Applied Biosystems

About: Applied Biosystems is a based out in . It is known for research contribution in the topics: Mass spectrometry & Nucleic acid. The organization has 1521 authors who have published 1579 publications receiving 285423 citations.

Large-Scale Economic Synthesis of Antisense Phosphorothioate Analogues of DNA for Preclinical Investigations

Abstract: The therapeutic potential of antisense oligonucleotides will heavily depend on a balance of two factors: pharmacologic effectiveness and cost of production. Pharmacologic optimization will be achieved to a limited degree in in vitro systems, but substantial progress can only be made in the context of appropriate in vivo models. The quantities of synthetic oligonucleotides required for modest in vivo testing are several thousandfold greater than can be produced by conventional DNA synthesis technology and 10(5)-10(7)-fold greater for preclinical and clinical evaluation. Cost-effective synthesis and purification cannot be achieved by extrapolating current technologies to scales commensurate with these quantities. Recent interest in anti-HIV (anti-rev) phosphorothioate analogues of DNA (approximately 28-mers) has prompted us to develop scale-up methodology for routinely producing gram amounts of such analogues. These results and considerations given to producing clinical and commercial quantities were discussed.

Determination of peptide sequences

Abstract: An apparatus and process are used to cyclicly degrade a peptide to be sequenced, arriving at a set of amino acid residues for each cycle. The amount of each amino acid residue is quantitatively measured in each set, then a background level is fit to each cycle to obtain a background fit. A measure of dispersion is then calculated for the background fit, and the measured amounts of amino acid residues in each cycle are normalized relative to the background fit. The largest normalized background-corrected residue amount in each cycle then provides a sequence assignment that can be used for further correction steps if desired.

5′ Nuclease Assays for the Loci CCR5-+/Δ32, CCR2-V64I, and SDF1-G801A Related to Pathogenesis of AIDS

Abstract: Background: Variations within the human genome play important roles in human disease. To study variations related to susceptibility to AIDS, we have developed 5′ nuclease assays that eliminate post-PCR molecular biology steps. Methods: TaqMan assays based on the 5′ nuclease activity of Taq polymerase and fluorescent resonance energy transfer were developed to score alleles at the biallelic loci CCR5 - + /Δ 32 , CCR2-V64I and SDF1-G801A . For each assay, 72 samples were analyzed. Data collection and analysis were performed on the Prism 7700 Sequence Detection System. For comparison with gel electrophoresis methods, each locus was also scored on a subset of 24 samples, using restriction enzymes or single-strand conformational polymorphism (SSCP). Results: Clear allelic discrimination was obtained on each of the 72 samples for all three TaqMan assays. The TaqMan scores for the subset of 24 samples were concordant with the restriction enzyme and SSCP scores. Conclusions: Because of its simplicity, speed, and potential for automation and miniaturization, TaqMan is an excellent candidate for investigation of genetic variation in clinical, research, and forensic settings.

Configurations, systems, and methods for optical scanning with at least one first relative angular motion and at least one second angular motion or at least one linear motion

Abstract: Methods and optical systems for scanning of a target sample, including methods and systems using a low mass scan head and methods and systems for conducting a scanned optically transduced assay where the scanning includes at least one first relative angular motion and at least one second angular motion or at least one linear motion. The present invention also relates to methods and systems for performing sample assays, and for producing and measuring optical responses and signatures.

Semi-automated PCR method for quantitating MDR1 expression

Abstract: The MDR1 gene is involved in drug resistance in man y hematopoietic and solid tumors The Quantitative PCR System 5000 ™ (QPCR-5000; Perkin-Elmer) is a new instrument system tha t uses electrochemiluminescence to automatically quantitate pol y merase chain reaction (PCR) products A comparative study b e tween radioactively labeled PCR ( 3 2 P-PCR) and QPCR was pe r formed to analyze the MDR1 gene expression in the drug-resistan t (Doxorubicin) cell lines Dox40, Dox6, the parental cell line 8226/S , CEM Dox1 and three acute myeloid leukemia (AML) patient sam ples Using the Dox40 and Dox6 resistant cell lines, we compared the sensitivities of QPCR and 3 2 P-PCR A strong signal was ob tained from QPCR at 20 to 25 cycles (which is in the linear range fo r quantitation), while a weak signal was obtained using 3 2 P-PCR a t the same cycle number Dilution experiments gave better precision with the QPCR than with the radioactive method AML samples wer e studied with the MDR1-specific MAbs MRK16 and 4E3, and the e f flux function was analyzed using Rh-123 retention in the absence o r presence of verapamil The three samples showed high (D = 079) , medium (D = 052) and negative (D = 008) p-glycoprotein (P-gp ) levels and correlated with efflux function The MDR1 / β 2 -M mRNA ratios for 3 2 P-PCR were 041, 040 and 012, respectively, and wer e 0127, 0097 and 0028, respectively, for QPCR There were signif i cant differences between the samples with high and medium P-gp levels comparing the two methods Very low levels of MDR1 in CEM Dox1 cells could be detected only by QPCR In conclusion, QPCR was found to be more reproducible, accurate and sensitive than