Gene analysis techniques最新文献

We measured local compositional complexity (LCC) of DNA sequences by calculating Shannon information content over mononucleotide frequencies. Eukaryotic DNA appeared to be “simpler” than bacterial DNA even at the level of short oligonucleotides. Moreover, different DNA functional domains displayed different compositional complexity in a systematic manner. In particular, the complexity of exon sequences was systematically higher than the complexity of corresponding introns. We therefore present examples of complexity charts (plots of complexity versus position in sequence) for pre-mRNA sequences from higher eukaryotes. By taking a window width of 100 nucleotides and a window step of 1 nucleotide, introns can be distinguished from exons in the majority of cases studied. Complexity charts of immunoglobulin variable regions allowed correct mapping of exons and introns in these sequences as well, a task was impossible with commercial programs available to date.

We have developed a simple and quick method (“wick blot”) for detecting the presence of specific DNA sequences i in plants, using radiolabeled DNA probes. The method requires only small amounts of tissue, about 15–25 mg. More than a hundred samples per day can be easily extracted and blotted. It works well on various species and tissues, including leaves, embryos, and callus. The method is ideally suited for screening large numbers of putative transformants, especially populations that have not been screened by prior selection.

Here we present the SequencesEditingAligner system for editing multiple, aligned genetic sequences. This is an interactive multi-window color system that displays more than 3500 nucleotides or amino acids. The system handles nucleic acid or protein sequences with or without secondary structure data. More than 300 sequences, each more than 1500 elements in length, may be analyzed together. With the system scientists can classify elements, align sequences, edit them, fund consensus patterns, and simultaneously generate oligomer frequency histograms and other statistics.

We describe a general method for the synthesis and cloning of cDNA, applicable to cases in which the availability of biological material for mRNA extraction is extremely limited. A protocol allowing amplification of a heterogeneous mixture of cDNAs by the polymerase chain reaction has been devised and applied successfully to the construction of an apparently representative cDNA library, using as a model of a scarce RNA source 50 mouse ovulated eggs that can yield a maximum of 1.75 ng of poly(A)⁺ RNA. However, about 5% of the material obtained after amplification was adequate for cloning. Using the cloned sequences, we have derived a preliminary indirect measurement of the sequence complexity of the maternal poly(A)⁺ RNA in this mammalian oocyte.

Two fast and effective methods for high-scale purification of linear phage λ DNA and circular double-stranded M13 replicative form are presented. A substantial reduction of time is attained by avoiding the long-term CsCl gradient centrifugations and dialysis common to standard procedures. Biologically active DNA preparations, free of chromosomal DNA and RNA, are obtained by including a simple gel filtration chromatography as the last step of purification. Yields are comparable to those from previously described methods.

Bacteriophage λgt11 has been used quite extensively for producing cDNA libraries. The cDNA inserts are usually subcloned into a plasmid vector for large scale production and analysis. However, isolating the recombinant DNA of interest from the phage clones can be a tedious task. Since the E. coli strain Y1088 used for λgt11 phage infection carries a pBR322-derived plasmid endogenously, we reasoned that this endogenous plasmid could be used directly for cloning the cDNA phage insert. In this report, we describe a method in which cDNA inserts from λgt11 phage were cloned directly into the pBR322 plasmid vector, by-passing the time-consuming procedures of preparing plasmid DNA as a subcloning vector. This method is likely to be extended to the cloning of DNA inserts derived from other phage λ vectors when bacteria containing endogenous pBR322 are used as host cells.

Rat fibroblast cells carrying an exogenous normal or mutant T24 human H-ras1 gene were transfected with plasmids carrying the normal or mutant T24 H-ras1 gene promoter linked to the reporter chloramphenicol acetyl transferase (CAT) gene and the cells were treated with insulin. We found that the H-ras1 gene was positively autoregulated and that insulin potentiated the response of the T24 ras p21 to the H-ras1 gene promoter. We have also examined the effect of insulin directly on the H-ras1 promoter by treating stable transfectants obtained after transfection of rat fibroblasts with plasmids carrying the normal or mutant T24 H-ras1 gene promoter linked to the reporter CAT gene and the selectable marker aminoglycoside phosphotransferase (aph) gene. We found that insulin appeared to have no direct effect on the H-ras1 promoter in this case, suggesting that the effect is mediated through the ras p21 oncogene product. We suggest that the mutant T24 H-ras p21 protein mediates the action of insulin.

A number of operator-binding proteins contain similar sequence features to Cro and cI repressors of bacteriophage and CAP protein of Escherichia coli, such as conserved amino acids at constant positions. However, these sequence patterns also occur in proteins that are not operator-binding. We use sequence analogy information in conjunction with a pattern recognition algorithm. The functional and structural properties, e.g., distributions of hydrophobicity, hydrophilicity, charged amino acids, electrostatic free energy, and helical structures of protein are also considered. Within the framework of discriminant analysis, we calculate the above variables and search for a better combination of variables. To assess the discriminatory power of these variables, we allocated additional sequences and predict DNA-binding regions of regulatory proteins not included in the training set.