The BiosearchTech Blog

Digital PCR – improving reproducible molecular methods in the clinic

Posted on Thu, Apr 06, 2017 @ 08:40 AM

A recent study coordinated by LGC and published in the journal Analytical Chemistry, has demonstrated the potential of digital PCR (dPCR) to improve the reproducibility of routine clinical testing between facilities.

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Topics: Real-time PCR

qPCR-based Molecular Diagnostics at the Forefront of Zika Surveillance

Posted on Tue, Aug 23, 2016 @ 02:00 PM

As the Zika virus outbreak spreads, a wave of international concern has grown, and scientists have scrambled to overcome the significant challenge of diagnosing the virus so it can be treated effectively. Fortunately, a new multiplexed-qPCR assay using Dual-Labeled BHQ® probes from LGC Biosearch Technologies has recently been developed that can distinguish between Zika and other viral infections that cause similar symptoms.

Zika is a single-stranded RNA arbovirus, spread by the Aedes aegypti and Ae. albopictus mosquitoes1. These mosquito species are also the same vectors that spread other viral pathogens such as Chikungunya and Dengue, both of which can present similar symptoms as those of Zika. It’s been a true clinical challenge to diagnose and differentiate between Chikungunya, Dengue, and Zika infections.

On February 1, 2016 the World Health Organization (WHO) released a statement of public health concerns over a link between Zika virus and prevalence of microcephaly in the offspring of infected individuals2. Of all the South American countries affected by Zika, Brazil has been hardest hit, with an estimated 1.5 million cases since 20153. Subsequent to the announcement, concern has grown internationally due to the 2016 Olympic games in Rio de Janeiro, Brazil, coinciding with the outbreak. Recently, Centers for Disease Control and Prevention (CDC) issued a historic travel advisory relating to the continental United States due to localized transmission within a region of Miami, FL4,5. Zika cases have also been reported in numerous other US locations, particularly in the territory of Puerto Rico which is under a public health emergency as of August 12, 2016 (see inset map).  CDC advises travelers to take precautions against Zika, and recommends those experiencing symptoms to meet with their physicians6.

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Topics: Real-time PCR

Photoblog: Behind the scenes of oligo synthesis

Posted on Wed, May 18, 2016 @ 03:00 PM

OLIGO
SYNTHESIS
PHOTO
GLIMPSE

We’ve recently captured our talented manufacturing teams hard at work building oligos. Please enjoy this short visual insight into LGC Biosearch Technologies.

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Topics: Molecular Diagnostics, Real-time PCR, Custom Oligos

Nova is the new black

Posted on Thu, Apr 14, 2016 @ 02:00 PM

LGC Biosearch Technologies has developed a new qPCR probe format powered by Black Hole Quencher® technology known as BHQnova™ probes. This probe format incorporates 5’ fluorophores and 3’ BHQ modifications as seen in standard BHQ® probes, but also introduces a novel Nova quencher placed internally between bases 9 and 10 from the 5’ end of the oligo.

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Topics: Real-time PCR

Introducing BHQnova Probes for qPCR - Join the Early Access Program

Posted on Mon, Feb 29, 2016 @ 02:00 PM

LGC Biosearch Technologies is announcing the upcoming release of a new qPCR probe format known as BHQnova™ probes. This is an exciting addition to the full range of BHQ qPCR probes including our standard BHQ® hydrolysis probes and our compact BHQplus® probes. The new BHQnova probe is a double-quenched probe, which includes the typical 5’ reporter dye and 3’ BHQ modifications, but also incorporates an additional internal “Nova” quencher. This new probe format allows for longer probe sequences, maintains excellent quenching efficiency, and improves signal-to-noise ratio (S:N) resulting in robust amplification curves. The BHQnova probe format presents yet another option that allows greater design flexibility to tackle almost any qPCR assay design challenge.

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Topics: Real-time PCR

Know Your Oligo Mod: 3' Spacer C3

Posted on Thu, Oct 15, 2015 @ 02:15 PM

This week, we continue our Know Your Oligo Mod series and we will focus on a very basic, yet extremely versatile modification: 3’ Spacer C3. This modification is just a short 3 carbon chain (C3), which is attached to the terminal 3’ hydroxyl group of the oligonucleotide.

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Topics: Real-time PCR, Oligo Modifications

And the Consensus (Sequence) is...

Posted on Thu, Jun 11, 2015 @ 02:31 PM

Studying the expression level of RNA transcripts is often complicated by the fact that many DNA sequences are transcribed into multiple RNA isoforms. Or, in cases with microbes, each strain can represent a different sequence variant due to the frequency of mutations in these organisms. Despite these complications, it is still possible (in some, but not all, cases) to design a functional assay to detect multiple variants or isoforms of a gene or transcript. In other words, design one assay to specifically detect multiple targets. In this article, we will go over the basics of designing your assay to detect multiple transcripts at once.

