genomic DNA

About: genomic DNA is a research topic. Over the lifetime, 15046 publications have been published within this topic receiving 663636 citations. The topic is also known as: genomic deoxyribonucleic acid & gDNA.

Barley: Genes and chromosomes

Abstract: The information on barley genes and chromosomes assembled consists of: {fx123-1}

Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS)

Abstract: Alterations of the DNA methylation pattern have been related to generalized chromosomal disruption and inactivation of multiple tumor suppressor genes in neoplasia. To screen for tumor-specific alterations and to make a global assessment of methylation status in cancer cells, we have modified the methylated CpG island amplification method to generate easily readable fingerprints representing the cell’s DNA methylation profile. The method is based on the differential cleavage of isoschizomers with distinct methylation sensitivity. Specific adaptors are ligated to the methylated ends of the digested genomic DNA. The ligated sequences are amplified by PCR using adaptorspecific primers extended at the 3′ end with two to four arbitrarily chosen nucleotidic residues to reduce the complexity of the product. Fingerprints consist of multiple anonymous bands, representing DNA sequences flanked by two methylated sites, which can be isolated and individually characterized. Hybridization of the whole product to metaphase chromosomes revealed that most bands originate from the isochore H3, which identifies the regions of the genome with the highest content of CpG islands and genes. Comparison of the fingerprints obtained from normal colon mucosa, colorectal carcinomas and cell lines revealed tumor-specific alterations that are putative recurrent markers of the disease and include tumor-specific hypo- and hypermethylations.

Strategies for Mutational Analysis of the Large Multiexon ATM Gene Using High-Density Oligonucleotide Arrays

Abstract: Mutational analysis of large genes with complex genomic structures plays an important role in medical genetics. Technical limitations associated with current mutation screening protocols have placed increased emphasis on the development of new technologies to simplify these procedures. High-density arrays of >90,000-oligonucleotide probes, 25 nucleotides in length, were designed to screen for all possible heterozygous germ-line mutations in the 9.17-kb coding region of the ATM gene. A strategy for rapidly developing multiexon PCR amplification protocols in DNA chip-based hybridization analysis was devised and implemented in preparing target for the 62 ATM coding exons. Improved algorithms for interpreting data from two-color experiments, where reference and test samples are cohybridized to the arrays, were developed. In a blinded study, 17 of 18 distinct heterozygous and 8 of 8 distinct homozygous sequence variants in the assayed region were detected accurately along with five false-positive calls while scanning >200 kb in 22 genomic DNA samples. Of eight heterozygous sequence changes found in more than one sample, six were detected in all cases. Five previously unreported sequence changes, not found by other mutational scanning methodologies on these same samples, were detected that led to either amino acid changes or premature truncation of the ATM protein. DNA chip-based assays should play a valuable role in high throughput sequence analysis of complex genes.

Characterization of the structural gene and putative 5′-regulatory sequences for human proopiomelanocortin

Abstract: It is now well established that the hormones corticotropin (ACTH) and β-lipotropin (β-LPH) are contained within a common precursor peptide called proopiomelanocortin (POMC), which is synthesized in the anterior and/or intermediate lobes of the pituitary1–3 and in the hypothalamus4. The recent cloning of a ‘full-size’ cDNA copy of bovine POMC mRNA has revealed the presence of additional peptides in the previously ‘cryptic’ segment of the precursor protein5. This cDNA has been used as a hybridization probe for the isolation and characterization of a bovine genomic DNA segment encoding the complete POMC mRNA6, and for isolation of part of the corresponding human genomic DNA sequence7. DNA sequence analysis of these isolates and of part of the rat POMC gene8 has shown that, in the species studied, certain segments of the POMC structural gene have been conserved during evolution, whereas the nucleotide sequences of other segments have diverged sharply. We have now isolated and characterized a 11.6-kilobase (kb) human genomic DNA fragment that encodes the complete POMC mRNA and putative regulatory sequences proximate to the gene (which is repressed by glucocorticoids in vivo9). We have also analysed the 800-base pair (bp) segment preceding the mRNA coding sequence, within which—at a position nearly 480 bp upstream from the mRNA start site—is a 21-bp segment that shares homology with a DNA sequence beginning 370 bp upstream from two other glucocorticoid-controlled genes. We speculate that these sequences may be involved in the regulation of POMC gene expression by glucocorticoids.