Stratagene

About: Stratagene is a based out in . It is known for research contribution in the topics: Nucleic acid & Gene. The organization has 161 authors who have published 232 publications receiving 17223 citations.

Methods of detecting a target nucleic acid

Abstract: The invention relates to compositions and methods of generating a signal indicative of the presence of a target nucleic acid in a sample, where the method includes forming a cleavage structure by incubating a sample comprising a target nucleic acid with a probe. The invention also includes the steps of cleaving the cleavage structure with a nuclease to release a nucleic acid fragment to generate a signal, wherein generation of the signal is indicative of the presence of a target nucleic acid in a sample.

Improved method for more efficient electroporation

Abstract: This invention provides improved electroporation methods for transferring nucleic acids of interest into host cells, wherein the host cells are (1) suspended in a substantially non-ionic solution comprising at least one sugar or sugar derivative, (2) mixed with the nucleic acids of interest, and (3) electrically treated. Also, this invention provides for kits used in the method for transferring nucleic acids into host cells.

Temperature sensitive mutant of bacteriophage T4 endonuclease VII

Abstract: The subject invention provides for a method of selectively cloning homoduplex nucleic acid molecules, in particular, by using a strain of host cells that contains a conditionally expressed and/or conditionally active mismatch-recognizing enzyme, e.g., a temperature sensitive variant of the gene encoding the endonuclease VII from phage T4. Using this host strain, the invention features a novel cloning method that selects for PCR products that are devoid of PCR-generated mutations.