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Topics: Real-time PCR, RNA FISH

MIQE Goes Digital with Open Access qPCR Guide

Posted on Thu, May 21, 2015 @ 02:00 PM

Since its inception, qPCR has been recognized as a powerful molecular method. However, the application of this technique in research has not always been straight-forward or standardized. In 2009, a group of qPCR experts published a series of standards for the execution, analysis, and reporting of qPCR data. These guidelines were dubbed the Minimum Information for Publication of Quantitative Real-Time PCR Experiments, or simply MIQE, and have now become the definitive reporting method adopted by a number of scientific journals.

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Topics: Real-time PCR

Molecular Methods Research Finds a New Home

Posted on Thu, Apr 30, 2015 @ 02:00 PM

The need for improved diligence in research reporting has been echoed in numerous publications which cast doubt on the validity of current scientific research and the reproducibility of published data. This notion in research has also been summarized in the popular acronym borrowed from computer science - G.I.G.O. standing for “garbage in, garbage out”. Meaning, the conclusions which can be derived from research are only as solid as the data those conclusions are based upon. A large step forward in combating ‘bad science’ was accomplished in late 2014 by the introduction of a new open access journal titled Biomolecular Detection and Quantification (BDQ).

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Topics: Real-time PCR

How Much is Your qPCR Assay Really Costing You?

Posted on Thu, Apr 02, 2015 @ 02:00 PM

In the setup of a qPCR experiment, one of the first decisions to make is which detection method to use. This generally boils down to two common options:

  1. DNA-binding Dyes
  2. Dual-labeled Probes

The DNA binding dyes, also known as intercalating dyes, are often referred to as SYBR® Green assays due to the popularity of this particular detection dye’s trade name. On the other hand, the most common probe-based format is the dual-labeled probe (hydrolysis probe) positioned internally to the amplicon sequence, containing the desired fluorophore on one end and a quencher at the other.

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Topics: Real-time PCR

BHQplus Probes Optimize Multiplex Competitive qRT-PCR in Diagnostics

Posted on Thu, Jan 29, 2015 @ 02:00 PM

In a recent webinar, Dr. James Willey describes a two color fluorometric assay for more robust quantitation of nucleic acids in highly degraded FFPE and FNA samples. Wiley’s method, described in a recently published article in the journal PLoS One, employs a patented mixture of internal and external standards paired with a pre-amplification step. This system enables measurement of transcription levels of three lung cancer-associated genes and a control gene in clinical samples. All of the fluorometric probes used in the method are labeled with Black Hole Quencher® dyes in BHQplus® probes. The compact design of BHQplus probes is optimal for this application as it confers enhanced sequence discrimination for each target. The webinar takes the audience through assay development, reagent preparation, and the analytical validation experiments.

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Topics: Real-time PCR

A Successful Duo for Accurate, Speedy, and Economical SNP Genotyping

Posted on Thu, Jan 08, 2015 @ 11:30 AM

Single Nucleotide Polymorphisms (SNPs) have been widely studied for over 15 years, and have applications in forensics, disease susceptibility studies, pharmacogenomic and other personalized medicine applications, crop and livestock breeding programs. Numerous genetic methods and companion platforms have been developed for SNP detection encompassing DNA sequencing, microarrays, mass spec, and PCR based techniques. For high sample throughput applications, PCR analysis has emerged as the method of choice for rapid targeted SNP analysis, facilitated by new platforms and reagent cost improvements. On October 30, 2014, Biosearch Technologies sponsored a webinar showcasing the utility of the BHQplus® probe technology for qPCR based SNP analysis. Presenter Cassie Keppel, Laboratory Operations Manager at Douglas Scientific, shared some compelling data showing the accurate and economical utility behind the use of Biosearch’s BHQplus probes on Douglas Scientific’s Array Tape® platform. In this article, we highlight some of Cassie’s findings on the dramatic cost-savings that the BHQplus probe and Array Tape platform combination offers.

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Topics: Real-time PCR, Product Information, SNP Genotyping

Check out our new website qPCR Design Lab @ qPCRdesign.com

Posted on Thu, Oct 23, 2014 @ 02:00 PM

Biosearch Technologies has launched qPCRdesign.com, a new microsite targeted specifically for your quantitative PCR needs. In the qPCR Design lab, users can design, analyze, experiment, and play with a variety of interactive tools at their disposal. This is an excellent resource for both new and seasoned qPCR users to access information, advice, or the tools to quickly perform calculations and begin performing assays in no time!

