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At least 757 records · Page 42Linked to original sources
PubMed2003

Capillary DNA sequencing: maximizing the sequence output.

Like most other DNA sequencing core facilities, one of our continuing goals is to improve our sequence output without substantially adding to cost. To minimize sample-to-sample variability in template DNA concentration, we implemented the rolling circle amplification (RCA) procedure for preparing our DNA templates. In addition to saving time and reducing the number of steps in template DNA preparation, the RCA method has the potential to normalize the DNA concentration in samples that can be sequenced directly without additional purification. In the present study, we used RCA-generated templates to test a recently reported procedure that increased sequence quality by resuspending the sequenced products in low concentrations of agarose before capillary electrophoresis (CE) on a MegaBACE 1000 platform. Although we did not obtain the expected result using the specified procedure, a modification resulted in up to 60% increase in total sequence yield per sample plate. A combination of agarose and formamide-EDTA in the resuspension solution enabled us to generate long-read and high-quality sequences for more than 38,000 templates with minimal additional cost.

DNA, Bacterial↗
PubMed1993

A strategy for the amplification, purification, and selection of M13 templates for large-scale DNA sequencing.

A strategy addressing various aspects of generating and processing DNA sequencing templates is described. The strategy is designed for large-scale DNA sequencing projects and involves procedures for the amplification, purification, and selection of M13 DNA templates. The amplification is based on growth in liquid culture, the purification is based on a novel thermoextraction method which replaces phenol extraction and ethanol precipitation, and the template selection is based on hybridization of gridded template arrays on membranes with chemiluminescent probes. All steps are currently carried out manually but the use of standardized formats (96-well format) throughout the entire strategy provides for possible transition to partial or full automation in the future. The strategy has been developed and tested within the ongoing project of sequencing the class II region of the human major histocompatibility complex but it should be equally applicable to any large-scale DNA sequencing project.

Centrifugation↗
PubMed1999

The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar.

The complete sequence of the Atlantic salmon (Salmo salar) mitochondrial genome has been determined. The entire sequence is 16665 base pairs (bp) in length, with a gene content (13 protein-coding, two ribosomal RNA [rRNA] and 22 transfer RNA [tRNA] genes) and order conforming to that observed in most other vertebrates. Base composition and codon usage have been detailed. Nucleotide and derived amino acid sequences of the 13 protein-coding genes from Atlantic salmon have been compared with their counterparts in rainbow trout. A putative structure for the origin of L-strand replication (O(L)) is proposed, and sequence features of the control region (D-loop) are described.

Animals↗
PubMed2004

Ultrasensitive detection of DNA sequences in solution by specific enzymatic labeling.

We present a newly developed technique for the direct detection of very low concentrations of specific nucleic acid sequences in homogeneous solution based on a polymerase extension reaction. This method consists of synthesizing a highly fluorescent nucleic acid reporter molecule using a sequence of the target as a template. Synthesis of the reporter molecule is accomplished by hybridizing a short complementary oligonucleotide primer to the target and extending the reporter using a polymerase and free nucleotides. One of these nucleotides is partially labeled with a fluorophore. The reaction sample is then flowed through the capillary cell of a single molecule detector. Detection of the reporter signifies the presence of the target being sought. Under carefully selected conditions, fluorescence from the reporter molecule is much stronger than that of the free nucleotide background over the detection time. We have derived practical equations that allow us to determine an optimal range of values for the relative reporter and free-nucleotide concentrations. This method allows for the rapid, direct detection of individual targets at femtomolar concentrations without the use of an amplification procedure, such as the polymerase chain reaction.

Affinity Labels↗
PubMedDate not supplied

Three new Lasiodiplodia spp. from the tropics, recognized based on DNA sequence comparisons and morphology.

Botryosphaeria rhodina (anamorph Lasiodiplodia theobromae) is a common endophyte and opportunistic pathogen on more than 500 tree species in the tropics and subtropics. During routine disease surveys of plantations in Australia and Venezuela several isolates differing from L. theobromae were identified and subsequently characterized based upon morphology and ITS and EF1-alpha nucleotide sequences. These isolates grouped into three strongly supported clades related to but different from the known taxa, B. rhodina and L. gonubiensis, These have been described here as three new species L. venezuelensis sp. nov., L. crassispora sp. nov. and L. rubropurpurea sp. nov. The three could be distinguished easily from each other and the two described species of Lasiodiplodia, thus confirming phylogenetic separations. Furthermore all five Lasiodiplodia spp. now recognized separated from Diplodia spp. and Dothiorella spp. with 100% bootstrap support.

