Shop All DNA⁄RNA Labeling Kits

SuperScript™ Plus Direct cDNA Labeling Module (no purification) with Alexa Fluor™-aha-dUTPs Invitrogen™

The SuperScript® Plus Direct cDNA Labeling System is a microarray labeling kit that combines the superior performance of SuperScript® III Reverse Transcriptase (RT) with the simplicity of direct labeling. In place of an enzyme spike-in, the streamlined protocol incorporates balanced sets of novel, array-optimized, nucleotides conjugated to Alexa Fluor® 555 and 647 dyes. This results in more reproducible array data with higher correlation coefficients than using standalone reagents. The SuperScript® Plus Direct cDNA Labeling System provides:

• Optimized, all-inclusive direct labeling with balanced aha-Alexa Fluor® nucleotides, enabling higher numbers of array positives
• Improved correlation coefficients for more accurate data (Figure 1)
• Low elution purification columns included for ease of use

In the SuperScript® Plus cDNA Labeling method, anchored oligo(dT) anneals to the mRNA template (Figure 2). SuperScript® III RT extends from the priming site, incorporating dUTP labeled with Alexa Fluor® dye directly to produce labeled cDNA. Template RNA is degraded by base hydrolysis. Free nucleotides and other contaminants are removed using low-elution volume purification columns before hybridization to the microarray.

SuperScript™ Plus Direct cDNA Labeling System with Alexa Fluor™-aha-dUTPs Invitrogen™

The SuperScript® Plus Direct cDNA Labeling System is a microarray labeling kit that combines the superior performance of SuperScript® III Reverse Transcriptase (RT) with the simplicity of direct labeling. In place of an enzyme spike-in, the streamlined protocol incorporates balanced sets of novel, array-optimized, nucleotides conjugated to Alexa Fluor® 555 and 647 dyes. This results in more reproducible array data with higher correlation coefficients than using standalone reagents. The SuperScript® Plus Direct cDNA Labeling System provides:

• Optimized, all-inclusive direct labeling with balanced aha-Alexa Fluor® nucleotides, enabling higher numbers of array positives
• Improved correlation coefficients for more accurate data (Figure 1)
• Low elution purification columns included for ease of use

In the SuperScript® Plus cDNA Labeling method, anchored oligo(dT) anneals to the mRNA template (Figure 2). SuperScript® III RT extends from the priming site, incorporating dUTP labeled with Alexa Fluor® dye directly to produce labeled cDNA. Template RNA is degraded by base hydrolysis. Free nucleotides and other contaminants are removed using low-elution volume purification columns before hybridization to the microarray.

North2South™ Biotin Random Prime DNA Labeling Kit Thermo Scientific™

Thermo Scientific North2South Random Prime DNA Biotinylation Kit uses random heptanucleotides, Klenow fragment and biotin-nucleotides to produce biotinylated DNA templates for DNA hybridization and detection methods.

Features of the North2South Random Prime DNA Biotinylation Kit:

• Works with as little as 100ng starting DNA template
• Exonuclease-free Klenow fragment in the DNA labeling kit produces higher yields
• Each reaction yields probe sufficient for approximately three (10 x 10 cm) blots

This random prime DNA labeling kit is based on the procedure of Feinberg and Vogelstein (Ref.4,5). Random heptanucleotides containing all possible sequences are annealed to a denatured DNA template. These act as primers for complementary strand synthesis by DNA Polymerase (Klenow fragment, 3'-5' exo-). Biotinylated dNTPs in the reaction mix are incorporated into the newly synthesized DNA. This protocol yields biotin-labeled DNA of high activity for use as probes in hybridization experiments such as Southern and Northern hybridizations. The resulting hybrids can be detected with streptavidin-horseradish peroxidase (HRP) and a chemiluminescent substrate kit such as North2South Chemiluminescent Hybridization and Detection Kit.

HT WT Terminal Labeling and Controls Kit Applied Biosystems™

The HT WT Terminal Labeling and Controls Kit is used with the WT Expression Kit for High-Throughput Robotics (sold separately). Both products can be combined with the HT WT Expression Assay Consumables for Biomek™ FXp Target Prep Express (sold separately) for customers who use the Beckman Coulter Biomek™ FXp Target Prep Express Instrument.

The HT WT Terminal Labeling and Controls Kit contains the GeneChip™ HT WT Terminal Labeling Kit, GeneChip™ Hybridization Control Kit, and GeneChip™ Poly-A Control Kit.