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Topics: Real-time PCR, Design Services

Delivering Oligos by Nanomole Units

Posted on Wed, Oct 15, 2014 @ 11:00 AM

Different oligonucleotide manufacturers deliver probes and primers in a variety of different measured units including moles (e.g. nmol), molarity (e.g. µM), optical density at 260 nm (e.g. OD), and even the number of reactions a scientist can perform.  Although these measured units are all technically correct, it is important to understand what each unit is telling you so you know exactly what you are receiving. In this article, we will quickly cover the basics of each oligo delivery unit to help you make the most informed decision when placing your next order for probes and primers.

Quantity in Moles - abbreviated mol, commonly nanomole; (nmol)

This is the default delivery unit Biosearch uses for delivering oligos.  The quantity of moles refers to the number of molecules present in the delivered amount. 5 nanomoles (nmol) of one probe will have the same number of molecules as 5 nanomoles (nmol) of another oligo even if the sequence and modifications are totally different. Because the quantity of moles is independent of the physical characteristics and sequence of each oligo compound it makes it a very convenient and transparent unit of measure. Similarly, the use of moles makes it very easy to dilute your oligos to a fixed molar concentration. When oligos are measured in moles, we know that we can compare one oligo to another very easily.  This is not the case with units such as OD as we will see below.

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Topics: Real-time PCR, Custom Oligos

RT-qPCR Molecular Diagnostics Assist Workers at the Forefront of Ebola Outbreak.

Posted on Thu, Sep 25, 2014 @ 11:30 AM

The largest recorded Ebola Virus Disease outbreak in history continues to devastate the West African region. This epidemic has presented a public health emergency to national and international disease control centers with aid workers tirelessly working to assist affected communities. Ebola is a single-stranded RNA virus that has five known strains, four of which are pathogenic to humans. The current outbreak is a result of the spread of the Zaire ebolavirus (EBOV) strain which previously averaged a 78% mortality rate 1. In a recent update from the World Health Organization, upwards of 2,600 deaths have been reported as result of the viral infection over the last several months 2.

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Topics: Molecular Diagnostics, Real-time PCR, Biodefense

One Step too Many? Simplify your qPCR Protocol.

Posted on Thu, Feb 27, 2014 @ 10:02 AM

Don’t waste time performing an extra step. Cut back on pipetting and order a ValuMix™ Assay to have your probes and primers delivered in one tube. The oligos are formulated according to the quantities you specify and delivered dry for maximal stability. ValuMix Assays expedites your research because they:

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Topics: Real-time PCR, Product Information

30 Years: The Impact of PCR

Posted on Thu, Sep 05, 2013 @ 09:29 AM

Do you remember when the most popular method of DNA amplification involved multiple hybridizations, followed by single or 2-primer extension and ligation steps? DNA amplification was a long and tedious process, and if people followed the saying “if it ain’t broke, don’t fix it” the world would certainly be in a different place today. Without rapid PCR assays, it could take several months for medical test results, innocent people would continue to overcrowd prisons, and less research will be achieved but more interns hired (someone needs to perform all those hybridizations).

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Topics: Real-time PCR

RT-qPCR and the Stellaris FISH Method

Posted on Fri, Apr 26, 2013 @ 10:32 AM

A "Referral from the Doctor" Blog Article-

Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is a sensitive and
robust method for analyzing RNA. It has been used to corroborate the findings of other genetic methods, such as microarray and RNAse protection assays, and has become the gold standard for quantifying changes in gene expression. Stellaris FISH is a new RNA detection method that provides direct quantification of transcripts in situ, with potential to become the standard for mRNA and lncRNA interrogation using microscopy.

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Topics: Real-time PCR, RNA FISH, Referral from the Doctor

qPCR Probes at work: Innovative CLIA test for NSCLC staging

Posted on Tue, Mar 06, 2012 @ 11:00 AM

Non-squamous, Non-small cell lung cancer (NSCLC), the most common cause of death in the US and globally, has recently been dealt a significant blow as a result of collaborations among teams from UCSF Thoracic Oncology, Kaiser Permanente Research, and the China Clinical Trials Consortium (CCTC) uniting hospitals and universities across mainland China.  

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Topics: Molecular Diagnostics, Real-time PCR

Factors affecting fluorophore performance in qPCR

Posted on Wed, Jan 11, 2012 @ 09:00 AM

A "Referral from the Doctor" Blog Article-

In qPCR, fluorescent modified oligos may be either linear or non-linear in structure. In either conformation, Förster resonance energy transfer (FRET) combined with the static quenching mechanism inhibits reporter dye emission until hybridization with the target (Read Quenching Mechanisms in Probes to learn more about FRET and static quenching). Upon hybridization the quencher and reporter dye are separated spatially, interrupting the quenching mechanisms and permitting fluorescence emission from the reporter dye. The increase in signal intensity with repeated PCR cycles indicates the accumulation of product and allows for accurate quantification of template. Gene expression analysis by qPCR is dependent upon direct comparisons between the normalized fluorescence emission of individual samples against a standard curve or through ‘relative’ comparison against expression of an internal calibrator gene.

