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INTEGRATED DNA TECHNOLOGIES
THE CUSTOM BIOLOGY COMPANY
PRODUCTS & SERVICES

THE CUSTOM BIOLOGY COMPANY

INTEGRATED DNA TECHNOLOGIES
PRODUCTS & SERVICES 2011

Integrated DNA Technologies (IDT) was founded as a biotechnology research
company in 1987 in Coralville, Iowa. Since then, IDT has been a major force
in advancing biological research, both as a leading supplier of custom
oligonucleotides and genes, and as a developer of innovative new technologies.
IDT is the largest supplier of custom nucleic acids in the world. Scientists select
IDT as their supplier of choice for quality, service, and price. IDT’s products
support a wide range of applications including DNA sequencing, DNA
amplification (PCR), expression profiling, microarray analysis, mutagenesis,
SNP detection, gene quantification, and functional genomics. Over 77,000
customers worldwide trust IDT for dependable products of the highest quality.
ABOUT
IDT
IDT’s Coralville, Iowa facility
IDT’s Commitment
IDT continuously strives to bring customers the best in oligonucleotide synthesis, quality control, and customer
service. IDT maintains strict methods and analysis to ensure that each and every product meets rigorous
standards. Products released to market will be of the highest quality, produced on time, and supported by
professional customer service.
3

Quality Guaranteed
IDT has pioneered the use of high-throughput quality control (QC) methods and is the only oligonucleotide
manufacturer that offers 100% QC and purity guarantees and provides QC documents
online. Today, every oligo synthesized at IDT undergoes QC by mass spectrometry. IDT also offers
CE and analytical HPLC as a routine tool for additional QC on purified oligos. In addition to DNA,
IDT has led the effort over the last decade to reduce the cost of high-quality custom RNA synthesis.
Through improvements to the traditional tBDMS chemistry and advances in instrumentation, IDT has
achieved the highest coupling efficiency in the industry. Only at IDT are customers guaranteed the
very best in quality synthesis with free mass spectrometry and CE traces on all purified oligos.
IDT’s manufacturing facilities in Coralville, IA; San Diego, CA; and Leuven, Belgium are ISO 9001:2008
certified. The Clinical and Commercial Manufacturing (CCM) suite within the Coralville facility also
has ISO 13485:2003 certification and uses current good manufacturing practices (cGMP) of the FDA’s
Quality System Regulation (QSR) 21 CFR Part 820 as guidance for manufacturing. ISO is the world’s
largest developer and publisher of International Standards. The success in achieving certification
reflects the strength of the company’s existing product quality procedures, as well as its clear commitment
to the manufacturing excellence and the ongoing development of its quality management
system. It also signifies the continuing commitment of IDT’s management to strengthen the company’s
ability to identify and exceed the expectations of its customers.
Locations
ABOUT
IDT
Innovation, Ongoing Research, and Development
In line with IDT’s mission to advance research in DNA-based technologies, the research staff at IDT
combines expertise in synthetic chemistry, biophysics, molecular biology, bioinformatics, and engineering.
IDT specializes in the areas of gene silencing based on RNAi, shRNA and antisense technologies,
transcription profiling, DNA sequencing, SNP detection, and DNA amplification. This expertise
has led to research and development collaborations with many leading biotechnology companies
and academic laboratories. For a list of papers published by IDT scientists, please visit the TechVault
on the IDT website.
4

Custom Oligonucleotide Synthesis
Custom DNA Synthesis in Tubes
Every oligo is deprotected and desalted to remove small molecule impurities. Desalted, custom synthesized
DNA oligos are shipped lyophilized or hydrated with LabReady Oligo Service. Oligos are
quantitated twice by UV spectrophotometry to provide an accurate measure of yield. All oligos are
quality control (QC) checked by mass spectrometry. Synthesis scales up to 1 μmole are shipped the
next business day; 5 μmole and 10 μmole scales are shipped within 5 business days. Large-scale synthesis
up to 10 grams is also available and and can be shipped in 10-15 business days.
CUSTOM
OLIGOS
Synthesis Scale
Length
25 nmole 15-60 bases
100 nmole 10-90 bases
250 nmole 5-100 bases
1 µmole 5-100 bases
5 µmole 5-50 bases
10 µmole 5-50 bases
SameDay® Oligo Service
For longer oligos, see
Ultramers on p. 7
Unmodified oligos between 15 and 45 bases are available for same-day shipping. SameDay oligos
ordered online before the deadline will ship the same day for quickest delivery. Check the IDT website
for order deadlines for your area. SameDay oligos have a 2 OD minimum guarantee (sufficient for
>250 PCR reactions), are deprotected and desalted, and shipped lyophilized in tubes.
LabReady Oligo Service
For convenience, IDT offers LabReady oligo services. For a small charge, we will ship 25 nmole, 100
nmole, or 250 nmole scale oligos in IDTE (1x TE buffer at pH 8.0) at a concentration of 100 μM.
Customized Labels
Customized labels are available as a replacement for the stock IDT label. Customers can easily sort
and identify oligos by creating their own customized labels. Many different fields are available, including
institution name, sequence, sequence name, date of synthesis, and order number.
5

Custom DNA Synthesis in Plates
Orders with 24 oligos or more can be packaged into 96-well plates and orders with 96 oligos or
more can be packaged into 384-well plates. Plates can be delivered lyophilized, or resuspended in
nuclease-free water or IDTE buffer. IDTE (1X TE buffer) is available at pH 7.5 or pH 8.0.
Synthesis Scale
Length
25 nmole Plate Oligo 15-80 bases
100 nmole Plate Oligo 10-90 bases
250 nmole Plate Oligo 5-100 bases
1 µmole Plate Oligo 5-100 bases
Plate Loading Options
IDT offers numerous options for customizing 96- and 384-well plates.
• Oligos normalized to the same concentration or volume across the plate
• Full synthesis yield
• Mixed, normalized oligos loaded in the same well
• Normalized oligos in one plate with the remainder of the synthesis yield shipped in a separate
plate
• Primer mix remainders can be shipped in two separate plates
• Replicate 96-well and 384-well plates
• Plates can be delivered lyophilized or at a pre-set volume in water or buffer
−−
IDTE (1X TE buffer) is available at pH 7.5 or pH 8.0
−−
Oligos shipped in water or buffer must ship on dry ice
CUSTOM
OLIGOS
Plate Service 96-Well Plate 384-Well Plate
Loaded with 100% synthesis yield FREE FREE
Loaded with fixed quantity FREE FREE
Loaded with fixed quantity, remainder in plates Inquire Inquire
Primer mix, with fixed amounts FREE FREE
Primer mix, with remainder in plates Inquire Inquire
Replicate plate Inquire Inquire
Primer mix, Replicate plate Inquire Inquire
HOTplates®
For high-throughput labs, IDT offers a HOTplate expedited oligo synthesis service. As with SameDay
oligo service, IDT has brought the same focus on speed, quality, and service without compromise
to the 96-well plate. Order online before the deadline and the entire 96-well plate will ship the next
business day.
This service is available for unmodified oligos from 15-60 bases with a minimum order of 48 oligos
per plate. Oligos are normalized to 2-10 nmoles/well or full synthesis yield and shipped in 300 μL V-
bottom plates. Check the IDT website for order deadlines for your area.
6

