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New Tm Algorithm Brings Greater Accuracy to Molecular Biology
Experiments.
Abstract IDT supersedes 40-year old industry standard with new equation that delivers improved melting
temperature (Tm) prediction for biotech researchers.
CORALVILLE, IA. (June 10, 2005) – Integrated DNA Technologies (IDT) today announces
the introduction of a more effective and more accurate oligonucleotide (oligo) melting
temperature (Tm) algorithm for researchers in molecular biology. IDT’s Tm Algorithm has
been developed to give researchers new levels of precision when designing, analyzing or
evaluating the nucleic acid molecules that are at the heart of the biotech industry.
The new IDT Tm Algorithm enables more accurate Tm prediction under the experimental
conditions used by researchers. This in turn allows for improved design of primers and
probes for use in polymerase chain reaction (PCR) applications, DNA sequencing, and in
functional genomics applications such as siRNA mediated gene knockdown. IDT, which has
been granted a patent on the Tm Algorithm (US06889143), has incorporated this new tool
into its web-based suite of oligonucleotide design tools, which are freely available to
researchers through the SciTools portal at http://www.idtdna.com/SciTools/SciTools.aspx.
“An oligonucleotide’s melting temperature is its most critical property,” noted Dr. Mark
Behlke, vice president for molecular genetics at IDT. “It’s the point at which half the oligo
strands are hybridized to complementary sequences and half are free in solution as single
strands. The problem is that existing algorithms can be off in their predictions by as much
as 5-10 degrees Celsius when estimating the temperature at which melting takes place.”
These inexact algorithms can have a serious impact on the work of biotech researchers.
“Imprecise Tm prediction can adversely affect the design of experiments,” said Dr. Richard
Owczarzy, who led the team of IDT scientists that developed the new algorithm. “Indeed,
the resultant errors can actually be large enough to ruin experiments, or, even worse, to
give misleading or inaccurate results. Accurate estimation of Tm is too important to be left
to 40-year old equations, so we built our own more accurate algorithm from the ground
up.”
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Whether molecular biologists are amplifying the amount of genetic material through PCR,
using hybridization, sequencing or antisense/RNAi applications the use of more accurate
design tools can eliminate some of the laborious ‘trial and error’ approaches that
researchers are now forced to undertake when reactions fail.
Most extant algorithms estimate the Tm for oligos under standard conditions of 1M salt,
and then scale from that to predict melting temperatures for the actual condition to be
used in the experiment. The key issue is that predictions are mostly based on a saltcorrection equation, developed in the 1960s during studies of bacterial genomic DNA, that
is known by researchers to have significant shortcomings when used with
oligonucleotides.
Dr. Owczarzy’s team of IDT scientists, in their quest for an improved melting temperature
equation, studied the Tm of oligos for a wide variety of sequences and conditions. After
performing over 4,000 melting curves, they succeeded in developing a new algorithm that
accurately predicts the Tm of oligos as salt concentration is varied.
The results of this work were published in the April 2004 issue of Biochemistry (43:3537)
and are the basis for the new improved sequence analysis and design software available
from IDT today.
About Integrated DNA Technologies, Inc. (IDT):
Integrated DNA Technologies, Inc. (IDT) is the largest supplier of custom nucleic acids in
the U.S. Serving the areas of academic research, biotechnology, and pharmaceutical
development, IDT’s primary business is the manufacturing of DNA and RNA
oligonucleotides (oligos) for research applications.
Started in 1987 by Joseph Walder, M.D., PhD (University of Iowa), Integrated DNA
Technologies, Inc. has grown average of over 50% every year during the past 10 years, to
where it is now synthesizing and shipping 15,000 – 25,000 oligos per day. Currently, over
60,000 customers worldwide turn to IDT to fulfill their oligo requirements.
IDT also makes licensure available for key design tools – including the new IDT Tm
Algorithm – for use in commercial applications.
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Integrated DNA Technologies
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Coralville, Iowa 52241 USA
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www.idtdna.com