How do I know how bright the dye will be?

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Topics: Real-time PCR, Referral from the Doctor

Fluorescence Quenching Mechanisms for Dual-Labeled Probes

Posted on Wed, Jun 29, 2011 @ 07:44 AM

A "Referral from the Doctor" Blog Article-

Fluorescent probes are used in biochemical assays to monitor specific events such as binding, cleavage or conformational changes. Dual-labeled probes with a fluorophore and a quencher have many applications in genetic analysis. The efficiency of fluorescence quenching is very distance dependent – if the reporter fluorophore and quencher are far apart, there is fluorescence; if the reporter and quencher are close together in space, fluorescence is suppressed. Typically, the reporter and quencher are placed at specific sites in an oligonucleotide such that a change in their distance will produce a maximal change in fluorescence and effectively signal the event being monitored (often hybridization or nuclease activity). The oligonucleotide acts as a flexible tether linking the fluorescent reporter and quencher. Below, we present fluorescence quenching mechanisms for dual-labeled oligonucleotides in genetic analysis.

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Topics: Real-time PCR, Referral from the Doctor

Multiplexing with Xanthenes

Posted on Wed, Jun 08, 2011 @ 09:13 AM

A "Referral from the Doctor" Blog Article-

Quantitative real-time PCR (qPCR) was developed as a means to detect the presence of target nucleic acids and is routinely used to quantify gene expression through reverse transcription of RNA transcripts.  The detection method depends on a signaling molecule, often a dual-labeled oligonucleotide with a fluorophore (reporter) dye at the 5’ end and quencher dye at the 3’ end. The development of new reporter dyes, true dark quenchers and advancements in probe sophistication enable researchers to improve their genetic analysis.  One significant improvement is in the application of multiplexed qPCR to yield additional data and confidence in the results.

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Topics: Real-time PCR, Referral from the Doctor

qPCR Troubleshooting

Posted on Thu, May 05, 2011 @ 10:23 AM

A "Referral from the Doctor" Blog Article-

Quantitative real-time PCR (qPCR) is based upon the fractional cycle number at which a replicating sample of target DNA accumulates sufficient fluorescence to cross an arbitrary threshold. The threshold is either manually selected or auto-selected to fall several standard deviations above baseline fluorescence and below the plateau phase, where the amplification begins to attenuate. Typically, the threshold is adjusted to the mid-point of the exponential phase of the PCR, at a location suitable for all samples in the experiment. The CT (cycles to threshold) value for a given reaction is defined as the cycle number at which the fluorescence emission intersects the fixed threshold.

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Topics: Real-time PCR, Referral from the Doctor

Biosearch Technologies and Intelligent Medical Devices, Inc. (IMDx) Finalize cGMP Oligo Supply and Licensing Agreements for Molecular Diagnostic Testing (IVD) Products

Posted on Tue, Mar 15, 2011 @ 10:01 AM

Biosearch Technologies, Inc. (Biosearch), a leading supplier of sophisticated oligonucleotide components to the rapidly growing molecular diagnostics industry, and IMDx (privately held), a developer and manufacturer of innovative, clinically impactful molecular test solutions, today announced that Biosearch has licensed access to the BHQ®, CAL Fluor® and Quasar® patents to IMDx.  In addition, Biosearch will manufacture cGMP oligonucleotides for IMDx for use in human in-vitro diagnostics.

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Topics: Announcement, Molecular Diagnostics, Real-time PCR

Between ROX and a Hard Place

Posted on Wed, Nov 10, 2010 @ 09:12 AM

A "Referral from the Doctor" Blog Article-

ROX in qPCR

Quantitative real-time RT-PCR was developed as a means of quantifying gene expression either relatively or absolutely, with accurate and reproducible results. Despite advances in dye chemistries, variability continues to haunt research scientists.  One effort to reduce the observed variability between technical replicates was to include the ROX dye (5- or 6-carboxy-X-rhodamine) as a passive reference in the PCR master mix.

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Topics: Real-time PCR, Referral from the Doctor

Biosearch Technologies and DuPont Qualicon Finalize Agreements for Food Safety Dx

Posted on Fri, Oct 29, 2010 @ 09:24 AM

Biosearch Technologies, Inc. (Biosearch), a leading supplier of sophisticated oligonucleotide components to the rapidly growing molecular diagnostics industry, today announced that the company has licensed access to the BHQ®, CAL Fluor® and Quasar® patents to DuPont Qualicon.