Ultramers
IDT’s proprietary synthesis systems and chemistries allow the high-fidelity synthesis of very long
oligos (up to 200 bases). Ultramers are suitable for demanding applications like cloning, shRNA,
mutagenesis and gene construction and can save researchers a great deal of time and trouble
through direct synthesis of entire target fragments.
Ultramers are delivered normalized and lyophilized in tubes or plates. Standard, desalted Ultramers
ship within 2-4 business days. PAGE-purified Ultramers ship within 4-7 business days.
Product Purification Guaranteed Yield
4 nmole Ultramer DNA Oligo Standard Desalt 4 nmoles
20 nmole Ultramer DNA Oligo Standard Desalt 20 nmoles
PAGE Ultramer DNA Oligo PAGE Purification Inquire
4 nmole Ultramer DNA Plate Oligo Standard Desalt 4 nmoles/well
Custom RNA Synthesis
CUSTOM
OLIGOS
IDT has the expertise to deliver custom-synthesized RNA with the yield and purity that meet the
demands of researchers today. RNA is shipped deprotected and desalted in 2-3 business days or deprotected
and purified in 4-6 business days. Please inquire for turnaround on 5 µmole and 10 µmole
RNA synthesis. Large-scale synthesis up to 10 grams is also available and can be shipped in 10-15
business days.
Scale and Lengths for Custom RNA
Synthesis Scale
Available Lengths
100 nmole 10-50 bases
250 nmole 5-50 bases
1 µmole 5-50 bases
5 µmole 5-50 bases
10 µmole 5-50 bases
2’-O-methyl RNA
2’-O-methyl RNA is a useful RNA analog that is resistant to degradation by single-stranded ribonucleases.
This modification is often used in antisense oligonucleotides to provide nuclease resistance or in
siRNAs where it can provide both nuclease resistance and prevent immune stimulation.
7

Modifications
A wide variety of modifications are available for addition to oligonucleotides. These include attachment
chemistry and linkers, fluorophores, quenchers, spacers, and modified bases. For a complete
list of modifications available at IDT, or for additional information on any of these modifications,
please visit the website at www.idtdna.com.
Modification 5’ Internal 3’ DNA RNA
Attachment Chemistry/Linkers
Adenylation /5rApp/ x x • x
Amino Modifier C12 /5AmMC12/ x x • •
Amino Modifier /5AmMC6/ /iAmMC6T/ /3AmMO/ • •
Biotin /5Biosg/ /iBiodT/ /3Bio/ • •
Digoxigenin (NHS Ester) /5DigN/ /iDigN/ /3Dig_N/ • o
Thiol Modifier S-S /5ThioMC6-D/ o /3ThioMC3-D/ • •
Phosphorylation
Phosphorylation /5Phos/ x /3Phos/ • •
Modified Bases
deoxyUridine /5deoxyU/ /ideoxyU/ /3deoxyU/ • •
deoxyInosine /5deoxyI/ /ideoxyI/ /3deoxyI/ • •
5-Methyl dC /5Me-dC/ /iMe-dC/ /3Me-dC/ • •
2'-O-Methyl RNA Bases mA, mG, mC, mU mA, mG, mC, mU mA, mG, mC, mU • •
Fluorophores
6-FAM (Fluorescein) /56-FAM/ x /36-FAM/ • •
Fluorescein dT /5FluorT/ /iFluorT/ /3FluorT/ • •
TET /5TET/ x o • •
HEX /5HEX/ x o • •
JOE (NHS Ester) /56-JOEN/ o /3Joe_N/ • o
MAX (NHS Ester) /5MAXN/ o /3MAX_N/ • •
TYE 563 /5TYE563/ x /3TYE563/ • •
Cy3 /5Cy3/ /iCy3/ /3Cy3Sp/ • •
6-TAMRA (NHS Ester) /56-TAMN/ /i6-TAMN/ /36-TAMTSp/ • o
ROX (NHS Ester) /56-ROXN/ o /3Rox_N/ • o
TEX 615 /5TEX615/ x /3TEX615/ • •
TYE 665 /5TYE665/ x /3TYE665/ • •
Cy5 /5Cy5/ /iCy5/ /3Cy5Sp/ • •
TYE 705 /5TYE705/ x o • •
Quenchers
Iowa Black® FQ /5IAbFQ/ o /3IABkFQ/ • •
Iowa Black® RQ /5IAbRQ/ o /3IAbRQSp/ • •
Black Hole Quencher® 1 /5BHQ_1/ o /3BHQ_1/ • o
Black Hole Quencher® 2 /5BHQ_2/ o /3BHQ_2/ • o
Dabcyl /5Dab/ x /3Dab/ • •
Spacers
Spacer 18 /5Sp18/ /iSp18/ /3Sp18/ • •
1',2'-Dideoxyribose (dSpacer) /5dSp/ /idSp/ /3dSp/ • •
C3 Spacer /5SpC3/ /iSpC3/ /3SpC3/ • •
• Available
o Inquire
x Not available
MODIFICATIONS
For a complete list and more information on all the modifications offered, please go to
www.idtdna.com
8

Oligonucleotide Purification
For demanding applications such as multiplex PCR, cloning, mutagenesis, or antisense/RNAi methods,
additional purification will significantly improve oligonucleotide performance. Every purified
oligo up to 60 bases in length receives QC to document final purity. Purity and yield may vary due to
oligo length, modifications, or sequence composition.
PAGE Purification
PAGE obtains extremely high purity, especially for unmodified oligos and Ultramers (see page 7).
PAGE purification is strongly recommended for oligos >60 bases in length. For unmodified oligos,
purity of >90% is guaranteed. PAGE purification is available at 100 nmole, 250 nmole, 1 µmole, 5
µmole, and 10 µmole scales.
HPLC Purification
All HPLC methods, except Rapid HPLC, are available at 100 nmole, 250 nmole, 1 µmole, 5 µmole, and
10 µmole scales. Purity may vary due to oligo length, modifications, or sequence composition.
PURIFICATION
Reverse-Phase HPLC is well suited to purify any modified or unmodified oligo sequence up to 60
bases in length. For unmodified oligos, purity of >85% is guaranteed.
Ion-exchange HPLC (IE-HPLC) is available to purify long DNA oligos. For unmodified oligos, purity of
>85% is guaranteed.
For the most demanding applications, IDT offers dual HPLC purification and dual PAGE and HPLC
purification.
RNase-Free HPLC purification is available for isolating RNA and DNA oligos which will be used in
applications with a high sensitivity to ribonucleases. RNase-Free HPLC purification is carefully performed
in an RNase-free environment; reagents, equipment, and lab surfaces are monitored for
RNase contamination using the RNaseAlert system. Guaranteed yields are provided for purified, unmodified
oligos from 20-50 bases in length.
Rapid HPLC Purification
IDT offers Rapid HPLC purification, which provides the fastest turnaround time available coupled with
excellent quality. Rapid HPLC oligos are purified using the same equipment and protocols as standard
HPLC purification. The resulting purity is routinely >85%. All oligos are quality control checked
by mass spectrometry and the trace is available free on the IDT website.
Rapid HPLC purification is available for oligos from 10-60 bases and is available at the 100 nmole or
250 nmole scales. Oligos are shipped lyophilized in tubes and are available with 5’ Phosphorylation
or 5’ Amino Modifier. Rapid HPLC oligos must be ordered online before the deadline and will ship the
next day for quickest delivery. Check the IDT website for order deadlines for your area.
9

Custom Analytical Methods
Mass Spectrometry
All oligos synthesized at IDT are analyzed by mass spectrometry. Matrix-Assisted Laser Desorption/
Ionization-Time of Flight (MALDI-TOF) mass spectrometry is suitable for use in a high-throughput QC
setting and can resolve oligonucleotides up to 50 bases in length (~15,000 Daltons). Electrospray
Ionization (ESI) mass spectrometry can resolve longer oligonucleotides. All mass spec traces are available
for free in customer accounts on the IDT website. See the technical report, Mass Spectrometry
Analysis of Oligonucleotide Syntheses, on the IDT website for more information on this method.
Capillary Electrophoresis
Capillary Electrophoresis (CE) provides quantitative analysis of purity. Nanoliter samples of oligonucleotides
are electrokinetically injected into a fused silica capillary filled with a denaturing gel under
an electric potential. The oligonucleotides move through the gel matrix and are separated according
to length. Absorbance at 260 nm is detected as the oligo passes through a window in the capillary.
The resulting electropherogram provides the percent purity of the full length product as well as
truncated products. See the technical report, Capillary Electrophoresis of Oligonucleotides, on the IDT
website for more information on this method.
CUSTOM
ANALYSIS
Channel A
Channel A
93263967
Migration Time
0.04
0.04
AU
AU
0.02
0.02
0.00
47.542
48.000
48.688
49.304
20 30 40 50 60 70 80
Minutes
0.00
Analytical HPLC
HPLC is a universally accepted method of sample quality assessment. IDT production scientists use
both Reverse-Phase and Ion-Exchange methods to assess product purity. These methods are employed
on purified oligos where the composition is incompatible with CE technology.
10