Using universal human reference RNA in microarray gene expression studies

Abstract: s: Session II 7 6 Norman, Sylvia [64] Analysis of TP53 mutations in human malignant gliomas Sylvia Norman1, Adrienne Scheck2 & Jeff Braman1 1Stratagene, La Jolla, California, USA 2Barrow Neurological Institute, Phoenix, Arizona, USA TP53 is involved in the regulation of the cell cycle, response to DNA damage and induction of apoptosis. Mutations in this gene are thought to contribute to the development, progression or both of a variety of tumors, including human malignant glioma. Molecular analyses of primary malignant gliomas have demonstrated cellular heterogeneity in gene loss, rearrangement, amplification, transcription and translation. Furthermore, the rapid recurrence of this tumor demonstrates the presence of cells that are intrinsically resistant to therapy. Whether mutations in TP53 contribute to therapy resistance and tumor recurrence in malignant gliomas is not known. To determine if TP53 mutations are indicative of cells with a selective advantage that contributes to the survival and/or recurrence of glial tumors, we undertook a study to compare matched cells from primary and recurrent tumors from the same patients. We will present results from our analysis of TP53 mutations present in cells derived from both primary and recurrent glial tumors using polymerase chain reaction and sequence analysis to screen for mutations in exons 5–8 of TP53. Novoradovskaya, Natalia [65] Using universal human reference RNA in microarray gene expression studies Natalia Novoradovskaya1, Nicki Chin2, Terry Payette1, Alexander Pergamenschikov2, Michael Fero2, David Botstein2 & Jeff Braman1 1Stratagene, La Jolla, California, USA 2Stanford University, Stanford, California, USA The expression profiles of thousands of genes can be analyzed simultaneously by hybridizing labeled complementary DNA targets to microarrays. Two-color hybridization allows comparison of two samples labeled with different fluorescent dyes on the same microarray. Normalized signals are expressed as the ratio of signals from Cy5 experimental and Cy3 reference probes. Use of a common reference sample across multiple experiments provides reliable data comparison. A reference sample should provide a hybridization signal at as many probe elements as possible. We chose 21 human cell lines, representing different tissues, to approximate the expression profile of all human genes. The expression profile of each individual cell line and that of a pool of RNAs from 21 cell lines were compared. Hybridization was performed using 24K probe element human microarrays (Stanford University) and GeneConnection Discovery microarrays (Stratagene). Signal distribution on these microarrays demonstrates that reference cDNA hybridizes to a larger number of tethered probes than cDNA from any single cell line. Ten different cell lines were chosen for Universal Human Reference RNA, providing optimal coverage on human microarrays; these can be used as a reference sample for any microarray experiment. Nuchtern, Jed [66] cDNA microarray analysis of differential gene expression in MYCN-amplified neuroblastoma tumor cells Jed Nuchtern1, Jason Shohet1, Susan Stuart2, M. John Hicks1 & Susan Burlingame1 1Baylor College of Medicine, Houston, Texas, USA 2Incyte Genomics, Palo Alto, California, USA Neuroblastoma is a common pediatric solid tumor that is frequently incurable. Biological risk stratification implicates amplification of the MYCN oncogene as a robust marker for poor prognosis. We have undertaken an analysis of gene expression in MYCN-amplified and non-amplified neuroblastoma tumors based on complementary DNA microarrays to advance our knowledge of the pathogenesis of this aggressive disease. We isolated messenger RNA from tumor cell primary cultures of two INSS stage 4 neuroblastoma patients, one with MYCN amplification and the other with normal MYCN copy number. Relative gene expression was determined after hybridization of the fluorophore-labeled cDNAs to a human cDNA microarray representing over 6,800 unique expressed genes. Using a differential gene expression ratio of 3.5 as a screening criterion, we identified 370 unique genes for further analysis. Of these, 78 were upregulated in the MYCNamplified neuroblastoma and 292 had decreased expression. Amplification correlated with increased transcript levels of genes associated with cell proliferation, including cell cycle regulatory genes such as CDC2 and CDC28 protein kinase, and the Ki-67 antigen, as well as many other annotated molecules not previously linked to MYCN amplification and several uncharacterized expressed sequence tag sequences. A coherent group of genes was downregulated in the MYCN-amplified cells, including the genes for the class I and class II major histocompatibility complex antigens, the gene for peptide antigen transporter TAP1, and several interferon responsive transcripts. MYCN amplification correlates with a distinct gene expression pattern in neuroblastoma that is consistent with the clinical phenotype of these tumors. Further characterization of this motif should enable the development of new therapies for these difficult tumors. O’Connor, Maureen [67] Identification of genes that are differentially expressed in response to EGF receptor signaling in A549 lung cancer cells using a combination of suppression subtractive hybridization and microarrays Maureen O’Connor, Alain Guimond, Christiane Cantin & Joanne Magoon Biotechnology Research Institute, Montreal, Quebec H4P 2R2, Canada Since current treatments for almost all patients with non-small-cell lung cancer are not satisfactory, and since prognosis is adversely affected by the overexpression of EGF receptors, we are attempting to identify new genes whose expression is modulated by the EGF signaling pathway in A549 lung carcinoma cells. The cells were treated with either EGF or C225 (a neutralizing antibody that blocks the EGF receptor). We have shown that these treatments affect the epithelial-to-mesenchymal transdifferentiation of these cells. We prepared complementary DNA libraries from EGF-treated, C225Ab-treated or control cells and subjected them to suppression subtractive hybridization to identify both upand downregulated genes. These enriched cDNAs were fluorescently labeled and used to screen 9,600 human © 20 01 N at u re P u b lis h in g G ro u p h tt p :/ /g en et ic s. n at u re .c o m © 2001 Nature Publishing Group http://genetics.nature.com

Electrophoresis temperature feedback controller

Abstract: A method of (and apparatus for) electrophoresis in which the gel temperature is controlled automatically. A sensor may measure a gel temperature and a processor may control a power supply for the electrophoresis process in response to that measurement. Measurements may be made at predetermined times (e.g., periodically) and the processor may determine control settings for the power supply based on a preferred temperature for the electrophoresis process. The preferred temperature for the electrophoresis process may be a predetermined temperature which is chosen so that the electrophoresis process operates at or near the highest speed which is unlikely to break the glass plates.