Ascomycota↗
PubMed1986

Presence of human papillomavirus type-16 and type-18 DNA sequences and their expression in cervical cancers and cell lines from Japanese patients.

Southern blot analyses of surgical specimens of cervical carcinoma from Japanese patients showed that 3/9 samples contained human papillomavirus (HPV) type-16 DNA sequences, and 2 contained HPV type-18 DNA sequences. By Northern blot analyses, RNA transcripts of HPV DNA sequences were demonstrated in some of the tissues containing HPV type-16 or HPV type-18 DNA sequences. Two cell lines established from cervical cancers of Japanese patients also contained HPV type-18 genomes and these cell lines contained HPV type-18 transcripts. Two other cervical cancer cell lines from a Japanese patient were found to contain HPV type-16 DNA sequences and their RNA transcripts.

Adenocarcinoma↗
PubMed1996

Fragment walking for long DNA sequencing by using a library as small as 16 primers.

A DNA sequence can be rapidly and efficiently determined by digesting it into segments small enough to be sequenced at one time, then assembling them into contigs by searching for overlaps. Fragment walking achieves this without subcloning or preparing many kinds of primers; fragments obtained by digesting a template DNA are sequenced in parallel directly from the fragment mixture by using a set of 16 primers. Since the sequence adjacent to each cutting site is determined together with the fragment sequence, the contiguous fragment can be easily determined. The complete template DNA sequence can thus efficiently determined. The sequencing of pUC19 (2.7 kb) from both sides was done in one step by using only 15 fragments. The redundancy was only about 1.3, greatly reducing base-reading redundancy. Automating this strategy would increase the speed and efficiency of large-scale DNA sequencing.

Base Sequence↗
PubMed1984

A DNA sequence analysis package for the IBM personal computer.

We present here a collection of DNA sequence analysis programs, called "PC Sequence" (PCS), which are designed to run on the IBM Personal Computer (PC). These programs are written in IBM PC compiled BASIC and take full advantage of the IBM PC's speed, error handling, and graphics capabilities. For a modest initial expense in hardware any laboratory can use these programs to quickly perform computer analysis on DNA sequences. They are written with the novice user in mind and require very little training or previous experience with computers. Also provided are a text editing program for creating and modifying DNA sequence files and a communications program which enables the PC to communicate with and collect information from mainframe computers and DNA sequence databases.

Amino Acid Sequence↗
PubMed1994

A comparison of 16S ribosomal DNA sequences from five isolates of Helicobacter pylori.

Other workers have found that clinical isolates of Helicobacter pylori exhibit very extensive DNA sequence polymorphisms when they are examined by ribotyping or some other genomic sequence characterization technique. In fact, it is rare to find similar clones, much less identical ones, among isolates. We found that the levels of divergence between the 16S ribosomal DNA sequences of individual organisms and the consensus sequence of the five isolates which we examined ranged from 0.2 to 0.5%. In contrast, other workers have shown that levels of divergence between the 16S ribosomal DNA sequence of H. pylori and the 16S ribosomal DNA sequences of four other Helicobacter species range from 2.7 to 8.0%. Our results show that the H. pylori 16S ribosomal DNA is not very polymorphic and support the conclusion that H. pylori is a unique species.

Base Sequence↗
PubMed1981

Repeated DNA sequences and kangaroo phylogeny.

Three highly repeated DNA sequences have been used to determine relationships of species within the Macropodidae (kangaroos and wallabies). Two highly repeated DNA sequences were isolated as buoyant density satellites in the red-necked wallaby and in the wallaroo-euro group. The third probe was a cloned representative of one class of highly repeated species from the red kangaroo. Radioactively labelled probes of these three repeated sequences were used to determine the incidence and distribution of each in number of macropodid species. The results were consistent with a monophyletic origin of the macropodid species and showed in particular, that the red-necked wallaby is closely related to the red kangaroo and to the euro-wallaroo group. In addition, the data indicated that the tammar and the agile wallaby were closely related. The results also favour the current taxonomic status of the eastern and western grey kangaroos as closely related but separate species.

Animals↗
PubMed1988

[Detection of human papillomavirus types 16 and 18 DNA sequences in the screening of the cells related with carcinoma in situ of the uterine cervix--application of in situ hybridization for cytologic diagnosis].