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Topics: Announcement, Real-time PCR, Food Safety

Biosearch Technologies and Seegene Finalize Oligonucleotide Supply and BHQ®, CAL Fluor® and Quasar® Licensing Agreements

Posted on Wed, Oct 20, 2010 @ 08:12 AM

Biosearch Technologies, Inc. (Biosearch), a leading supplier of sophisticated oligonucleotide components to the rapidly growing molecular diagnostics industry, today announced that the company has licensed access to the BHQ®, CAL Fluor® and Quasar® patents to Seegene (KOSDAQ; Korea Securities Dealers Automated Quotations).

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Topics: Announcement, Real-time PCR

Biosearch Technologies Expands Licensing of QIAGEN Scorpions® Patents

Posted on Thu, Aug 12, 2010 @ 08:41 AM

Biosearch Technologies today announces that it has entered into a new license relationship with QIAGEN (NASDAQ: QIA, Frankfurt Prime Standard) providing broad commercialisation rights to Scorpions Primers.  This agreement allows Biosearch the right to manufacture, catalog, and sell Scorpions primer assays into the research, applied, and infectious disease testing markets.

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Topics: Announcement, Real-time PCR, Product Information

Taq Facts

Posted on Tue, Aug 03, 2010 @ 08:14 AM

A "Referral from the Doctor" Blog Article-

When the polymerase chain reaction (PCR) was first described, the Klenow fragment derived from the Escherichia coli DNA Polymerase I was the paramount enzyme for sequence extension. Due to its lack of stability at high temperature, it needs be replenished before each cycle. Upon the discovery of thermophilic bacteria which thrive at temperatures greater than 45 °C, heat-stable polymerases which function at higher temperatures were investigated in an effort to eliminate the need to replenish enzyme following each denaturation cycle.

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Topics: Real-time PCR, Referral from the Doctor

Pipetting for qPCR

Posted on Wed, Jun 09, 2010 @ 08:41 AM

A "Referral from the Doctor" Blog Article-

Research trends in laboratories today increasingly steer towards gene expression analysis and genetic testing, often in the form of qPCR. As reproducibility is essential to genetic research it is imperative that scientists know the fundamentals of micro-volume pipetting.

Forward and Reverse Pipetting: This discussion is limited to the use of manual pipettors. Electronic pipettors are capable of other pipetting techniques such as dispensing, sequential dispensing and diluting which are not discussed here.

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Topics: Real-time PCR, Lab Method, Referral from the Doctor

Easier Online Ordering through RealTimeDesign™ Software

Posted on Wed, May 26, 2010 @ 08:32 AM

RealTimeDesign (RTD TM) Software from Biosearch Technologies is an easy to use, yet powerful assay design application for real-time qPCR. This user-friendly software is available free of charge through our website and requires NO installation. We have recently updated RealTimeDesign software with more options and improvements to the ordering process:
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Topics: Real-time PCR, Design Services

Buy One qPCR Probe & Get One FREE

Posted on Fri, May 14, 2010 @ 09:21 AM

Buy one CAL Fluor® or Quasar® -BHQ® Probe and get a FREE ValuProbeTM BHQ Probe* and calibration standard ($190 in savings!). Simply enter promo code CFQVP upon checkout to receive this offer. Take advantage of this promotion before it expires on June 30, 2010.

Biosearch Technologies offers CAL Fluor and Quasar dyes that span the spectrum, for 2-plex, 3-plex, 4-plex, 5-plex, and even 6-plex PCR. They perfectly complement the Black Hole Quencher dyes, a true dark quencher that extinguishes signal from any fluorophore.

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Topics: Announcement, Real-time PCR

New Product Line! ValuPanel™ Reagents

Posted on Tue, Apr 06, 2010 @ 08:52 AM

We are pleased to introduce ValuPanel Reagents, a new product line of mission-critical probe and primer sets that discriminate different strains of pathogens. This product line culminated from our successful collaboration with Centers for Disease Control and Prevention* (CDC) in response to the 2009 H1N1 pandemic. As of now, ValuPanel Reagents are available for both 2009 H1N1 and seasonal Influenza A subtyping.

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Topics: Announcement, Real-time PCR, Product Information, Biodefense

Black Hole Scorpion® Primers - Killer probes for qPCR

Posted on Wed, Mar 24, 2010 @ 08:57 AM

A "Referral from the Doctor" Blog Article-  

Scorpions®Primers are dual-labeled FRET probes that combine a Molecular Beacon®-like probe structure and a PCR primer element in a single oligonucleotide, allowing for specific target amplification and advanced target detection through a unimolecular or single oligonucleotide driven mechanism.

