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At least 937 records · Page 52Linked to original sources
PubMed2000

Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.

Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers, and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology. In this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited. Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region. Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another. The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology, this new approach can improve branch length estimations when using parsimony.

Alligators and Crocodiles↗
PubMed2004

Positive selection scanning of parasite DNA sequences.

Parasites successfully exist within the host as a result of highly specific genetic adaptations. Therefore, detecting genes that contain relevant adaptive mutations can provide a guide to biological processes that are potentially essential to the parasite. Random genetic mutations that confer selective advantage can act to alter amino acids so as to confer gain of function that has positive impact on the survival of the parasite. Directional selection of advantageous mutations results from an elevated rate of nonsynonymous substitutions in rapidly evolving genes. Genes on which this positive selection operates are considered to have an evolutionary characteristic such that the normalized number of nonsynonymous (dn) substitutions is greater than that of synonymous (ds) substitutions. By searching in a statistically robust way for genes that contain this characteristic, it is possible to apply a stringent method to identify genes that may be under positive selection and thus to identify biological processes involving those genes that are essential to the survival of the parasite. Genes detected typically class into those under host immune surveillance and those intrinsic to pathways essential to survival of the parasite within the host. Depending on their function and location of protein expression, such genes have the potential to provide exceptional vaccine and drug candidates.

Amino Acid Sequence↗
PubMedDate not supplied

[Optimal chips for megabase DNA sequencing].

The SHOM method (Sequencing by Hybridization with Oligonucleotide Matrix) developed in 1988 is a new approach to nucleic acid sequencing by hybridization to a octanucleotide matrix composed of an array of immobilized oligonucleotides. The original matrix proposed for sequencing by SHOM had to contain at least 65,536 octanucleotides. The present work describes a new family of matrices for sequencing, which allows one to reduce the number of synthesized oligonucleotides 5-15 times without essentially decreasing the resolving power of the method.

Base Sequence↗
PubMedDate not supplied

Semi-automated solid-phase DNA sequencing.

Increasing the efficiency of DNA sequencing necessitates the development of systems which reduce the need for manual operations by integrating template preparation, sequencing reactions, product separation and detection. A semi-automated system, whereby PCR-amplified biotinylated genomic or plasmid DNA is immobilized on streptavidin-coated magnetic beads, has been developed.

Automation↗
PubMed1986

DNA sequence selectivity of guanine-N7 alkylation by three antitumor chloroethylating agents.

The DNA sequence selectivities of guanine-N7 alkylation produced by three chloroethylating antitumor agents, 1-(2-chloroethyl)-3-(cis-2-hydroxy) cyclohexyl-1-nitrosourea (cis-2-OH CCNU), 2-chloroethyl (methylsulfonyl)methanesulfonate, and 8-carbamoyl-3-(2-chloroethyl)imidazo-[5,1-d]-1,2,3,5-tetrazin-4(3H )-one (mitozolomide), were examined using a modification of the Maxam and Gilbert sequencing technique. In a region of pBR322 DNA, 2-chloroethyl (methylsulfonyl)methanesulfonate produced approximately the same degree of alkylation at all guanines. cis-2-OH CCNU, however, preferentially alkylated the middle guanines in runs of three or more guanines; the intensity of the reaction increased with the number of adjacent guanines in the DNA sequence. Mitozolomide produced the same pattern of preferential alkylation but not as intensely as cis-2-OH CCNU. Three other nitrosoureas, 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea, 1-(2-fluorethyl)-3-cyclohexyl-1-nitrosourea, and 1-(2-chloroethyl)-1-nitrosourea gave similar patterns of alkylation to that of cis-2-OH CCNU at pH 7.2. The ratio of 7-hydroxyethylguanine to 7-chloroethylguanine was approximately the same following treatment of the synthetic polymers dGn X dCn and (dG X dC)n with cis-2-OH CCNU, indicating that 7-chloroethylation and 7-hydroxyethylation were enhanced similarly by the presence of adjacent guanines. Ethylnitrosourea produced relatively little alkylation preference. The results suggest that the alkylating intermediates, 2-chloroethyldiazohydroxide and 2-hydroxyethyldiazohydroxide, tend to react preferentially with those guanine-N7 positions the electronegativity of which is enhanced by the presence of neighboring guanines. This is consistent with the presence of cationic character in the alkylating centers of these intermediates. 2-Chloroethyl (methylsulfonyl)methanesulfonate and ethyldiazohydroxide would not be expected to have strong cationic character, in agreement with their lack of sequence selectivity.

Alkylating Agents↗
PubMed1984

Introduction of restriction enzyme sites in protein-coding DNA sequences by site-specific mutagenesis not affecting the amino acid sequence: a computer program.

Structure/function relationship studies of proteins are greatly facilitated by recombinant DNA technology which allows specific amino acid mutations to be made at the DNA sequence level by site-specific mutagenesis employing synthetic oligonucleotides. This technique has been successfully used to alter one or two amino acids in a protein. Replacement of existing DNA sequence coding for several amino acids with new synthetic DNA fragments would be facilitated by the presence of unique restriction enzyme sites in the region of interest. This computer program provides a means of searching the DNA sequence of interest for restriction enzyme sites that could be introduced by site-specific mutagenesis not affecting the amino acid sequence of the protein. Alternately, the program will also allow single amino acid changes to be made.

Amino Acid Sequence↗
PubMed1995

Molecular and cytological characterization of a highly repeated DNA sequence in Raphanus sativus.