SciTools®
IDT offers a number of free design and analysis tools in the online SciTools suite. The suite is comprised
of tools for designing assay components as well as determining the properties of any sequence
entered. Tools include OligoAnalyzer® (for analyzing oligonucleotide melting temperature,
hairpins, dimers, and mismatches), the RealTime PCR design tool (design custom assays for qPCR experiments)
and PrimerQuest® (design primers and probes for PCR and qPCR reactions). Other design
tools for life science researchers include:
••
Pre-designed DsiRNA – Pre-designed siRNA duplexes and TriFECTa® Kits
••
RNAi design – Design duplexed RNA oligos for RNA Interference experiments
••
454 FusionPrimers – Design primers for 454 Sequencing applications
••
UNAFold – Secondary structure prediction tool
••
DilutionCalc – Calculate volume needed to dilute down to a lower concentration
••
ResuspensionCalc - Calculate how much volume (µL) to resuspend a dry lyophilized oligo
SCITOOLS
OligoAnalyzer®
OligoAnalyzer provides analysis of the physical properties of any oligo sequence. Users simply enter
the sequence and initiate the calculations. The sequence can include standard and mixed bases, as
well as DNA, RNA, methylated, locked, and phosphorothioated bases. The OligoAnalyzer will calculate
the properties of the sequence including length, GC content, melting temperature range,
molecular weight, extinction coefficient, and optical density (OD). From there, users can run the
UNAFold program to measure the folding properties of the sequence and determine the likelihood
of hairpin structure or self-dimer formation. The NCBI Blast icon within the program initiates a comparison
between the sequence entered and sequences in the NCBI database and will calculate the
statistical significance of the matches.
OligoAnalyzer accommodates
• DNA
• RNA
• Mixed bases
• Methylated bases
• Locked Nucleic Acids (LNA)
• Phosphorothioated bases
Provides analysis
• Length
• GC content
• Melting temperature range
• Molecular weight
• Extinction coefficient
• Optical density
11

PrimerQuest®
The PrimerQuest program designs primers
and probes for PCR and qPCR reactions. To use
PrimerQuest, users enter a sequence or RefSeq
accession number and configure the primer/
probe options to fit their specific reaction
conditions. The program will then provide options
for sets of oligo primers and probes. Users
select the set they like best and can order
directly from the design tool.
Customizable parameters
• Melting temperature
• Length
• GC content
• Primer-dimer possibilities
• PCR product size
• Positional constraints
SCITOOLS
RealTime PCR Design Tool
The highly flexible RealTime PCR Design Tool designs custom PrimeTime qPCR Assays and allows
for complete control of design parameters. To use the RealTime PCR Design Tool, users enter Ref-
Seq accession numbers or gene sequences and then select the assay location, such as the entire
coding region or specific exons. The tool will design multiple assays across different exons. Users
then select the set they want to order. Prior to purchase, the tool provides the customer with details
about the assay that competitors have previously not divulged; these include the primer and
probe locations, amplicon length, melting temperature and, most importantly, actual primer and
probe sequences.
Customizable parameters
• Melting temperature targets
• Amplicon length
• Key master mix ingredient
concentrations
12

cGMP Manufacturing
IDT’s Clinical and Commercial Manufacturing (CCM) suite is a “facility within a facility” dedicated to
the GMP manufacture of diagnostic oligos. The CCM suite specializes in servicing customer relationships
that feature customer-defined product specifications and require customer control over
the manufacturing processes. The CCM suite parallels IDT’s proven research line which simplifies
the transition of oligos and products from research to clinical applications.
The CCM suite is ISO 13485:2003 certified, registered with the US Food & Drug Administration
(FDA), and is a contract manufacturer for in vitro diagnostic devices (IVDs), analyte-specific reagents
(ASRs) and nucleic acid tests (NATs). The CCM service includes dedicated ordering, production,
final-fill, and shipping systems that meet the elevated quality standards required for the
product’s use in clinical or commercial applications.
cGMP
MANUFACTURING
Benefits
• GMP oligo manufacturing minimizes customer regulatory and vendor auditing burdens
• Transparent, customer-defined and controlled manufacturing process
• Flexible, customer-defined ordering methods
• Customer relationship managed by a single point of contact
• Long-term pricing stability through supply agreements
Customer Service
13
A dedicated CCM customer representative will act as the single point of contact within IDT for all
account management needs.
• Representatives will serve as a project coordinator to gather and route all necessary information
from product development through product consumption.
• Orders will be placed directly with the representative and workflow verified with manufacturing
for accuracy prior to production.
• CCM pricing can be quoted per customer-defined unit of measure (e.g., per nanomole, per
aliquot, per kit, etc.).
• In CCM “we will learn to speak your language” to facilitate and improve purchasing and
inventory management. Examples of actual customer supplied ordering units of measures:
“X tests”, “X reactions”, “X tubes”.

Benefits of cGMP Manufacturing
• Capability to provide 10 nmole to 1 gram final deliverable utilizing dedicated production
equipment
• Product stability programs as well as retain lot capability are also offered
• Three synthesis platforms to meet all scale and modification needs
• Liquid handling robots, plate reading spectrophotometers and IDT exclusive dry down equipment
are all designed to increase the throughput of oligos
• Multiple HPLC purification methods are available including IE-HPLC, RP-HPLC, and both modern
and traditional buffer and column systems
• Equipment and Process Validations are transparent to the customer and are often referenced
in relevant Oligo Master Records (OMR)
• Validated electronic batch record capability for each Manufacturing Lot (individual syntheses,
HPLC fractions, etc.)
Finish and Fill
IDT offers a full range of final-fill, labeling and OEM solutions with services including:
• Customer-specified formulation
• Custom packaging
• OEM and kitting solutions
• Third-party labeling
• Plate packaging
• Stability programs available
• Functional QC
cGMP
MANUFACTURING
Contact
Our friendly and professional customer service is ready to handle any questions you may have as you
take your product from development to final delivery.
For questions about the services we offer for clinical or commercial applications:
• Email ccminfo@idtdna.com
• Call +1-319-626-8400
• Email your IDT sales representative
14