Structure

Q. What parts are similar to dual-labeled Black Hole Quencher® (BHQ) probes?
A BHQ dye and a 5'-fluorophore covalently bound to the oligonucleotide termini.

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Topics: Real-time PCR, Product Information, Referral from the Doctor

Molecular Beacons - Lights in the storm

Posted on Wed, Mar 10, 2010 @ 11:05 AM

A "Referral from the Doctor" Blog Article-

Molecular Beacons are a special type of dual-labeled oligonucleotide probe. Beacons are hairpin loop structures with a 5'-fluorophore and a 3'-quencher dye. The stem region is a short sequence of 5-7 complementary bases. The loop sequence is complementary to the target sequence. In the absence of target or prior to amplification, the stem anneals to form a closed hairpin conformation which holds the reporter and quencher close together to enable efficient FRET quenching and to promote contact or static quenching. The beacon is engineered such that the probe-target hybrid is more stable than the closed hairpin conformation, which is respectively more stable than a probe-mismatch hybrid. Therefore it is only in the event of a perfect-match hybridization that signal occurs, allowing beacons to discriminate mismatches as small as a single nucleotide polymorphism (SNP).

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Topics: Real-time PCR, Referral from the Doctor

Dual-labeled BHQ probes - Performance to “dye” for

Posted on Wed, Feb 24, 2010 @ 10:20 AM

A "Referral from the Doctor" Blog Article-  

A BHQ® probe is a dual-labeled oligonucleotide covalently labeled with a fluorophore and a Black Hole Quencher® (BHQ) dye.

Structure
 

Q. What are the main components of a dual-labeled Black Hole Quencher® (BHQ) probe?

  • An oligonucleotide, typically 30 bases long
  • A 3' BHQ dye
  • A 5'-fluorophore (reporter) dye
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Topics: Real-time PCR, Referral from the Doctor

This Year's MVP (Most Valuable Practice): Touchdown PCR

Posted on Thu, Feb 04, 2010 @ 10:39 AM

A "Referral from the Doctor" Blog Article-  

The aim of the Polymerase Chain Reaction (PCR) method is to amplify or increase the number of copies of a target sequence. Most often that sequence is part of a gene of interest and the total copy number or relative copy number of that transcript will impart some knowledge to the researcher regarding the impact of a drug, disease status of a sample or may represent a control condition. In some situations, the copy numbers of a particular transcript are very low and it may be necessary to nudge the PCR reaction in favor of amplifying the exact splice variant, family member or a construct the researcher wishes to examine.

 

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Topics: Real-time PCR, Referral from the Doctor

The Grand Ballet: Wine and Biotechnology

Posted on Wed, Jan 27, 2010 @ 11:15 AM

At the third qPCR Symposium, held November 9th -12th in Millbrae, CA, ETS laboratories (ETS) scientist Rich DeScenzo gave a compelling presentation describing the inherent difficulties associated with wine production and quality control. Biosearch Technologies, Inc. is proud of its collaborative efforts with ETS to produce the world's first wine spoilage test kit. Biosearch manufactures the biotechnology used in these test kits, namely Scorpions® Primers, designed by ETS scientists for the identification and quantification of microbes at each stage of fermentation in the maturing wine product. Before we present the technology and methods used in wine spoilage testing, we want to present an overview of what role genetic testing has in the development of aromas and flavors in our favorite dinner libation. The Grand Ballet is an extraction taken from the presentation of Dr. DeScenzo, paraphrased and presented with a bit of artistic license, with permission from ETS. We hope you enjoy it.
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Topics: Real-time PCR

An Alternative to DNAse I heat inactivation: LiCl precipitation

Posted on Wed, Jan 13, 2010 @ 10:04 AM

A "Referral from the Doctor" Blog Article-

Genomic DNA contamination has been a hot topic for qPCR researchers since the beginning. It is impossible to remove all DNA from RNA preparations without additional steps. The most commonly used technique is to incubate with DNAse I. The deoxyribonuclease I (DNAse I) enzyme catalyzes the hydrolytic cleavage of phosphodiester linkages adjacent to a pyrimidine nucleotide. It acts on single-stranded DNA, double-stranded DNA, and chromatin. DNAse I activity will degrade trace amounts of genomic DNA (up to 10 µg/mL) that could otherwise result in falsely positive signals in subsequent RT-PCR reactions. DNAse I is a heat-inactivated nuclease, requiring both the presence of EDTA and temperatures of 75oC for 5 minutes for complete inactivation. The extreme temperatures associated with heat-inactivation of the enzyme may cause damage to the RNA through chemical mediated degradation if even small amounts of metal ions are present. Lower temperatures will not fully inactivate the DNAse before reverse transcription of the RNA to cDNA. Because we cannot discriminate between cDNA and DNA amplification products, initial copy number determination is compromised.

