Application Note
TimeLogic Solutions
For Sensitive, High-performance Oligonucleotide Searching
The DeCypher® and CodeQuest " biocomputing systems deliver the sensitivity
and high-throughput searching required for microarray probe design, SNP mapping,
and RNA interference. These systems process searches on the DeCypher
Engine" accelerator card to deliver performance of hundreds to thousands of
CPUs within a single computer. Our accelerated Tera-BLAST algorithm (1) meets or
exceeds the sensitivity and performance of both NCBI BLAST (2) and
Smith-Waterman for oligonucleotide searches. Profilesearch is also available on
these systems and has been used to increase the speed of Osprey probe design
applications by nearly 100-fold.
Microwave-Assisted
Synthesis of 2,4,6-Trisubstituted Pyrimidines from Acid Chlorides via in situ
Formed Alkynones Utilizing Encapsulated Pd(II) as a Catalyst
By Panagiotis Ioannidis , Ronny Lundin , Pino Pilotti
Pyrimidines constitute a prominent class of heterocyclic compounds; their
derivatives show interesting pharmacological properties. One synthesis approach
that has attracted attention is the reaction of alkynones and amidinium salts
(1).
Comparison
of Insect Cell Expression Systems: Baculovirus vs. InsectDirect" System
By Katie Loomis , Courtney Rockwell , Keith Yaeger , Robert Novy
The InsectDirect" System requires only 48 hours for transient
expression screening in Spodoptera insect cells and can be scaled up to produce
miligram quantities of protein.
Dynamic Arrays: Higher
Throughput than Conventional Platforms for Real-time QPCR
By Chris Heid
Fluidigm has developed a system for real-time quantitative PCR (RT QPCR),
comprised of instrumentation and dynamic arrays—nanofluidic chips for
combining any N samples and and M assays. After a dynamic array is loaded with
cDNA samples and sets of primers and FRET probes, instrumentation automatically
combines samples and assays into all possible pairings within discrete 10 nL
reaction chambers. Our Dynamic Array Reader continuously monitors reactions. In
this note, we describe experiments demonstrating that dynamic arrays yield
reproducibility and dynamic range of detection equivalent to conventional
platforms while offering orders of magnitude higher throughput than 96-well
plates.
A Nanofluidic Chip for
Absolute Quantification of Target Nucleic Acid Sequences
Fluidigm has developed a novel nanofluidic chip that provides reliable
single-copy sensitivity and absolute quantification of target nucleic acid
sequences. The Digital Isolation and Detection (DID) chip works by partitioning
a sample/assay (TaqMan® assays) mixture into hundreds to tens of thousands of
reaction chambers, where real-time QPCR reactions are continuously monitored by
our Dynamic Array Reader.
Automating
the digital ProteomeChip" -Filling Process: Microchip Technology,
Synchronized Fluidics, and Motion Control
An adaptive fluidic and motion control MetaModule" from Parker Life
Sciences ensures the accurate and reproducible formation and deposition of
200-nL volumes for the automated protein-profiling system, digital ProteomeChip"
(dPC), from Protein Forest, Inc.
The iPLEX" Assay: A
Genotyping Application for High-level Multiplexing on the MassARRAY® System
By Martin Beaulieu, PhD
Sequenom recently released a novel genotyping assay termed iPLEX" whose
increase in design efficiency and flexibility is possible through the use of
novel, mass-modified terminator nucleotides.
Panorama" Human p53 Functional
Protein Array: A Useful Tool for Accurate Identification of p53 Interactions
By Alicia Pruett
The Panorama Human p53 Protein Functional Microarray contains 49 p53 SNP
variants and one wild-type control. This array utilizes a proprietary biotin-carboxy
carrier protein-tagging technology that ensures only functional proteins are
printed on the microarray slides. The protein sequences are derived from the
Mammalian Gene Collection (MGC), expressed in insect cells, and analyzed to
verify protein sequence.
Gene Expression Analysis
without RNA Isolation
By L. Scott Basehore , Natalia Novoradovskaya , Jeff Braman
We developed a cell lysis buffer that immediately stabilizes nucleic acids for
use in Quantitative Reverse Transcription-PCR (QRT-PCR) without further
processing. Using lysate dilutions as templates, the generated signal is
equivalent to that of purified nucleic acids; RNA in the lysate is stable for
storage up to six months at –20°C.
Articles
Gene Expression Analysis Using
Methods of Computational Intelligence
By Gary B. Fogel
The ever-increasing application of microarrays for gene expression analysis has
led to similar expansion in the number of algorithms and methods used for data
interpretation. Microarray techniques make it possible to monitor the expression
of thousands of genes simultaneously from a given cell type.
Immobilization
of Oligonucleotides on a Silicon Surface
By Patrizia Di Pietro , Enrico Alessi , Floriana San Biagio , Luigi La
Magna , Gaetano Panvini , Gianfilippo Scicolone , Salvatore Oliveri , Salvo
Coffa
A new method for affixing DNA oligonucleotides to silicon surfaces increases
signal intensity 20-fold compared to glass, enabling a silicon field-effect
electrolyte-insulator-semiconductor (EIS) sensor that directly detects DNA
hybridization.