Synthetic Biology
Custom Gene Synthesis
By ordering genes from IDT, researchers not only save money spent on reagents necessary for construction,
cloning, and sequencing, but can also save time by outsourcing the manufacture of hardto-clone
gene sequences, which often result in repeated failures. At IDT, all genes are constructed
using Ultramers, the highest fidelity next generation synthesis technology available (see page 7).
Genes arrive in a plasmid cloning vector and are ready for use in a variety of applications. Sequence
information is always secure and confidential at IDT. Non-disclosure agreements are available
through IDT’s legal services upon request.
Turnaround Time
miniGENES (up to 400 bp) Genes (401-1500 bp) Genes (>1500 bp)
4-8 business days 8-12 business days Inquire
Turnaround time is dependent on gene length, complexity, and vector choice.
SYNTHETIC
BIOLOGY
Cloning Vectors
All genes, unless otherwise specified, will be delivered in IDT’s proprietary cloning vector, pIDTSmart.
This vector has been specifically engineered to remove most common restriction endonuclease
cleaving sites and does not contain a promoter within the cloning region. If you require restriction
sites or promoters for your application, it is important to include these when ordering the gene of
interest by appending the desired restriction sites or promoters to the ends of the desired gene
sequence. The default version of pIDTSmart contains a kanamycin resistance cassette. An ampicillin
version is also available upon request. IDT also offers a pIDTBlue vector that does contain restriction
sites as well as T7 and T3 promoters. However, it is important to note that this is not an expression
vector. Additional subcloning will be required for expression.
Vector
pIDTBlue
Endogenous
Enzymes
Sequence
# of
Cuts
ApaLI GTGCAC 2
BspDI ATCGAT 1
ClaI ATCGAT 1
EagI CGGCCG 1
PvuI CGATCG 3
PvuII CAGCTG 2
RsaI GTAC 2
Comments
Doesn't exist in
≤ 400 version
Restriction sites not present in plasmid
Acc65I, AgeI, ApaI, AscI, Asp718I, AvaI, AvrII, BamHI,
BglII, BmgBI, BstBI, DraII, Ecl136II, EcoRI, EcoRV,
HindIII, HpaI, KpnI, MluI, NcoI, NdeI, NheI, NotI, NsiI,
PacI, PaeR7I, PspOMI, PstI, SacI, SacII, SalI, SmaI,
SnaBI, SpeI, SphI, TliI, TspMI, XbaI, XhoI, XmaI
15

Vector
pIDTSmart
Endogenous
Enzymes
Sequence
# of
Cuts
ApaL GGGCCC 1
ApaLI GTGCAC 2
BspDI ATCGAT 1
ClaI ATCGAT 1
DraII RGGNCCY 2
NsiI ATGCAT 2
PspOMI GGGCCC 1
PvuI CGATCG 3
RsaI GTAC 2
SnaBI TACGTA 1
Comments
Doesn't exist in
> 400 version
or pIDTSmart-
KAN
Contains 1 in
pIDTSmart-
KAN
Contains 2 in
pIDTSmart-
KAN
Contains 2 in
pIDTSmart-
KAN
Contains 1 in
pIDTSmart-
KAN
Restriction sites not present in plasmid
Doesn't exist in
≤ 400 version
Doesn't exist in
> 400 version
or pIDTSmart-
KAN
Acc65I, AgeI, ApaI, AscI, Asp718I, AvaI, AvrII, BamHI,
BglII, BmgBI, BstBI, DraII, Ecl136II, EcoRI, EcoRV, HindIII,
HpaI, KpnI, MluI, NcoI, NdeI, NheI, NotI, NsiI, PacI, PaeR7I,
PspOMI, PstI, SacI, SacII, SalI, SmaI, SnaBI, SpeI, SphI, TliI,
TspMI, XbaI, XhoI, XmaI
SYNTHETIC
BIOLOGY
Custom Vector Requests
IDT has the ability to subclone into almost any customer-supplied vector. To start the process, go
to IDT’s website and complete the Custom Vector Request Sheet or contact IDT Gene Support at
genes@idtdna.com.
16

Gene Expression
PrimeTime® qPCR Assays and Probes
IDT offers PrimeTime qPCR Assays and Probes designed for 5’ nuclease assays, the gold standard for
quantitative gene expression studies.
PrimeTime® qPCR Assays
PrimeTime qPCR Assays consist of a forward primer, a reverse primer, and a hydrolysis probe delivered
in a single tube. With the added capability of selecting from multiple dye-quencher combinations,
primer-to-probe ratio, and qPCR design parameters, optimizing qPCR reactions is no longer
complicated or expensive. PrimeTime qPCR Assays are offered in three different sizes to meet any
qPCR experimental need. In addition, for the Standard and XL sizes, selection of dye-quencher combination
and primer-to-probe ratio can be specified to meet unique experimental demands.
Each Assay ships in 2 to 4 days from order placement. Each oligo undergoes 100% QC by mass spectrometry
and all QC results are provided free of charge on the IDT website.
GENE
EXPRESSION
Reactions
(20 µL)
PrimeTime® Mini qPCR Assay 100
PrimeTime® Standard qPCR Assay 500
PrimeTime® XL qPCR Assay 2500
Estimated
Ship Date
2-4 business
days
2-4 business
days
2-4 business
days
1
The primer-to-probe ratio may be specified by the customer for Standard and XL Assays.
Probe
(nmoles)
Primers
(nmoles) 1
0.5 1.0
2.5 2.5-10
12.5 12.5-50
Available Dye and Quencher Combinations
5' Dye 3' Quencher Mini Standard XL
FAM ZEN/Iowa Black® FQ 2 • • •
FAM TAMRA • •
HEX Iowa Black® FQ • •
TET Iowa Black® FQ • •
Cy5 Iowa Black® RQ • •
2
ZEN/Iowa Black FQ is a double-quenched probe that provides superior performance to
traditional dual-labeled probes.
ZEN Double-Quenched Probes
17
IDT has developed a new internal ZEN quencher that enables the production
of double-quenched probes with less background and increased
signal. Double-quenched probes contain a 5’ FAM fluorophore, a 3’ IBFQ
quencher, and an internal ZEN quencher. While traditional probes have
around 20-30 bases between the fluorophore and the quencher, the internal
ZEN quencher decreases the length to only 9 bases. This shortened
distance, particularly when combined with the traditional 3’ end
quencher, leads to extremely efficient quenching with significantly less
background, and enables the use of much longer probes for designing
AT-rich target regions. In addition to the greatly decreased background,
the double-quenched probes also have consistently reduced Cq values
and improved precision when compared to traditional probes. Use of the
double-quenched probes can allow users to experience both increased
sensitivity and precision in their qPCR experiments.
D
D
3’ Quencher Distance
from Dye: 20-30bp
3’ Quencher Distance
from Dye: 20-30bp
Z
Q
ZEN Distance from Dye: 9bp
Q