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Topics: Real-time PCR, Referral from the Doctor

A Quick Jump Start to Multiplexing qPCR

Posted on Wed, Jan 06, 2010 @ 10:01 AM

By now, you've no doubt read about the reductions in error, cost and time that can be achieved by multiplexing real time PCR. A common complaint about multiplexing is that, despite its benefits, it is sometimes considered too much of a hassle. This post will address some key factors to consider when planning a multiplexed qPCR assay.

1. Instrumentation and Dye Selection
This one is pretty easy. For a successful multiplex, your instrument needs to be able to excite each of your reporter dyes. Although there are dyes on the market that excite in the far red, you'll be safe using an instrument which excites over the visible spectrum (350-750nm). Biosearch Technologies has developed two essential tools to assist you with dye selection:

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Topics: Real-time PCR, Design Services

Slope Efficiency Equals Manageable and Corrected PCR

Posted on Wed, Dec 09, 2009 @ 12:01 PM

A "Referral from the Doctor" Blog Article-  

ε = m.c.2 (shall I explain? slope efficiency equals manageable and corrected PCR)

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Topics: Real-time PCR, Referral from the Doctor

On the Set of "Making of the Swine Flu Test Kit - Inside Biosearch Technologies"

Posted on Thu, Nov 19, 2009 @ 08:29 AM

Biosearch Technologies recently launched a video, Making of the Swine Flu Test Kit - Inside Biosearch Technologies, which had debuted last week at qPCR Symposium 2009 held in Millbrae, California.  This video is an accurate re-enactment of Biosearch Technologies' rapid production of the H1N1 (Swine Flu) test kit that was developed by the Centers for Disease Control and Prevention (CDC).

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Topics: Molecular Diagnostics, Real-time PCR, Biodefense

Bringing Back a Champion: Competitive Quantitative Real-time RT-PCR

Posted on Wed, Nov 18, 2009 @ 08:08 AM

A "Referral from the Doctor" Blog Article-

Competitive qRT-PCR has become a lost art. Early titans of probe-based PCR used this technique to minimize variability between samples and experiments due to differences in reverse transcription and amplification efficiency. This technique facilitates the absolute measurement of initial gene target copy number based on known copy numbers of a control template.

This is accomplished through the addition of an internal control, a competitor sequence to the mRNA target in the sample. The competitor sequence is similar enough to use the same primer pairs as the target sequence but has a unique central sequence allowing for analysis with a different probe and reporter. Plasmid DNA or in-vitro transcribed RNA is commonly used as a competitor sequence and standard for quantification. To detect the initial copy number of a gene of interest, multiple replicates of a fixed amount of the target mRNA are dispensed into tubes. In the same tubes, 10 fold serial dilutions of competitor RNA are "spiked" in sequentially. Using one set of primers and two fluorogenic probes labeled with different dyes, real-time PCR data can be collected for both sequences simultaneously.

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Topics: Real-time PCR, Referral from the Doctor

BIOSEARCH TECHNOLOGIES TAKES LICENSE TO CDC H1N1 SIGNATURES AND INFLUENZA A SUB-TYPING PATENT

Posted on Wed, Nov 04, 2009 @ 07:47 AM

Biosearch Technologies announced today that the company has licensed from the CDC the novel H1N1 Influenza signatures along with the Influenza A sub-typing panel signatures.  This licensing agreement with the CDC makes Biosearch Technologies the first oligo manufacturer to have the right to manufacture and sell dual-labeled probes and primers bearing the H1N1 and Influenza A sub-typing signatures.

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Topics: Announcement, Molecular Diagnostics, Real-time PCR, Biodefense

Micronics Acquires License to Biosearch Technologies’ Nucleic Acid Assay Chemistries

Posted on Wed, Oct 28, 2009 @ 01:16 PM

 

 

Micronics, Inc., a leading developer of point-of-care molecular diagnostic products, announced today that it has entered into a license agreement with Biosearch Technologies, Inc. for the right to make, have made, use and sell Micronics' products that incorporate Biosearch's proprietary fluorophores and quencher dyes for nucleic acid assays. Under the terms of the worldwide license, Biosearch has granted Micronics a royalty-free use of certain of its chemistries for inclusion in Micronics' infectious disease tests for sale in underdeveloped countries.

