence of an intra-specific variation of mitochondrial DNA in the G. spinigerum population.

Animals↗
PubMed2005

Single-strand conformational polymorphism analysis: basic principles and routine practice.

Single-strand conformational polymorphism (SSCP) analysis is a simple and sensitive technique for mutation detection and genotyping. The principle of SSCP analysis is based on the fact that single-stranded DNA has a defined conformation. Altered conformation due to a single base change in the sequence can cause single-stranded DNA to migrate differently under nondenaturing electrophoresis conditions. Therefore wild-type and mutant DNA samples display different band patterns. SSCP analysis involves the following four steps: (1) polymerase chain reaction (PCR) amplification of DNA sequence of interest; (2) denaturation of double-stranded PCR products; (3) cooling of the denatured DNA (single-stranded) to maximize self-annealing; (4) detection of mobility difference of the single-stranded DNAs by electrophoresis under non-denaturing conditions. Several methods have been developed to visualize the SSCP mobility shifts. These include the incorporation of radioisotope labeling, silver staining, fluorescent dye-labeled PCR primers, and more recently, capillary-based electrophoresis. Silver staining is simple, rapid, and cost-effective, and can be routinely performed in clinical laboratories. The use of SSCP analysis to discover and genotype single-nucleotide polymorphisms (SNPs) has been widely applied to the genetics of hypertension, including both monogenic (e.g., Liddle's syndrome) and polygenic disorders (e.g., essential hypertension).

DNA↗
PubMed2000

Raman spectroscopic study of oat globulin conformation.

Analysis of Raman spectra of oat globulin showed that extreme pH values caused an increase in the amide and C-H stretching band intensity, indicating changes in the secondary structures of the protein due to denaturation. Similar changes were observed when oat globulin was treated with chaotropic salts and several protein perturbants. Sodium dodecyl sulfate, beta-mercaptoethanol, and ethylene glycol also caused a shift in the amide III' band, suggesting a transition from beta-sheet to a random coil conformation. Heating at temperatures near the denaturation temperature of oat globulin led to increases in the amide and C-H band intensity, indicating unfolding of the protein. The data indicate that FT-Raman spectroscopy is suitable for studying the secondary structure of plant proteins such as oat globulin.

Avena↗
PubMed1991

Two dimensional single-strand conformation polymorphism analysis: a useful tool for the detection of mutations in long DNA fragments.

A new two-dimensional gel system for the analysis of single strand conformational polymorphisms has been developed to identify point mutations, deletions and insertions in long DNA fragments (e.g. 2.7 kb) generated by the polymerase chain reaction. In this procedure, such DNA fragments are first restricted with frequent-cutter enzymes. The resulting small fragments are then separated in the first dimension according to their size by electrophoresis under denaturing conditions; these single stranded DNA fragments are subsequently fractionated in the second dimension by electrophoresis on a non denaturing slab gel based on their fold-back conformation which is completely sequence-dependent. The method was tested on three previously characterized pH 4.5 resistant mutants of HRV14 and was then used to determine changes in three further mutants.

Base Sequence↗
PubMed1993

The conformations of cyclic (1-->2)-beta-D-glucans: application of multidimensional clustering analysis to conformational data sets obtained by Metropolis Monte Carlo calculations.