PrimeTime® qPCR Probes
PrimeTime qPCR Probes are available with a large selection of dye-quencher combinations. The
prices and estimated turnaround time for these probes will depend on the degree of complexity.
Standard Level probes will ship in approximately 3-5 business days, while Complex Level probes will
ship in approximately 4-6 days. The minimum guarantees are listed for probes that are 15-35 bases in
length. Please inquire about yield for probes 36-45 bases in length.
Standard Level
Scale
Minimum Guarantee
100 nmole 10 nmoles
250 nmole 25 nmoles
1 µmole 50 nmoles
5’ Reporter Dye(s) Quencher Family
FAM
HEX
TET
ZEN/Iowa Black® FQ 1
Iowa Black® FQ
TAMRA
Black Hole Quencher®
Iowa Black® FQ
Black Hole Quencher®
1
ZEN/Iowa Black FQ is a double-quenched probe that
provides superior performance compared to traditional duallabeled
probes.
Complex Level
Scale
Minimum Guarantee
100 nmole 2 nmoles
250 nmole 8 nmoles
1 µmole 20 nmoles
5’ Reporter Dye(s) Quencher Family
FAM
MAX (NHS ester)
Cy3
TEX 615
Cy5
TYE 563
TYE 665
JOE (NHS Ester)
TAMRA (NHS Ester)
ROX (NHS Ester)
Texas Red-X (NHS Ester)
TAMRA NHS Ester
Iowa Black® FQ or RQ
Black Hole Quencher®
Iowa Black® FQ or RQ
Black Hole Quencher®
GENE
EXPRESSION
PrimeTime® Mini qPCR Probes
The PrimeTime Mini qPCR probes are probes available on a small scale. The smaller scale and lower
price make them ideal for testing new probes, for screening the expression levels of many genes, or
for testing the conversion to FAM/IBFQ and FAM/ZEN/IBFQ from other FAM-related quenchers. Mini
probes are offered with a 5’ FAM and the option of a 3’ IBFQ quencher alone or in combination with
the internal ZEN quencher. The delivery amount is 0.5 nmoles and the estimated turnaround time is
3-5 days.
PrimeTime® Performance Data
Integrated DNA Technologies and Agilent
Competitor A
3 5
A C T B S tandard C urve
4 0
T B P S tandard C urve
3 0
18S S tandard C urve
3 5
B 2M S tandard C urve
3 0
3 5
2 5
3 0
C q Va lue
2 5
2 0
C q Va lue
3 0
2 5
C q Va lue
2 0
1 5
C q Va lue
2 5
2 0
1 5
2 0
1 0
1 5
1 0
-2 .5 -2 -1 .5 -1 -0 .5 0 0 .5 1 1 .5 2 2 .5
Log(S a mple A mount)
1 5
-2 .5 -1 .5 -0 .5 0 .5 1 .5 2 .5
Log(S a mple A mount)
5
-2 .5 -2 -1 .5 -1 -0 .5 0 0 .5 1 1 .5 2
Log(S a mple A mount)
1 0
-2 .5 -2 -1 .5 -1 -0 .5 0 0 .5
Log(S a mple A mount)
F luo r e sce nce (dR n)
Agilent and IDT
8 .5
Competitor A
7 .5
6 .5
5 .5
4 .5
3 .5
2 .5
1 .5
0 .5
-0 .5
1 3 5 7 9 1 1 1 3 1 5 1 7 1 9 2 1 2 3 2 5 2 7 2 9 3 1 3 3 3 5 3 7 3 9
C ycle s
C t (dR n)
Agilent and IDT
Competitor A
3 .3 5 5 *L O G - (X ) + 2 1 .6 2 , Eff. = 9 8 .6 , Rsq = 0.99
3 .6 0 1 *L O G -(X ) + 2 3 .1 3 , Eff. = 8 9 .5 %, Rsq = 0.99
3 2
3 1
3 0
2 9
2 8
2 7
2 6
2 5
2 4
2 3
2 2
2 1
2 0
1 9
1 8
1 7
1 6
1 5
1 4
0 .0 1 0 .1 1 1 0
I nitial Q uantity (nano gr am s)
C a lc u la te d q P C R E ffi c ie n c y C o m p a ris o n ID T a n d
A gile n t + ID T
A gile n t P ro d u c ts vs . Competitor A
C o mp e tito r A
1 1 0 %
1 0 4 %
1 0 2 %
1 0 3 %
9 7 %
9 9 %
9 9 %
9 7 % 9 9 %
1 0 0 %
9 5 %
9 6 %
9 3 %
9 0 % 9 0 % 9 0 %
9 0 % 9 1 %
9 1 %
9 0 %
8 6 %
A ssay Efficie ncy
8 0 %
7 0 %
6 0 %
5 0 %
1 8 s A C TB B 2 M G A P D H G U S B H P R T P S G 8 TB P 8 Ta r ge t
A ve r a ge
Targe t G e ne
B2M amplification plots and standard curve are shown along with efficiency comparison for assays across 8 targets. In the B2M assay the
Agilent/IDT assay resulted in 1.5x higher fluorescence and detected each standard 1-2 C q earlier than Competitor A. The standard curve efficiency
values are higher for 7 of 8 Agilent/IDT assays and on average 8% higher. Note: 5 of the 8 Competitor A assays are at or below 90%
efficiency.
18

PrimeTime® Express qPCR Probes
PrimeTime Express qPCR Probes allow researchers the opportunity to have their qPCR probes ship in
just one working day! All oligos are HPLC purified and quality control checked by mass spectrometry.
All Express orders will be shipped the day after the order is placed. Check the IDT website for order
deadlines for your area. All Express Probes must be 18-35 bases and are shipped lyophilized with a
minimum guarantee of 5 nmoles.
Express Probes
Scale
Minimum Guarantee
100 nmole 5 nmoles
5’ Reporter Dye Quencher Family
ZEN/Iowa Black® FQ *
FAM
Iowa Black®
Black Hole Quencher® 1
GENE
EXPRESSION
*ZEN/Iowa Black FQ is a double-quenched probe that provides superior performance
over traditional dual-labeled probes.
Molecular Beacons
Molecular Beacons are a special class of dual-labeled probes having self-complementary ends
that form a stem-loop structure (hairpin) in their native state. The hairpin forces the reporter and
quencher into proximity so that the quencher absorbs the fluorescence emitted by the reporter.
Upon hybridization to the target, reporter and quencher are separated and the Molecular Beacon
emits fluorescence.
Molecular Beacons are custom oligos (up to 45 bases in length) containing a reporter and quencher,
and are HPLC purified. The turnaround time is 5-7 business days for standard Molecular Beacons.
5’ 6-FAM TM
Reporter
Quencher
3' Black Hole Quencher® 1
3' Iowa Black® FQ
3' Dabcyl
5’ HEX TM 3’ Iowa Black® FQ
5’ TET TM 3’ Iowa Black® FQ
5’ TYE TM 563 3’ Iowa Black® RQ
5’ TYE TM 665 3’ Iowa Black® RQ
Synthesis
Scale
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
Minimum
Guarantee
10 nmoles
40 nmoles
10 nmoles
40 nmoles
10 nmoles
40 nmoles
10 nmoles
40 nmoles
10 nmoles
40 nmoles
5 nmoles
20 nmoles
5 nmoles
20 nmoles
19

Genotyping
PrimeTime® Dual-Labeled LNA Probes
Locked Nucleic Acids (LNAs) can be incorporated into dual-labeled probes to detect single nucleotide
polymorphisms (SNPs). Since LNA bases significantly increase oligonucleotide Tm, LNA duallabeled
probes (DLPs) are shorter than standard DNA DLPs. These probes offer an improved ability to
distinguish mutations or SNPs. A DNA DLP typically has a ΔTm of ~5 o C between perfect match and
mismatch hybridization. An LNA DLP can have a ΔTm of >15 o C, greatly increasing accuracy of allele
discrimination by real-time PCR or other methods that use differential hybridization to distinguish
polymorphisms.
The custom oligo can be up to 25 bases in length and include up to 6 LNA base insertions, a reporter
and a quencher. Dual-Labeled LNA probes are HPLC purified and turnaround time is 4-6 business days.
Reporter
Quencher
3' Iowa Black® FQ
5’ 6-FAM TM 3' Black Hole Quencher® 1
3' Iowa Black® FQ
5’ HEX TM 3' Black Hole Quencher® 1
3’ Iowa Black® RQ
5’ TYE TM 563
3’ Black Hole Quencher® 2
3’ Iowa Black® RQ
5’ Cy3 TM 3’ Black Hole Quencher® 2
3’ Iowa Black® RQ
5’ TEX TM 615
3’ Black Hole Quencher® 2
3’ Iowa Black® RQ
5’ TYE TM 665
3’ Black Hole Quencher® 2
3’ Iowa Black® RQ
5’ Cy5 TM 3’ Black Hole Quencher® 2
Synthesis
Scale
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
250 nmole
1 µmole
Minimum
Guarantee
8 nmoles
20 nmoles
8 nmoles
20 nmoles
8 nmoles
20 nmoles
8 nmoles
20 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
4 nmoles
10 nmoles
GENOTYPING
20