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Topics: Announcement, Molecular Diagnostics, Real-time PCR

The New Favorite Reference Gene: 36B4, a.k.a. RPLP0

Posted on Wed, Oct 14, 2009 @ 08:06 AM

A "Referral from the Doctor" Blog Article-

Ribosomes are comprised of two subunits, one small (40S) and one large (60S). The 36B4 gene encodes an acidic ribosomal phosphoprotein P0 (RPLP0), which forms tight associations with the smaller 40S protein (L12). 36B4 protein is part of a pentameric complex that forms a stem-like structure, protruding into the cytoplasm, off of the 60S subunit. This protrusion functions to support the GTPase steps in the translocation of protein synthesis. Why is 36B4 fast becoming the new reference gene for probe-based real time RT-PCR?
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Topics: Real-time PCR, Custom Oligos, Referral from the Doctor

DoD Issues SBIR Grants to Biosearch Technologies

Posted on Thu, Oct 08, 2009 @ 08:13 AM

Biosearch Technologies has been selected for two Small Business Innovative Research (SBIR) grants from the Department of Defense (DoD). Both Phase 1 grants calls for the development of highly sensitive analyte specific reagents (ASRs) for a total of twelve pathogens.  The ASRs are qPCR based, but modified for field deployment.  Both grants include the following target pathogens: Dengue, Rift Valley Fever, Sand Fly Fever, Crimean-Congo Hemorrhagic Fever, Tick-Borne Encephalitis, Chikungunya, causative agents of typhus, spotted fever, anaplasmosis, Ehrlichioses, and Q fever.  If Phase I turns out to be a success, Biosearch expects this project to lead into a multiyear Phase II award.

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Topics: Announcement, Molecular Diagnostics, Real-time PCR

What Genes are Hot, What Genes are Not

Posted on Wed, Oct 07, 2009 @ 02:41 PM

 A "Referral from the Doctor" Blog Article-

 Top 10 Reference Genes for probe-based Real-time PCR in 2009:

• Acidic Ribosomal Phosphoprotein P0 (RPLP0 or 36B4)
• ATP-synthase subunit 5B (A5B)
• Tumor Protein Translationally controlled 1 (TPT1)
• Signal Recognition Particle 14kDa (SRP14)
• TATA-Binding Protein (TBP)
• Eukaryotic Elongation Factor 1A1 (EEF1A1)
• Hypoxanthine Phosphoribosyl-Transferase 1 (HPRT1)
• poly-Ubiquitin (Ubi)

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Topics: Real-time PCR, Referral from the Doctor

Labeling Oligos with Internal BHQ Dyes

Posted on Tue, Sep 29, 2009 @ 08:16 AM

 

When to use an internal Black Hole Quencher (BHQ) label in a fluorescence-quenched probe for real-time qPCR.

When the sequence length of your probe is 30 bases or shorter, we recommend selecting a conventional BHQ label for the 3' end of your probe. We have noticed, however, that probe lengths longer than 30 bases exhibit high background noise and are frequently nonfunctional. They are too long for efficient FRET quenching, a mechanism that is highly dependent upon the distance between the fluorophore and quencher. A shorter average distance between fluorophore and quencher is optimal for a FRET quenching environment, which is common in real-time qPCR experiments.

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Topics: Real-time PCR, Product Information, Custom Oligos

Salt-Free Primer Pair Option Now Available

Posted on Tue, Sep 22, 2009 @ 08:08 AM

Biosearch Technologies will now be offering the option of salt-free primer pairs for purchase with any probe order. A more affordable option for real-time qPCR, these primers offer a higher yield at a faster turnaround time in comparison to cartridge-purified primers.

We have done extensive research to show that the difference in purity specifications does not compromise the quality or performance in assays using the salt-free primer pairs instead of the cartridge purified primer pairs. You can review the Biosearch-conducted purification study by downloading this report.

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Topics: Real-time PCR, Product Information, Custom Oligos

Biosearch Technologies is adding more COLOR to qPCR

Posted on Mon, Sep 21, 2009 @ 02:07 PM

Since its introduction in 2005, the ValuProbe BHQ Probe has become Biosearch Technologies' most popular product sold to the real-time qPCR industry.  Many molecular biologists choose the ValuProbe BHQ Probe because they are quality, superior performing fluorescence-quenched probes that work great for validating and optimizing real-time qPCR assays.

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Topics: Announcement, Real-time PCR, Product Information

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About LGC, Biosearch Technologies

LGC, Biosearch Technologies is the complete Genomics portfolio from LGC. Providing genomic analysis tools, instrumentation and services to the genomic scientific discovery sector worldwide, with focus on across ag bio, pharma and molecular diagnostics. Visit our home page to view our products and services.

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