Sets containing up to 1.3 x 10(6) energetically accessible conformations of linear (1-->2)-beta-D-glucan oligosaccharides were obtained by Metropolis Monte Carlo (MMC) calculations performed with the GEGOP (GEometry of GlycOProteins) program. Quantitative analyses of the data sets (which were expressed in terms of the glycosidic dihedral angle coordinates) were obtained by two different clustering methods: (i) the three-distance hierarchical clustering method (3-DM), published by Jure Zupan, and (ii) a nonhierarchical clustering method (Population-Density Projection, PDP) which, through a segmentation analysis of two-dimensional projections of the population-density surface, establishes a partitioning of conformational space into a set of "cluster regions", followed by a clustering step where each conformation of the data set is assigned to one of these regions. Computer programs (MCLUST and PDPCLUST) were developed to perform the 3-DM and PDP analyses, respectively. The two types of analysis provided very similar sets of conformational families (clusters), which could be expressed as combinations of distinct conformations of the glycosidic torsional angles (phi, psi) centered at (50 degrees, 10 degrees) for conformation A, (40 degrees, 160 degrees) for conformation B, (55 degrees, -160 degrees) for conformation B', and (170 degrees, 10 degrees) for conformation C. The analysis provided the populations of the families, along with relative rates for transitions between families. Examination of the frequencies of the A, B, and C glycosidic bond conformations with respect to their relative positions in the sequence revealed the tendency of the (1-->2)-beta-D-glucan to adopt conformational repeating structures of the general form [AnB], where n = 3 or 6. These repeating structures combine in an energetically cooperative fashion to give low-energy cyclic conformations having, for example C5 symmetry [AAAB]5 for the eicosamer, and C3 symmetry [AAAAAAB]3 for the heneicosamer.

Carbohydrate Conformation↗
PubMed1992

[Detection of mutant adenine phosphoribosyltransferase genes by polymerase chain reaction-single strand conformation polymorphism analysis].

Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis is a rapid and sensitive method to identify point mutations in a given sequence of genomic DNA. We tried to apply the PCR-SSCP to the diagnosis of adenine phosphoribosyltransferase (APRT) deficiency, which is an autosomal recessive hereditary disease leading to 2,8-dihydroxyadenine urolithiasis. Genomic APRT genes, with or without mutations, were amplified and labeled simultaneously with 32P-dCTP by PCR. When run in a 6% polyacrylamide gel containing 10% glycerol, two types of mutant genes, APRT*Q0 and APRT*J, gave bands clearly distinct from those of the respective normal APRT genes. Since heterozygotes as well as homozygotes for these mutant APRT genes can be detected in 2 days, PCR-SSCP should be a valuable method in the diagnosis of APRT deficiency and in screening a large population for APRT mutant genes.

Adenine Phosphoribosyltransferase↗
PubMed2002

Oligomeric proanthocyanidins: naturally occurring O-heterocycles.

This review covers the flavan-3-ols (catechins), flavan-4-ols/flavan-3,4-diols (leucoanthocyanidins), A-type proanthocyanidins, B-type proanthocyanidins including the procyanidins, prodelphinidins, propelargonidins, proteracacinidins, promelacacinidins, procassinidins, probutinidins, and non-proanthocyanidins with flavan-3-ol constituent units. Newly isolated proanthocyanidins, structure elucidation, syntheses, HPLC/MS analysis, NMR/ conformational analysis, and the effects of proanthocyanidins on human nutrition and health are reported. The literature from January 1999 to December 2001 is reviewed, and 130 references are cited.

Animals↗
PubMed1998

Quantification of relative expression of genes with homologous sequences using fluorescence-based single-strand conformation polymorphism analysis--application to lactate dehydrogenase and cyclooxygenase isozymes.

The combination of reverse transcribed-PCR and fluorescence-based single strand conformation polymorphism analysis has been proposed for the quantitative determination of ratio of mRNA molecules with homologous sequences. We applied this procedure to lactate dehydrogenase subunits M and H, and cyclooxygenase 1 and 2. We designed fluorescence labeled common PCR primers in the sequences highly homologous between two subunit and isozyme cDNAs, and performed reverse transcribed-PCR and fluorescence-based single strand conformation polymorphism analysis. PCR efficiency was almost the same for the different target sequences, so analysis of mixtures of known amounts of lactate dehydrogenase M and H revealed linear and precise proportions of lactate dehydrogenase M mRNA. It was shown that template concentrations and number of PCR cycles did not affect the determination of proportions of lactate dehydrogenase M to total lactate dehydrogenase. The procedure was applicable to a determination of cyclooxygenase-2 proportion; furthermore, the present procedure could be easily applied to investigation of expression levels of genes encoding mRNAs with homologous sequences.