Key Features
• Low RNA input requirements — as little as 100 ng total RNA for a single round of amplification
• No separate rRNA depletion step
• Magnetic bead purification for enhanced recovery and ease of use
• StreamLined workflow for simplified protocol and reduced hands-on time
• Unbiased coverage of the transcriptome

The WT Expression Kit for High-Throughput Robotics includes:
• All reagents needed to generate sense cDNA ready for fragmentation and labeling
• Magnetic beads for enhanced purification efficiency

The HT WT Terminal Labeling and Controls Kit includes:
• WT Fragmentation and Labeling Kit required for target produced by the WT Expression Kit for High-Throughput Robotics
• Poly-A controls are added to input RNA to measure efficiency of target amplification by the WT Expression Kit for High-Throughput Robotics
• Hybridization controls that monitor the hybridization process for troubleshooting purposes

Related Links
HT WT Expression Assay Consumables for Biomek™ FXp Target Prep Express
HT WT Terminal Labeling and Controls Kit

Nick Translation System Invitrogen™

The Nick Translation System is ideal for both radioactive and non-radioactive labeling of DNA. The Nick Translation System:

• Provides five pre-mixed nucleotide solutions for flexibility in labeled nucleotide incorporation
• Yields >108 cpm/µg control DNA using [ - 32 P]-dCTP
• Labels 1 µg of DNA in one reaction

BioPrime™ Total Genomic Labeling System Invitrogen™

The BioPrime® Total Genomic Labeling System is a complete genomic DNA labeling system designed for use in array comparative genomic hybridization applications (aCGH) that allows for better call rates with precious samples.

Note: The BioPrime® Total Genomic Labeling System includes PurelinkTM Genomic DNA purification columns and purification buffers. The BioPrime® Total Genomic Labeling Module does not.

The BioPrime® Total Genomic Labeling System offers users the following advantages:

- Higher signal to noise with Alexa Fluor® 3 and 5 dyes
- Less channel bias due to novel reaction formulation
- Widest range of input material (50 ng - 3 µg)
- Simplified workflow with master mix formulation

This complete, all-inclusive kit is optimized to work across the widest range of sample input material with no need for pre-amplification. Highly concentrated exo-Klenow fragment of DNA polymerase I in a component-limited reaction allows for consistent, robust DNA yields of ~ 8 µg with as little as 50 ng of genomic DNA input. An optimized dye-labeled nucleotide mix with new dNTP linkers, novel application-specific Alexa Fluor® 3 and 5 dyes, and improved buffer chemistry reduce labeling variation and increase signal to noise on arrays. Excitation and emission spectra of Alexa Fluor® 3 and 5 dyes are suited for conventional two color scanners with no need to change settings. New master mix formulation streamlines reaction set-ups, increasing consistency. Complete kits are batch tested to assure quality in performance from lot to lot.

Contents and Storage:
The BioPrime® Total Genomic Labeling System contains Alexa Fluor® 3 and Alexa Fluor® 5 2x reaction mix, Exo-Klenow fragment (40 U/ µl), 5 mM EDTA, TE Buffer, and control DNA (Salmon Sperm). Store at -80°C for long term storage. The 2X Reaction Mixes may be stored at +4°C for up to 4 weeks and should be protected from light. The BioPrime® Total Genomic Labeling System also contains PurelinkTM Genomic DNA purification columns and purification buffers (the BioPrime® Total Genomic Labeling Module does not). Store at room temperature. All components are guaranteed for 6 months when properly stored.

SuperScript™ Indirect cDNA Labeling System Invitrogen™

The SuperScript® Indirect cDNA Labeling System is an array labeling kit based on proven methods of indirect cDNA labeling. The optimized system provides:

• SuperScript® III RT for generating high cDNA yields
• A proprietary nucleotide mixture to increase signal intensity
• A convenient kit format that saves valuable time

In this indirect labeling method, mRNA or total RNA is reverse transcribed using SuperScript® III RT, incorporating amino-modified dUTP and dATP into the synthesized cDNA. The template RNA is then degraded by base hydrolysis, and the reaction is neutralized with acid. The amino-modified cDNA is then purified to remove unincorporated nucleotides, primers, and buffers. In the second step, the modified cDNA is coupled with the active form of a fluorescent dye. The fluorescently labeled cDNA is purified with a S.N.A.P.™ spin column to remove any unreacted dye. The resulting fluorescently labeled cDNA is ready for hybridization to microarrays (Figure 1).