In order to investigate the relationship between the presence of human papillomavirus (HPV) DNA and cervical carcinoma, we examined the cervical screening cells as well as the biopsy specimens obtained from 3 cases of severe dysplasia, 13 cases of carcinoma in situ (CIS) and 2 cases of microinvasive carcinoma for the presence of HPV types 6, 11, 16 and 18 DNA by DNA-DNA in situ hybridization using the biotinylated HPV DNA probes. The results of in situ hybridization analysis revealed that HPV 16 DNA sequences were detected in the nuclei of koilocytosis of severe dysplasia and CIS cases. The nuclei of atypical cells obtained from cervical screening cells were positive for HPV 16 or 18 DNA sequences. Two CIS cases were positive for the presence of HPV 16 and 18 DNA sequences. None of them contained HPV 6/11 DNA sequences. Eighteen cervical screening cases were examined and 10 contained HPV 16 DNA sequences and 6 contained HPV 18 DNA sequences. We suggest that the identification of HPV DNA types in cervical screening cells by in situ hybridization might be of diagnostic and prognostic value in early cervical neoplasia.

Carcinoma in Situ↗
PubMed1994

Complete DNA sequence of yeast chromosome II.

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

Base Composition↗
PubMed2004

Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure.

Molecular dynamics (MD) computer simulations have been carried out on four systems that correspond to an infinite array of parallel ordered B-DNA, mimicking the state in oriented DNA fibers and also being relevant for crystals of B-DNA oligonucleotides. The systems were all comprised of a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charges. The sequence of the double helical DNA decamer was d(5'-ATGCAGTCAG)xd(5'-TGACTGCATC). The counterions were the two natural polyamines spermidine(3+) (Spd(3+)) and putrescine(2+) (Put(2+)), the synthetic polyamine diaminopropane(2+) (DAP(2+)), and the simple monovalent cation Na(+). This work compares the specific structures of the polyamine- and Na-DNA systems and how they are affected by counterion interactions. It also describes sequence-specific hydration and interaction of the cations with DNA. The local DNA structure is dependent on the nature of the counterion. Even the very similar polyamines, Put(2+) and DAP(2+), show clear differences in binding to DNA and in effect on hydration and local structure. Generally, the polyamines disorder the hydration of the DNA around their binding sites whereas Na(+) being bound to DNA attracts and organizes water in its vicinity. Cation binding at the selected sites in the minor and in the major groove is compared for the different polyamines and Na(+). We conclude that the synthetic polyamine (DAP(2+)) binds specifically to several structural and sequence-specific motifs on B-DNA, unlike the natural polyamines, Spd(3+) and Put(2+). This specificity of DAP(2+) compared to the more dynamic behavior of Spd(3+) and Put(2+) may explain why the latter polyamines are naturally occurring in cells.

Base Sequence↗
PubMed1986

Small tandemly repeated DNA sequences of higher plants likely originate from a tRNA gene ancestor.

Several monomers (177 bp) of a tandemly arranged repetitive nuclear DNA sequence of Brassica oleracea have been cloned and sequenced. They share up to 95% homology between one another and up to 80% with other satellite DNA sequences of Cruciferae, suggesting a common ancestor. Both strands of these monomers show more than 50% homology with many tRNA genes; the best homologies have been obtained with Lys and His yeast mitochondrial tRNA genes (respectively 64% and 60%). These results suggest that small tandemly repeated DNA sequences of plants may have evolved from a tRNA gene ancestor. These tandem repeats have probably arisen via a process involving reverse transcription of polymerase III RNA intermediates, as is the case for interspersed DNA sequences of mammalians. A model is proposed to explain the formation of such small tandemly repeated DNA sequences.

Base Sequence↗
PubMed1993

Heritable unstable DNA sequences and hypermethylation associated with fragile X syndrome in Japanese families.

Fragile X syndrome, associated with the fragile site at Xq27.3 (FRAXA), is the most common form of familial mental retardation. The fragile X mutation has recently been characterized as a heritable unstable DNA sequence, p(CCG)n/p(CGG)n, in the FRAXA locus. In the present study, a correlation between fragile X-genotypes in the FRAXA locus and hypermethylation of an adjacent CpG island was examined in four Japanese families with fragile X syndrome. We show here that the heritable unstable DNA sequences in the fragile X chromosome usually increase in size when transmitted by female carriers, and that the degree of methylation in the CpG island correlated with the increased sizes of the unstable DNA sequences. When a hypermethylated full mutation was transmitted by a male to his daughters, both the size of the unstable DNA sequence and the degree of the methylation reduced to the premutation range. Our observations suggest that female meiosis has a greater potential for amplifying unstable DNA sequences and that amplified DNA sequences can be transmitted through germ cells, while male germ cells seem not to be able to tolerate highly amplified unstable DNA sequences.

Base Sequence↗