A highly repeated DNA sequence with a repeat unit of ca. 180 bp was found in genomic DNA HindIII-digests of Raphanus sativus. The repeating units of six isolated, independent clones were sequenced. These units have 177 or 178 bp, are 36% G+C in their DNA base composition, and show 90% sequence homology. The copy number of this 180-bp repeat unit is about 0.5 x 10(6) per diploid genome. In situ hybridization analysis with the repeating units as the probe and C-banding analysis indicated that the repeated DNA sequence of R. sativus is closely associated with the major C-heterochromatins in the proximal regions of all 18 chromosomes at mitotic metaphase.

Base Composition↗
PubMed1988

A DNA sequencing strategy.

A modification of Lin's systematic DNA sequencing strategy is described. A method based on the religation of compatible cohesive ends generated by Sau3AI and BamHI was developed. The original procedure has been simplified and the yield of transfectant has been greatly improved. After complete digestion with BamHI and limited cleavage with Sau3AI, the single-cut linear DNA does not have to be separated from the supercoil or the open circular DNA on an agarose gel. After ligation, the DNA is digested with the restriction enzyme between the cloning site and BamHI site again. The original intact DNA is linearized, whereas the deleted subclone is not. Therefore the background is decreased to an undetectable level. This DNA sequencing strategy was tested on a 1.4-kb cDNA fragment containing the haptoglobin-related sequences. It is not necessary to purify large amounts of RF DNA (500 ng is enough) to get enough subclones. A set of subclones was produced in 1 day and the yield of plaques was about sixfold higher than that published.

Base Sequence↗
PubMed1996

DNA sequences that activate isocitrate lyase gene expression during late embryogenesis and during postgerminative growth.

We analyzed DNA sequences that regulate the expression of an isocitrate lyase gene from Brassica napus L. during late embryogenesis and during postgerminative growth to determine whether glyoxysomal function is induced by a common mechanism at different developmental stages. beta-Glucuronidase constructs were used both in transient expression assays in B. napus and in transgenic Arabidopsis thaliana to identify the segments of the isocitrate lyase 5' flanking region that influence promoter activity. DNA sequences that play the principal role in activating the promoter during post-germinative growth are located more than 1,200 bp upstream of the gene. Distinct DNA sequences that were sufficient for high-level expression during late embryogenesis but only low-level expression during postgerminative growth were also identified. Other parts of the 5' flanking region increased promoter activity both in developing seed and in seedlings. We conclude that a combination of elements is involved in regulating the isocitrate lyase gene and that distinct DNA sequences play primary roles in activating the gene in embryos and in seedlings. These findings suggest that different signals contribute to the induction of glyoxysomal function during these two developmental stages. We also showed that some of the constructs were expressed differently in transient expression assays and in transgenic plants.

Arabidopsis↗
PubMed1991

Real time automated simultaneous double-stranded DNA sequencing using two-color fluorophore labeling.

We determined the base sequences of both strands of duplex DNA simultaneously with an automated DNA sequencer. Primers for each strand were labeled with two different dyes and chain extension reactions for both strands produced four DNA families: "A", "C", "G", and "T". An image splitting-prism and band-pass filters were mounted on a real time DNA sequencer to detect fluorescences from the two different dyes separately. As a result, one thousand bases of a clone could be determined at the same time.

Automation↗
PubMed1985

Novel rearrangements of herpes simplex virus DNA sequences resulting from duplication of a sequence within the unique region of the L component.

We constructed insertion mutants of herpes simplex virus type 1 that contained a duplication of DNA sequences from the BamHI-L fragment (map units 0.706 to 0.744), which is located in the unique region of the L component (UL) of the herpes simplex virus type 1 genome. The second copy of the BamHI-L sequence was inserted in inverted orientation into the viral thymidine kinase gene (map units 0.30 to 0.32), also located within UL. A significant fraction of the progeny produced by these insertion mutants had genomes with rearranged DNA sequences, presumably resulting from intramolecular or intermolecular recombination between the BamHI-L sequences at the two different genomic locations. The rearranged genomes either had an inversion of the DNA sequence flanked by the duplication or were recombinant molecules in which different regions of the genome had been duplicated and deleted. Genomic rearrangements similar to those described here have been reported previously but only for herpes simplex virus insertion mutants containing an extra copy of the repetitive a sequence. Such rearrangements have not been reported for insertion mutants that contain duplications of herpes simplex virus DNA sequences from largely unique regions of the genome. The implications of these results are discussed.

Base Sequence↗
PubMed2006

A tandemly repetitive centromeric DNA sequence of the fish Hoplias malabaricus (Characiformes: Erythrinidae) is derived from 5S rDNA.

A substantial fraction of the eukaryotic genome consists of repetitive DNA sequences that include satellites, minisatellites, microsatellites, and transposable elements. Although extensively studied for the past three decades, the molecular forces that generate, propagate and maintain repetitive DNAs in the genomes are still discussed. To further understand the dynamics and the mechanisms of evolution of repetitive DNAs in vertebrate genome, we searched for repetitive sequences in the genome of the fish species Hoplias malabaricus. A satellite sequence, named 5SHindIII-DNA, which has a conspicuous similarity with 5S rRNA genes and spacers was identified. FISH experiments showed that the 5S rRNA bona fide gene repeats were clustered in the interstitial position of two chromosome pairs of H. malabaricus, while the satellite 5SHindIII-DNA sequences were clustered in the centromeric position in nine chromosome pairs of the species. The presence of the 5SHindIII-DNA sequences in the centromeres of several chromosomes indicates that this satellite family probably escaped from the selective pressure that maintains the structure and organization of the 5S rDNA repeats and become disperse into the genome. Although it is not feasible to explain how this sequence has been maintained in the centromeric regions, it is possible to hypothesize that it may be involved in some structural or functional role of the centromere organization.

Animals↗