Next-Generation Sequencing
In an exclusive agreement with 454 Life Sciences, a Roche Company, IDT is able to provide researchers
with 454 Fusion Primer design software, custom primers for the Genome Sequencer FLX System,
and Molecular Identifier (MID) tags for multiplexed library sequencing.
454 Fusion Primers are required for a number of 454 Sequencing applications. These applications
include “ultra-deep” amplicon sequencing for detection of low-frequency mutations, and the comprehensive
identification and quantification of common and rare sequences within a population.
These studies are easily initiated with 454 Fusion Primer design software to target individual exons or
all exons from one or more genes.
For more information on 454 Life Sciences' products, visit their website at www.454.com.
454
SEQUENCING
SEQUENCING
GS FLX Standard Fusion Primers
GS FLX Fusion Primers consist of a 20-25 bp target-specific sequence (3’ end) and a 19 bp fixed sequence
(Primer A or Primer B on the 5’ end).
Amplicon sequencing projects use 454 Fusion Primers to incorporate specific identifying sequences
into your gene-specific primers. This allows the process to proceed directly into emulsion PCR for
sequencing and is often associated with Ultra-Deep sequencing applications.
• The software enables an investigator to initiate the survey in one or more gene loci
• 454 Fusion Primers are optimized across all workflow steps, not just the initial PCR
• Users can create sequencing primers for large surveys as well as specific, focused projects
GS FLX Titanium Fusion Primers
GS FLX Titanium Fusion Primers have a 25 bp fixed sequence (Primer A or Primer B on the 5’ end) and
an optional Multiplex Identifier (MID) sequence. This design allows for:
• Longer amplicons to be sequenced
• An increase in the number of reads per run
• An improvement in read representation for bidirectional sequencing
• More simplified choices for reagent kits and protocols
Titanium Fusion Primers can also be used to sequence existing amplicon libraries that were created
using Standard Fusion Primers. Roche highly recommends transitioning amplicon library designs to
the new format to achieve optimal performance.
GS FLX Titanium Rapid Library MID Adaptor Extended List
Tagging multiple libraries with different MIDs allows them to be amplified and sequenced together
in a single region of the PicoTiterPlate device. For customers that need more MIDs than the twelve
supplied by 454 in the GS FLX Titanium Rapid Library MID Adaptors Kit, this Extended List provides
additional sequences that have been optimized for MID applications.
Each MID sequence contains at least 4 changes (insertion, deletion, or substitution) to make it unique
from other members of 454’s original twelve and the Extended MID Set. This means that, for any of
these MIDs, it is possible to either detect up to 2 errors and correct 1 error, or alternatively, detect 3
errors and correct none.
454 miRCat® and miRCat®-33 Adaptor Primers
21
454 Adaptor Primers are designed to convert the small RNA libraries generated by miRCat ligations
(Set I) or by miRCat-33 ligations (Set II) into 454-compatible PCR libraries for deep sequencing. For
more information on the miRCat® Kit, see page 24.

Gene Silencing
DsiRNA – Dicer-substrate siRNAs
Dicer-substrate siRNAs (DsiRNAs) are chemically synthesized Dicer-substrate duplex RNAs that have
increased potency in RNA interference compared to traditional siRNAs and were developed as a collaborative
effort between John Rossi (Beckman Research Institute of the City of Hope) and IDT. Traditional
21-mer siRNAs are designed to mimic Dicer products and therefore bypass interaction with the
enzyme Dicer. Dicer has been recently shown to be a component of RISC and involved with entry of
the siRNA duplex into RISC. Dicer-substrate siRNAs are designed to be optimally processed by Dicer
and show increased potency by engaging this natural processing pathway. Using this approach, sustained
knockdown has been regularly achieved using sub-nanomolar concentrations. New design
rules specific to DsiRNAs have been developed and are available only from IDT.
DsiRNA Duplexes are available at 2 nmole, 10 nmole, and 40 nmole.
A schematic model of the initial steps in
the RNAi pathway after introduction of
dsRNA into a cell. A) Dicer-substrate duplexes
are bound and cleaved by Dicer,
then passed into the RISC assembly in
a sequence-specific orientation. B) Synthetic
siRNAs (19-22mers) are bound by
Dicer, and passed to RISC without any
specific orientation.
GENE
SILENCING
A graphical representation of the
Dicer-substrate duplex design. The
Dicer activity (light green) is blocked
by the two DNA bases on the 3’ end
(red), and therefore consistently
binds to the opposite 3’ end. It then
cleaves the 27mer in a unidirectional
manner to produce a predictable
21mer (blue).
22

TriFECTa®
IDT’s TriFECTa kit contains three Dicer-substrate siRNA duplexes that are specific for a single target
gene. Duplexes are provided in individual tubes and can be used individually or pooled, if desired.
Sequences are selected from a predesigned library of optimized siRNAs. The TriFECTa sequence
library includes seven of the genomes in the RefSeq collection, including human, mouse, and
rat. TriFECTa duplexes are selected using a rational design algorithm that integrates both traditional
21-mer siRNA design rules as well as new 27-mer-specific criteria. Additionally, analysis is
performed to ensure that the chosen sites do not target alternatively spliced exons and do not
include known single nucleotide polymorphisms.
IDT guarantees that at least two of the three Dicer-substrate duplexes in the TriFECTa kit will give
at least 70% knockdown of the target mRNA*
TriFECTa Kit Contents:
• Three target-specific Dicer-substrate siRNA duplexes (2 nmoles each)
• Fluorescent-labeled transfection control duplex: TYE 563 (1 nmole)
• HPRT-S1 DS positive control duplex (1 nmole)
• NC1, negative control duplex (1 nmole)
• RNase-free duplex buffer (100 mM KAc/30 mM HEPES pH 7.5)
GENE
SILENCING
* as measured by qPCR and when used at a 10 nM concentration, the fluorescent transfection control duplex indicates
that >90% of the cells have been transfected, and the HPRT positive control works with the expected efficiency.
TriFECTa® Kit Performance
Relative mRNA Levels
120
100
80
60
40
20
0
Dose Response Curves
Control
0.1 nM
1 nM
10 nM
HPRT1 SSB STAT1 HNRPH1
Target
Figure 1. Transfection controls and dose optimization.
(a) NIH3T3 cells were transfected with the
TriFECTa Cy3 transfection control duplex. Cells
were washed and examined at 24h after transfection.
Fluorescence and phase-contrast images are
overlaid. Scale bar, 100 µm. (b) HeLa cells were
transfected using TriFECTa duplexes specific for
HPRT1, SSB, STAT1, and HNRPH1 at the concentrations
indicated. Relative mRNA levels were measured
using qRT-PCR at 24h post-transfection;
data were normalized against an internal RPLP0
control using the ‘DS scrambled neg’ duplex as
baseline (100%). Con, control. (Nature Methods 3
(2006), Application Note published online)
23

miRNA
miRNA StarFire® Labeling System
StarFire is a proprietary labeling system for generating radiolabeled oligo probes for miRNA applications
such as in situ hybridization, Southern blotting, isoform detection, and more. The system
generates labeled probes with 10-fold greater specific activity than traditional 5’-end labeling
with polynucleotide kinase. It is based on 3’-end labeling with DNA polymerase. This labeling
method is particularly appropriate for probes used to identify small regulatory RNA and analyze
the expression of microRNA genes.
Product
miRNA StarFire® Complete Kit
miRNA StarFire® Custom Probes
miRNA Universal Template
miRNA StarFire® Refill Kit
Size
Sufficient for 25 labeling reactions
Up to 50 bases
Sufficient for 300 labeling reactions
Sufficient for 25 labeling reactions
miRCat® Small RNA Cloning Kit
Small RNA cloning using the miRCat Kit is based on the pre-activated, adenylated RNA linkering
method that has been used successfully in many labs since its development in 2001. This method
permits cloning from any RNA source in any species and is used primarily for miRNA discovery.
The process consists of isolating miRNAs, attaching cloning linkers to the miRNAs, and amplifying
and cloning miRNA+linker sequences.
The miRCat Kit provides reagents sufficient for ten cloning experiments.
miRNA
PRODUCTS
miRCat-33® Conversion Kit
miRCat-33 is an adaptation of the miRCat Kit for the purpose of carrying out 5’ ligation-independent
small RNA cloning. This kit uses the method of Pak and Fire (2007) and circumvents cloning
problems created by non-standard 5’ ends.
454 miRCat and miRCat-33 Adaptor Primers
454 Adaptor Primers and miRCat-33 Adaptor Primers are designed to convert the small RNA libraries
generated by miRCat ligations (Set I) or by miRCat-33 ligations (Set II) into 454-compatible PCR
libraries for deep sequencing.
24