The SuperScript® Indirect cDNA Labeling System provides a complete system that includes both the core kit reagents (except dyes) and a purification module. The SuperScript® Indirect cDNA Labeling Module includes just the core kit reagents. Both provide the flexibility to use fluorescent nucleotides of your choice.

BioPrime™ Total Genomic Labeling Module Invitrogen™

The BioPrime® Total Genomic Labeling Module is a complete genomic DNA labeling system designed for use in array comparative genomic hybridization applications (aCGH) that allows for better call rates with precious samples.

Note: The BioPrime® Total Genomic Labeling Module does not include PurelinkTM Genomic DNA purification columns and purification buffers. The BioPrime® Total Genomic Labeling System does include these components.

The BioPrime® Total Genomic Labeling Module offers users the following advantages:

- Higher signal to noise with Alexa Fluor® 3 and 5 dyes
- Less channel bias due to novel reaction formulation
- Widest range of input material (50 ng - 3 µg)
- Simplified workflow with master mix formulation

This complete, all-inclusive kit is optimized to work across the widest range of sample input material with no need for pre-amplification. Highly concentrated exo-Klenow fragment of DNA polymerase I in a component-limited reaction allows for consistent, robust DNA yields of ~ 8 µg with as little as 50 ng of genomic DNA input. An optimized dye-labeled nucleotide mix with new dNTP linkers, novel application-specific Alexa Fluor® 3 and 5 dyes, and improved buffer chemistry reduce labeling variation and increase signal to noise on arrays. Excitation and emission spectra of Alexa Fluor® 3 and 5 dyes are suited for conventional two color scanners with no need to change settings. New master mix formulation streamlines reaction set-ups, increasing consistency. Complete kits are batch tested to assure quality in performance from lot to lot.

Contents and Storage:
The BioPrime® Total Genomic Labeling Module contains Alexa Fluor® 3 and Alexa Fluor® 5 2x reaction mix, Exo-Klenow fragment (40 U/ µl), 5 mM EDTA, TE Buffer, and control DNA (Salmon Sperm). Store at -80°C for long term storage. The 2X Reaction Mixes may be stored at +4°C for up to 4 weeks and should be protected from light. All components are guaranteed for 6 months when properly stored.

Turbo Labeling™ Kit, biotin Applied Biosystems™

The ARCTURUS® Turbo Labeling™ Kits offer a proprietary, non-enzymatic technology optimized for the labeling of unmodified, amplified RNA (aRNA) for gene expression profiling. The unmodified aRNA is labeled post-amplification, thereby avoiding the need to incorporate modified nucleotides during RNA amplification. The use of unmodified nucleotides in the amplification process results in unmodified aRNA with higher yields and longer aRNA fragments, thus providing better representation of the mRNA transcript for downstream analysis (Figures 1 and 2).

Key product features:
• Simple – platform-independent aRNA labeling protocol typically takes less than 30 minutes
• Efficient – unlabeled aRNA can be preserved for downstream validation
• Effective – use of unmodified nucleotides permits exceptional representation of mRNA transcripts
Arcturus® Turbo Labeling™ Kits include reagents to support labeling of 12 samples with either Cy3*⁄Cy5 dyes (Figure 3) or with biotin for hybridization to cDNA or oligonucleotide arrays (Figure 4).

For Research Use Only. Not for use in diagnostics procedures.

GeneChip™ DNA Labeling Reagent, 7.5 mM Applied Biosystems™

The GeneChip™ DNA Labeling Reagent is used with the Prokaryotic Target Labeling Assay for 3' expression studies with GeneChip prokaryotic Brand Arrays. The assay utilizes reverse transcriptase and random hexamer primers to produce DNA complementary to the RNA. The cDNA products are then fragmented by DNase I and labeled with terminal transferase and biotinylated GeneChip DNA Labeling Reagent at the 3' termini.

Functionally tested on GeneChip Brand Arrays, we recommend the Prokaryotic Target Labeling Assay and associated reagents for use in prokaryotic gene expression studies.

Prokaryotic Target Labeling Assay components include:
Control Oligo B2, 3nM
GeneChip DNA Labeling Reagent
GeneChip Poly-A RNA Control Kit

Detailed instructions for using this reagent are described in Section 3, Chapter 1 of the GeneChip Expression Analysis Technical Manual.

Each kit contains 1 vial of 60 µL of the GeneChip DNA Labeling Reagent, 7.5 mM, sufficient for 30 labeling reactions.

