Read and Reviews
Article -A Beacon in the Night
By Sarah Goforth
[Published 28th May 2001]
10 great reasons to buy Beacon
1. Innovative Algorithms
a) Statistical Optimization: The sophisticated search algorithm calculates
all properties of every possible primer and
probe within the allowed length and positional
boundaries. Every selected primer and probe
must meet all specified criteria. It is rejected
if any parameter falls outside of its tolerance
limits. Beacon Designer™ makes the task of
choosing the best possible oligo set as easy
as clicking a button. For expert users a list
of alternate oligo sets is available and is
sortable by several key parameters.
products use the consecutive screening technique
to choose oligos. Possible oligos are screened
for each parameter in an arbitrary order for
acceptable parameter values and outliers are
eliminated in each screen. The result is highly
dependent on the order of screening and does
not result in the selecting the best oligo.
b) Avoid Cross Homologies: This function is one of the most unique features
of Beacon Designer™ and it ensures that the
oligo sets designed result in specific amplification
and exact detection, BLAST search is run for
the templates against the non-redundant database
of the organism and the results are interpreted
to identify regions of significant cross homologies
Note: We are not
aware of any product that offers this functionality.
c) Default Parameter Selection: Beacon Designer™ provide default parameter
values based on considerable research and
private communications with several experts
and some of the inventors of the qPCR technique.
The default parameters work well for most
assays. For more challenging assays, complete
manual control is available.
Note: This is a
quote from Alex Ryncarz, Epigenomics Inc.,
a long time customer of Beacon Designer™-"Unless
the sequence is exceptionally GC rich or repetitive,
I found that I could simply use the default
parameters. It is not a surprise that some
sequences, especially those shorter than 500
bases and or having a high GC content, do
not provide primer sets or probes with the
default conditions. The inability of the software’s
default conditions to provide primer or probe
designs is an attribute to the consistently
high quality of primer and probe designs that
are produced using Beacon Designer™. Other
design software may also provide good results,
but I have only seen excellent consistency
with Beacon Designer™, which saves both money
2. Many qPCR Assay Technologies
SYBR® Green, TaqMan®, MethyLight, beacons, FRET: Beacon Designer™ enables you to design almost all the popular qPCR technologies including SYBR® Green, TaqMan®, MethyLight, molecular beacons and FRET assays. You can even first test the primers
with a SYBR® Green assay before taking the
next step of purchasing the more expensive
fluorescent labeled probes for any of the
three dual labeled technologies.
software offers only the technology the vendor
recommends and expects the user to buy the
reagents from them. Primer Xpress supports
only TaqMan® assays and Light Cycler software
supports FRET exclusively.
NASBA®, a highly sensitive and specific amplification
reaction that offers several advantages over
other mRNA amplification methods. NASBA® is
an isothermal reaction performed at 41C, which
obviates the need for a thermal cycler and
may facilitate the production of point-of-test
devices. A single-stranded antisense RNA product
is produced during NASBA®, which can be directly
hybridized by a probe sequence to accelerate
post-amplification interrogation of the product.
In contrast to PCR, background DNA does not
interfere with the NASBA® reaction, as single-stranded
RNA sequences are specifically targeted. It
holds a great promise in diagnostic assay
Note: No other
program, to our knowledge, offers NASBA® qPCR
Nucleic Acid or LNA probes are gaining popularity
rapidly for SNP detection qPCR Assay because
of improved real-time PCR assay success. Incorporation
of the LNA bases significantly increases thermal
stability, making shorter probes possible
for standard reaction conditions.
Note: No other
program, to our knowledge, offers easy to
use design capability for qPCR assays with
LNA substituted probes.
5-methylcytosine is the most frequent covalent base modification of the DNA of eukaryotic cells. The development of MethyLight assay for DNA methylation analysis has significantly helped understanding biological processes such as transcription regulation, genetic imprinting, and tumorigenesis. MethyLight assay accurately determines the relative prevalence of a particular pattern of DNA methylation. The oligonucleotides designed for MethyLight assays allows high degree of specificity, sensitivity, and flexibility for methylation studies.
Using Beacon Designer™, design Scorpions® to achieve sequence-specific priming and PCR product detection using a single oligonucleotide. Scorpions® represent the most recent development in real-time PCR chemistry. The stem-loop format is a common approach for specific detection of PCR products in which the probe element and primer element are physically coupled during the reaction. It is ideally suited for many applications that require rapid detection such as viral load testing and RNA profiling.
7. Multiplex Reactions
Beacon Designer™ helps you design an optimum
set of primers and probes for single tube
multiplex Taqman® and molecular beacon assays
having up to four sequences.
It first designs the best 50 or so primer
and probe assays for each sequence. Then the
fluorescent probe in each assay is checked
for cross dimerization with the primers and
probes of all the assays of the other sequences
in the reaction. Potential multiplex sets
are created by grouping one successful assay
for each sequence in all possible combinations.
Each multiplex set is then rated according
to the formula described earlier, but with
the addition of the various cross dimer energy
and Tm mismatch terms. The resultant multiplex
set rating is a function of the rating of
each of the component assays and the compatibility
of each assay with the other assays of the
With 50 or so assays for each of the four
sequences, there are more than 6 million multiplex
sets possible. Each multiplex set has a total
of 108 cross compatibility terms in its rating.
Thanks to fast computers, efficient programming,
and innovative algorithms, nearly a billion
interactions are resolved in a flash.
reactions are crucial in the diagnostic assay
development, which is one of the most important
applications of qPCR technology. No other
program, to our knowledge, has the required
8. Continuous Improvement & Unlimited Free Support
We continuously improve the software based on
the latest scientific developments and your
feedback. We have a team of five software engineers
and one biologist for Beacon Designer™ working
full time, dedicated to continuous improvement. Telephone, e-mail and fax support for the
life of the product free of charge.
9. Versatile Output
You can control what is output. The results
are available in a format that can be used in
many ways, e.g. synthesis ordering, loading in
your own database, printing, sharing results
10. Thousands of Satisfied
Since the first version,
Beacon Designer™ has become a premier qPCR design
tool for many researchers around the world.
The Inventor of Molecular Beacon technology
Dr. Sanjay Tyagi uses Beacon Designer™ in his
here to see what people are saying
about Beacon Designer™.