Genomic DNA sequences

Amplification of endoPG genomic DNA sequences by PCR and isolation of genomic clones... 

Fluorescently labeled DNA probes can be used for detection, localization, or quantification of target DNA sequences. In situ hybridization mapping of genomic DNA sequences can be... 

Transcript discovery Find transcripts (genes) in genomic sequence In these experiments, arrays are made from genomic DNA sequences, rather than from complementary DNAs (cDNAs). Such studies can be used to confirm computational gene predictions and characterize alternative splicing and die boundaries of exons (DNA sequences destined to become part of die mature messenger RNA [mRNA]). 

Vector A plasmid containing either a cDNA or genomic DNA sequence or interest... 

The genomic DNA sequences used in these tests are generally regions containing repetitive DNA... 

In this chapter, methods developed for the detection of human papillomaviruses and repetitive genomic DNA sequences (individually and in combination) in cultured cells and routinely processed surgical biopsies are described. 

With the completion of genomic DNA sequencing for various species, attention has shifted towards the structural and functional characteristics of proteins. However, rapid progress in proteomics requires the following (a) availability of many proteins, and (b) availability of sufficient amounts of proteins in naturally folded states. To meet these requirements, various existing protein production technologies have been adopted for genome-wide protein translation. 

Celis, J. E. Rasmussen, H. H. Leffers, H. Madsen, P. Honore, B. Gesser, B. Dejgaard, K. Vandekerckhove, J. 1991. Human cellular protein patterns and their link to genome DNA sequence data usefulness of two-dimensional gel electrophoresis and microsequencing. FASEB J., 5,2200-2208. 

Gao Q. and Chess A. (1999) Identification of candidate Drosophila olfactory receptors from genomic DNA sequence. Genomics 60, 31-39. 

Fig. 7.4. Phylogenetic analysis of the ADP/ATP carriers (AACs) has so far revealed that only the hydrogenosomes of chytrids and ciliates possess genuine mitochondrial AACs, which cluster with the mitochondrial homologues of their aerobic, mitochondria-bearing relatives (2, 3) (Voncken 2001 Voncken et al. 2002a van der Giezen et al. 2002 Tjaden et al. 2004). The AAC of the mitochondrial remnant of Cryptosporidium clusters with the mitochondrial transporters of the distantly related Plasmodium (the closest relative from which a complete genome DNA sequence is available) (1). Trichomonas (5) and Entamoeba (4) use alternative members of the mitochondrial carrier family for the transport of ATP across the hydrogenosomal/mitosomal membranes (Dyall et al. 2000 Tjaden et al. 2004 Chan et al. 2005 Tjaden and Leroch, unpublished results)...

If either of the methods gives evidence for a terminal repeat it is then relatively easy to discover the flanking sequences at the point of insertion. In addition, there is usually a short direct repeat of the genomic DNA sequence at the insertion site. To confirm the terminal repeats, and whether the total element has been determined, a second element has to be isolated from the genomic library using the repetitive sequence as a probe. DNA sequence analysis of the second element will confirm the completeness of the element first isolated. 

Snyder, E. E. Stormo, G. D. (1993). Identification of coding regions in genomic DNA sequences an application of dynamic programming and neural networks. Nucl Acids Res 21, 607-13. 

After numerous complete genomic DNA sequences had been established and after these had been interpreted to a great extent in terms of protein sequences, it became evident that about 20% of all proteins are located in membranes (Liu and Rost, 2001). This number was derived from a search for transmembrane a-helices with a computerized prediction system, the results of which are known to come with a high confidence level. Such helices can be recognized from a continuous stretch of 20 to 30 nonpolar residues with a predominance of aliphatic side chains at the center and aromatic residues at both ends (Sipos and von Heijne, 1993). The number of transmembrane a-helices per protein is broadly distributed and averages around six. 

Storhoff JJ, Lucas AD, Garimella V et al (2004) Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticles probes. Nat Biol 22 883-887... 

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