Molecular Biology Reagents
ReadyMade Primers, Random Hexamers and Nonamers
IDT offers pre-stocked oligos for sample prep, sequencing, and gene expression analysis of common
genes. Each primer contains 10 μg >95% pure product to ensure optimum performance. Identity
is confirmed by mass spectrometry and purity is established by capillary electrophoresis. Because
these primers are pre-stocked, they can be shipped as soon as they are ordered and therefore provide
a fast turnaround time. Examples of ReadyMade products include GAPDH primers, Oligo dT,
random hexamers, and random nonamers. For the complete list of ReadyMade products, please visit
the IDT website at www.idtdna.com.
Nuclease-Free Buffers and Reagents
REAGENTS
While many researchers continue to store oligonucleotides in water, resuspension in a buffered solution
such as TE is recommended. Any solution used to resuspend and store DNA or RNA should
be nuclease-free. It is recommended that stock oligo solutions be made at high concentration and
stored frozen. More dilute working solutions can be made from the stocks at intervals as needed.
See the technical report, Oligonucleotide Yield, Resuspension, and Storage, on the IDT website for more
information on this method.
IDT offers a number of solutions for resuspension and dilution of oligos. Each lot is tested using our
RNaseAlert and DNaseAlert reagents and is guaranteed to be nuclease-free. The water is DEPCfree.
Individual lots are screened for endotoxins using a Limulis Amebocyte Lysate (LAL) assay.
IDTE (10 mM Tris, pH 7.5 or 8.0, 0.1 mM EDTA)
IDTE is a 1X TE buffer for initial resuspension and storage of DNA oligos. IDTE pH 7.5 and pH 8.0 are
both available in 1 L, 10 x 2 mL, 300 mL, or 4 x 1 L sizes.
Nuclease Decontamination Solution
A variety of nucleases are employed in routine molecular biology methods and can accidentally
contaminate lab surfaces and equipment at very high levels. Nuclease Decontamination Solution
irreversibly inactivates nucleases and can be applied to most lab surfaces to remove nuclease contamination.
Just spray, rinse, and let dry. Nuclease Decontamination Solution eliminates the need to
bake glassware and can be applied to plastic surfaces that are difficult to sterilize.
Nuclease Decontamination Solution is available in 250 mL and 6 x 250 mL sizes.
25

Nuclease-Free Water (DEPC-free)
Nuclease-Free Water is intended for initial resuspension and storage of single-stranded RNA oligos
and is also suitable for making dilute working solutions from stock oligos.
Nuclease-Free Water is available in 1 L, 10 x 2 mL, 300 mL, and 4 x 1 L sizes.
Duplex Buffer (30 mM Hepes, pH 7.5, 100 mM Potassium Acetate)
Duplex Buffer is intended for initial resuspension, annealing, and storage of duplex RNAi products.
Duplex Buffer is available in 1 L, 10 x 2 mL, 300 mL, and 4 x 1 L sizes.
Nuclease Detection Products
Nucleases are widely present in the laboratory environment and can interfere with many experiments.
IDT has developed reagents that allow for rapid, sensitive detection of RNases and DNases.
These reagents are fluorescence-quenched oligonucleotide probes that emit a fluorescence signal
only after nuclease degradation. The assay can be read visually or measured and quantitated using
fluorometry.
Two oligonucleotide substrates are available: one designed to detect RNases and the second designed
to detect DNases. The RNaseAlert substrate employs a FAM reporter (Em 520 nm). The DNaseAlert
substrate employs a HEX reporter (Em 555 nm). DNaseAlert and RNaseAlert are each available
in kit format, in 2 bulk tubes, or in 25 single-use tubes. 10X Buffer is also available.
REAGENTS
R
RNA
Q
Incubate with Test Sample
R
Q
R
RNA
Q
Bright = Positive Assay
Probe Cleaved
RNase Contamination Present
Dark = Negative Assay
Probe Intact
RNase Contamination Absent
Oligo Length Standards
Oligo Length Standards are two distinct mixtures of oligonucleotides for use as gel electrophoresis
size/mass standards. The marker oligos in each mixture have balanced base content, are purified,
and are provided in equal mass amounts (10 μg of each oligo per tube) to normalize band intensity.
Each tube contains enough marker for 25-100 loadings, depending on gel configuration and stain
employed. The recommended loading mass varies with the precise stain used and dimensions of
the gel comb.
10/60 ladder
10, 15, 20, 25, 30, 40, 50, 60 base marker oligos
20/100 ladder
20, 30, 40, 50, 60, 70, 80, 90, 100 base marker oligos
26

Usage, Warranty and Licenses
LICENSING
Usage
Research Purposes Only: Oligonucleotides and nucleic acid products (“IDT Products”) are manufactured and
sold by IDT for the customer’s research purposes only. Except pursuant to a separate, written agreement with
IDT, IDT Products are not sold (and have not been approved) for use in any clinical, diagnostic, or therapeutic
applications. Obtaining any license(s) or other approvals necessary to use IDT Products in proprietary applications
or in any non-research (e.g., clinical) applications is the customer’s exclusive responsibility. IDT will not be
responsible or liable for any losses, costs, expenses, or other forms of liability arising out of the unauthorized or
unlicensed use of IDT Products. By using any IDT Product for any purpose, purchasers and users of IDT Products
agree to indemnify and hold IDT harmless for any and all damages and/or liability, however characterized, related
to the unauthorized or unlicensed use of IDT Products. Under no circumstances shall IDT be liable for any
consequential damages resulting from any use (approved or otherwise) of IDT Products. No Resale: The sale or
resale of IDT Products by any person other than IDT is strictly prohibited without the express, written consent of
IDT. IDT accepts all orders for and makes all sales of IDT Products subject to the foregoing use restrictions and
the customer’s indemnification of IDT.
Warranty
IDT’s products are guaranteed to meet or exceed IDT’s published specifications for identity, purity, and yield
as measured under normal laboratory conditions. If an IDT Product fails to meet such specifications, IDT will
promptly replace the product. DISCLAIMER OF WARRANTIES – NO OTHER WARRANTIES: IDT makes no warranty
of any kind whatsoever other than the foregoing General Warranty. Specifically, but without limitation,
IDT expressly disclaims any implied warranties of merchantability or fitness for a particular purpose, and any
warranty that IDT Products, or the use of IDT Products, will not infringe the patents of one or more third-parties.
IDT accepts all orders for and makes all sales of IDT Products subject to the foregoing disclaimers of warranties.
Licenses/Trademarks
Black Hole Quenchers®, BHQ-1®, and BHQ-2®, are trademarks of Biosearch Technologies, Inc. (BTI), and all BHQ
products are licensed and sold under agreement with BTI. These products are sold exclusively for research and
development use by the purchaser. They may not be used for any human or veterinary clinical or diagnostic purposes
without express permission from BTI and they may not be re-sold, distributed, re-labeled or re-packaged.
Cy Dyes and Cy labeled oligonucleotides are covered by U.S. Patent Numbers 5,556,959 and 5,808,044 and
are licensed and sold for non-commercial research purposes only. Any other use including diagnostic, therapeutic
or in vivo applications requires a license from Amersham Biosciences, Inc. Cy is a trademark of Amersham
Biosciences.
TYE Dyes: are sold under license from Thermo Fisher Scientific (Milwaukee) LLC.
PrimeTime® qPCR Probes and Assays: NOTICE TO PURCHASER: LIMITED LICENSE. A license to perform the
patented 5’ Nuclease Process for research is obtained by the purchase of (i) both Licensed Probe and Authorized
5’ Nuclease Core Kit, (ii) a Licensed 5’ Nuclease Kit, or (iii) license rights from Applied Biosystems. This product
contains Licensed Probe. Use of this product is covered by one or more of the following US patents and corresponding
patent claims outside the US: 5,538,848, 5,723,591, 5,876,930, 6,030,787, 6,258,569, and 5,804,375
(claims 1-12 only). The purchase of this product includes a limited, non-transferable immunity from suit under
the foregoing patent claims for using only this amount of product for the purchaser’s own internal research.
The right to use this product in the 5’ Nuclease Process under the applicable claims of US Patents Nos. 5,210,015
and 5,487,972, and corresponding patent claims outside the United States, can be obtained through purchase
of an Authorized 5’ Nuclease Core Kit. Except under separate license rights available from Applied Biosystems,
no right under any other patent claim, or to perform commercial services of any kind, including without limitation
reporting the results of purchaser’s activities for a fee or other commercial consideration, or to sublicense,
repackage with other products, or resell in any form, is conveyed expressly, by implication, or by estoppel. This
product is for research use only. Diagnostic uses under Roche patents require a separate license from Roche.
Further information on purchasing licenses may be obtained from the Director of Licensing, Applied Biosystems,
850 Lincoln Centre Drive, Foster City, California 94404, USA.
Dual–Labeled Probes: NOTICE TO PURCHASER: DISCLAIMER OF LICENSE No license is conveyed with the
purchase of this product under any of US Patents Nos. 5,210,015, 5,487,972, 5,804,375, 5,994,056, 6,171,785,
6,214,979, 5,538,848, 5,723,591, 5,876,930, 6,030,787, and 6,258,569, and corresponding patents outside the
United States, or any other patents or patent applications, relating to the 5’ Nuclease and dsDNA-Binding Dye
Processes. For further information contact the Director of Licensing, Applied Biosystems, 850 Lincoln Centre
Drive, Foster City, California 94404, USA.
Molecular Beacons are licensed under patents owned by The Public Health Research Institute of the City of New
York, Inc. and come with licensed rights for use only in the purchaser’s research and development activities. A
probe which has a hairpin (stem-and-loop) structure with a fluorophore, quencher, or other label on each arm
of the hairpin stem is a Molecular Beacon Probe and must be ordered as a Molecular Beacon Probe. No license
is conveyed with the purchase of this product under any of US Patents Nos. 5,210,015, 5,487,972, 5,804,375,
5,994,056, 6,171,785, 6,214,979, 5,538,848, 5,723,591, 5,876,930, 6,030,787, and 6,258,569, and corresponding
patents outside the United States, or any other patents or patent applications, relating to the 5’ Nuclease and
27