Amino Acid Sequence↗
PubMed1991

Inactivation of the retinoblastoma gene in a human lung carcinoma cell line detected by single-strand conformation polymorphism analysis of the polymerase chain reaction product of cDNA.

Combined use of a simple, sensitive method of DNA analysis of nucleotide substitutions, namely, single-strand conformation polymorphism analysis of polymerase chain reaction products (PCR-SSCP), and the reverse transcriptase reaction (RT) is an effective method for mRNA analysis. We used this RT-PCR-SSCP method to detect abnormal retinoblastoma (RB) gene transcripts in human tumor cell lines. Results showed the presence of two types of RB gene transcripts in a giant cell lung carcinoma cell line Lu65: a minor mRNA species with a base substitution that created a stop codon in the nucleotide sequence corresponding to exon 2 of the gene, and a major species of mRNA without the nucleotide sequence corresponding to that of exon 2. PCR-SSCP analysis of the genomic DNA also revealed that Lu65 cells contained the mutated RB allele, but not the normal allele. These results suggested that in Lu65 cells, both RB alleles were inactivated. The transcript without the exon 2 sequence, probably due to alternative splicing, was also found in all the other human cells examined, as a very minor species.

Base Sequence↗
PubMed1993

Diresidue-monopeptide (DRMP) model for analysis of peptide and protein conformation.

The paired torsional angle representation phi i, psi i in protein conformational analysis is only one type of correlation with a focus on a given C alpha residue and gives the relative orientation of a pair of peptide planes sandwiching a given residue (referred as mono-residue dipeptide model, MRDP). A shift of emphasis from a residue site to a given peptide plane (termed as diresidue monopeptide model, DRMP) leads to examination of pairs such as phi i, psi i-1 and other parameters derived therefrom. General sum (alpha n = phi i + psi i-n) and the difference (beta n = phi i - psi i-n) parameters are introduced, of which, n = 0 and n = 1 relate to MRDP models and DRMP models respectively. Apart from the helical regions, where 'alpha 0' is found to be relatively stable, the sum parameters have been found to be more useful in the analysis of beta-turns. The 'alpha 0' at the second and third residue sites and 'alpha 1' at the middle peptide plane of the four residue corner is found to offer a numerical triplet code for resolving various beta-turn types. Besides these, an additional parameter introduced under the DRMP model is a virtual torsion angle 'sigma 1' involving C beta i-1 ... C'i-1 - Ni ... C beta i, which is expected to reflect the effect of interaction of the side chain atoms. The sigma 1, alpha 1 pair is found to play a role parallel to phi, psi at a given residue site.(ABSTRACT TRUNCATED AT 250 WORDS)

Dipeptides↗
PubMed1990

Detection of ras gene mutations in human lung cancers by single-strand conformation polymorphism analysis of polymerase chain reaction products.

A simple, sensitive method of DNA analysis of nucleotide substitutions, namely, single-strand conformation polymorphism analysis of polymerase chain reaction products (PCR-SSCP analysis), was used for detection of mutated ras genes in surgical specimens of human lung cancer. Of a total of 129 tumors analysed, 22 contained a mutated ras gene. Of the 66 adenocarcinomas analysed, 14 contained an activated c-Ki-ras2 gene (the mutations in codon 12 in 6, in codon 13 in 4, in codon 18 in one, and in codon 61 in 3), one contained a c-Ha-ras1 gene with a mutation in codon 61 and 3 contained N-ras genes with mutations (in codon 12 in one and in codon 61 in 2). Mutated rats genes were also found in 2 of 36 squamous cell carcinomas (c-Ha-ras1 genes with mutations in codon 61) and 2 of 14 large cell carcinomas (c-Ki-ras2 genes with mutations in codon 12). No mutation of the ras gene was detected in 8 small cell carcinomas and 5 adenosquamous cell carcinomas. These results indicate that activation of the ras gene was not frequent (17%) in human lung cancers, that among these lung cancers mutation of the ras gene was most frequent in adenocarcinomas (27%) and 73% of the point mutations were in the c-Ki-ras2 gene in codon 12, 13, 18 or 61.

Base Sequence↗