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.

Measurement of locus copy number by hybridisation with amplifiable probes

Abstract: Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicroscopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader–Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications.

A new DNA extraction method for high‐throughput marker analysis in a large‐genome species such as Triticum aestivum

Abstract: Gene mapping and marker-assisted selection in complex, polyploid genomes still relies strongly on restriction fragment length polymorphism (RFLP) analysis, as conversion of RFLP to polymerase chain reaction (PCR) markers can be very difficult. DNA extraction in amounts suitable for RFLP analysis represents the most time-consuming and labour-intensive step in molecular marker analysis of plant populations. In this paper, a new flexible method for plant DNA extraction is presented. It allows a high-throughput of samples in a short time without the need for freezing or lyophilizing the plant material. The method allows the isolation of genomic DNA with a yield of 100 μg for a minimal amount of 200 mg of leaf material. This is sufficient for work with large-genome plant species such as hexaploid wheat, where 20 μg of genomic DNA are required for a single RFLP analysis.

Expression of an Arabidopsis Potassium Channel Gene in Guard Cells

Abstract: The Arabidopsis thaliana KAT1 cDNA encodes a voltage-gated inward-rectifying K+ channel. A KAT1 genomic DNA clone was isolated and sequenced, and a 5[prime] promoter and coding sequences containing eight introns were identified. Reporter gene analysis of transgenic plants containing the KAT1 promoter fused to bacterial [beta]-glucuronidase showed robust [beta]-glucuronidase activity primarily in guard cells.

A method to assess genomic dna methylation using high-performance liquid chromatography-electospray ionization mass spectrometry

Abstract: The present invention provides a method for quantitative determination of 5-methyl-2'-deoxycytidine in human DNA using liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS). The method comprises the steps of enzymatically hydrolyzing the DNA sample by sequential digestion with enzymes; separating the DNA hydrolyzates by reverse-phase high-performance liquid chromatography in isocratic mode wherein the four major DNA bases and 5-methyl-2'-deoxycytidine are resolved and eluted; identifying the 2'-deoxycytidine and 5-methyl-2'-deoxycytidine by combining diode array UV spectra analysis and mass spectra of chromatographic peaks. The isotopomes 15N3 2'-deoxycytidine and methyl-D3, ring-6-D1 5-methyl-2'-deoxycytidine are used as internal standards. Ions of m/z 126 and 130 are used to detect 5-methyl-2'-deoxycytidine and its isotopomer, and ions of m/z 112 and 115 are used to detect 2'-deoxycytidine and its stable isotopomer, respectively. The DNA methylation status is consequently calculated based on the amount of 5-methyl-2'-deoxycytidine per µg DNA with percent relative standard deviations (%RSD) for method precision of 7.1 (within-day) and 5.7 (day-to-day). The method of the present invention also allows the measurement of 5-methyl-2'-deoxycytidine expressed as a percentage of total deoxycytidine residues in genomic DNA with % RSD for method precision of 1.9 (within-day) and 1.7 (day-to-day). The LC/MS method for quantitative determination of genomic DNA methylation status is rapid, sensitive, selective and precise.

The Complete Sequence of 340 kb of DNA around the Rice Adh1–Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4

Abstract: A 2.3-centimorgan (cM) segment of rice chromosome 11 consisting of 340 kb of DNA sequence around the alcohol dehydrogenase Adh1 and Adh2 loci was completely sequenced, revealing the presence of 33 putative genes, including several apparently involved in disease resistance. Fourteen of the genes were confirmed by identifying the corresponding transcripts. Five genes, spanning 1.9 cM of the region, cross-hybridized with maize genomic DNA and were genetically mapped in maize, revealing a stretch of colinearity with maize chromosome 4. The Adh1 gene marked one significant interruption. This gene mapped to maize chromosome 1, indicating a possible translocation of Adh1 after the evolutionary divergence leading to maize and sorghum. Several other genes, most notably genes similar to known disease resistance genes, showed no cross-hybridization with maize genomic DNA, suggesting sequence divergence or absence of these sequences in maize, which is in contrast to several other well-conserved genes, including Adh1 and Adh2. These findings indicate that the use of rice as the model system for other cereals may sometimes be complicated by the presence of rapidly evolving gene families and microtranslocations. Seven retrotransposons and eight transposons were identified in this rice segment, including a Tc1/Mariner–like element, which is new to rice. In contrast to maize, retroelements are less frequent in rice. Only 14.4% of this genome segment consist of retroelements. Miniature inverted repeat transposable elements were found to be the most frequently occurring class of repetitive elements, accounting for 18.8% of the total repetitive DNA.