dsDNA-Binding Dye Processes. For further information contact the Director of Licensing, Applied Biosystems,
850 Lincoln Centre Drive, Foster City, California 94404, USA.
Locked Nucleic Acids (LNAs). IDT is licensed under patents and patent applications assigned to Exiqon A/S to
sell oligonucleotides incorporating LNAs for research purposes only. Resale of LNA-oligos and their use in humans
or in therapeutic applications are all prohibited.
RNAi. IDT’s products are licensed under U.S. and international patent rights owned by the Carnegie Institution
of Washington that cover RNA interference. These products are accompanied by a limited non-exclusive worldwide
license under the Carnegie Institution of Washington’s patent rights for researchers at academic or other
not-for-profit institutions to use the products for non-profit research. However, use of dsRNA for RNA interference
by for-profit organizations requires a license from the Carnegie Institution of Washington.
siRNA. This product is licensed under European Patents 1144623, 121945 and foreign equivalents from Alnylam
Pharmaceuticals, Inc., Cambridge, USA and is provided only for use in academic and commercial research whose
purpose is to elucidate gene function, including research to validate potential gene products and pathways
for drug discovery and development and to screen non-siRNA based compounds (but excluding the evaluation
or characterization of this product as the potential basis for an siRNA-based drug) and not for any other
commercial purposes. Information about licenses for commercial use (including discovery and development of
siRNA-based drugs) is available from Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge MA 02142, USA.
DsiRNA Duplexes. IDT is exclusively licensed under patents owned by the City of Hope and IDT to make and sell
DsiRNA Duplex products for use in research and development. Use of DsiRNA Duplex products or technology in
humans or for human or veterinary diagnostic, prophylactic or therapeutic purposes requires a separate license
from City of Hope Medical Center.
OTHER DISCLAIMERS
Click-Chemistry enabled, modified oligos are manufactured and sold under license from Baseclick GmbH, using
Base-click’s proprietary Click Chemistry. All such modified products are sold by IDT for the end-user’s internal
research purposes only. See www.baseclick.org for further details.
Digoxigenin is licensed by Roche Diagnostics GmbH. The use of digoxigenin technology to label nucleic acids is
licensed under patents (EP 0 324 474, US 5.344.757, US 5.702.888, US 5.354.657, JP 1999884 and HK 1169) owned
by Roche Diagnostics GmbH. For further information on products to label and detect digoxigenin-modified
nucleic acids refer to www.roche-applied-science.com/dig/.
End-Blocked Oligos. This product is covered by US Patent No. 6,197,944 and sold under license from the University
of Iowa Research Foundation for the customer’s internal research purposes only.
RNaseAlert compositions and methods are protected under U.S. Patent No. 6,773,885 and other pending IDT
patent(s). RNaseAlert is a trademark of Ambion, Inc.
StarFire® is a trademark of IDT, and its compositions and methods are protected under pending IDT patent(s).
IDT Trademarks
Iowa Black®, PrimeTime®, TYE, MAX, TEX 615, Rapid HPLC, Express DLP, SameDay®, Hot Plate®, Ultramer,
Mini Gene, Ready Made Primers, OligoCard® , I-Linker, DNaseAlert, RNaseAlert, PrimerQuest®,
Oligo Analyzer®, LabLinker®, StarFire® and SciTools®.
Other Trademarks
FAM, HEX, ROX, TAMRA and TET are trademarks of Applied Biosystems, Inc.
TaqMan® is a registered trademark of Roche Molecular Systems that is licensed exclusively to Applied Biosystems
Inc. for use in certain non-diagnostics field.
Shipping Information
Orders shipped to customers located outside of the United States, Canada, Belgium, Australia, and the United
Kingdom may be subject to import taxes, customs duties, and fees levied by the destination country upon importation;
these charges are the recipient’s responsibility. Such commercial transactions require customs clearance,
and as the importer you are responsible for making customs clearance arrangements. Any corresponding
charges for brokerage/customs clearance will also be borne by you, the importer. Customs policies vary widely
from country to country; please contact your local customs office for further information.
When ordering from IDT, the recipient is the importer of record and must comply with all laws and regulations of
the destination country. You are responsible for assuring that the product(s) can be lawfully imported to the destination
country, and are also responsible for obtaining any necessary import permits. IDT must provide certain
order, shipment, and product information to our international carriers, and such information may be communicated
by the carriers to customs authorities in order to facilitate customs clearance and comply with local laws.
Please be aware that cross-border shipments may be subject to opening and inspection by customs authorities.
LICENSING
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Ordering
IDT’s San Diego, California facility
IDT offers convenient online ordering:
CONTACT
www.idtdna.com
Email orders are also accepted. See the IDT website for email templates and instructions.
An order confirmation is sent via email shortly after an order is placed on the website. IDT
offers many online ordering features, including pricing, yield guarantees and estimated ship
date shown as products are ordered, access to oligo specification sheets, mass spectrometry
and analytical traces, and order and shipment tracking.
For payment, IDT accepts purchase orders, all major credit cards, Electronic Funds Transfer,
and OligoCards.
See IDT's website for a list of distributors worldwide.
Customer Care & Technical Services
Our staff includes experts in molecular biology, oligonucleotide design, sequencing,
mutagenesis, PCR and related research applications who are available for consultation
about an application before or after an order is placed.
Americas
custcare@idtdna.com
1-800-328-2661
Europe
eutechsupport@idtdna.com
+32 (0) 16 28 22 60
Other Locations
international@idtdna.com
Web chat is available at www.idtdna.com.
IDT’s Leuven, Belgium facility