Related Links
GeneChip™ Wash Buffer A

GeneChip™ WT Terminal Labeling Kit Applied Biosystems™

GeneChip™ WT Sense Target Labeling and Control Reagents (900652) and GeneChip WT cDNA Synthesis and Amplification Kits (900672 and 900673) are being discontinued in June 2010.

The Whole Transcript (WT) Sense Target Labeling Assay has an updated protocol. The GeneChip WT (Whole Transcript) Terminal Labeling Kit is optimized to be used for the fragmentation and labeling steps of the GeneChip WT Sense Target (ST) Labeling Assay.

The WT Terminal Labeling Kit employs a strategy for reproducible DNA fragmentation with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1). The typical input material is random-primed, single-stranded DNA

Following fragmentation, the resulting fragmented DNA can then be labeled using terminal deoxynucleotidyl transferase (TdT) in the presence of a proprietary biotinylated compound, GeneChip DNA Labeling Reagent. Both components are also provided in the WT Terminal Labeling Kit. The final labeled DNA target is ready to be added to the cocktail for hybridizing to the arrays such as the GeneChip Human Exon 1.0 ST Array.

BioPrime™ Total FFPE Genomic Labeling System Invitrogen™

The BioPrime® Total FFPE Genomic Labeling System is a complete genomic DNA labeling kit designed for use in array comparative genomic hybridization applications (aCGH) using formalin-fixed paraffin-embedded (FFPE) samples. Previous protocols have required large amounts of very high quality DNA, which is often difficult to obtain from FFPE material. With a random prime amplification (RPA) method, using labeling mixes specifically formulated for FFPE samples, BioPrime® Total FFPE Genomic Labeling System generates high yields of labeled DNA which is most representative of the starting sample.. Increased call accuracy is achieved with higher yields of labeled material on the array, giving you more accurate calls. The BioPrime® Total FFPE Genomic Labeling System offers users the following advantages:

- Improved call rate with higher signal to noise ratios from Alexa Fluor® 3 and 5 dyes
- Easy cleanup with PureLink™ purification eliminates the need for complicated volume-reduction steps
- Less channel bias due to enhanced reaction formulation for FFPE samples
- Lower requirements for input material using enzymatic RPA method


This complete, all-inclusive kit is optimized to work across a wider range of sample input material with no need for pre-amplification. Highly concentrated exo-Klenow fragment of DNA polymerase I in a component limited reaction allow for consistent, robust DNA yields of genomic FFPE DNA input. BioPrime® Total for Agilent® aCGH is supplied with Purelink™ purification which allows for low elution, eliminating the need for complicated volume-reduction steps. Purelink™ purification also reduces background due to dye bled found in other purification systems An optimized dye labeled nucleotide mix with new dNTP linkers, novel, application-specific Alexa Fluor® 3 and 5 dyes, and improved buffer chemistry reduce labeling variation and increase signal to noise on arrays. Excitation and emission spectra of Alexa Fluor® 3 and 5 dyes are suited for conventional two color scanners with no need to change settings. Complete kits are batch tested to assure quality in performance from lot to lot.

Random Primers DNA Labeling System Invitrogen™

The Random Primers DNA Labeling System is ideal for radioactively labeling DNA, particularly fragments <1 kb. The Random Primers DNA Labeling System:
––Yields >109 cpm/µg control DNA using [ α-32 P]-dCTP
–25 ng of DNA in one reaction


Performance and Quality Testing: Incorporation of a radioactively labeled nucleotide is verified using control DNA in a random primers labeling reaction.

Biotin DecaLabel DNA Labeling Kit Thermo Scientific™

Thermo Scientific Biotin DecaLabel DNA Labeling Kit is an advanced system for the efficient synthesis of biotin-labeled DNA probes, based on an improved random-primed labeling method developed by Feinberg and Vogelstein. The primary improvement over traditional random-primed method involves the use of random decamers instead of hexamers, ensuring more efficient annealing with DNA at 37°C. Klenow Fragment, exo-, included in the kit, is genetically engineered enzyme with no detectable exonuclease activity. The enzyme does not degrade the labeled probe during reaction, which results in a high labeling yield even with low amounts of template. You can uniformly label any length DNA fragments.

Biotin-labeled DNA is detected with the Biotin Chromogenic Detection Kit or conventional biotin-avidin or biotin-streptavidin detection systems.

Highlights

Non-radioactive labeling of DNA
Efficient priming of labeling reactions with random decamers
High yields with Klenow Fragment, exo-: no degradation of a labeled probe during reaction

Applications

• Generation of biotin-labeled DNA probes for a variety of non-radioactive hybridization experiments, including Southern and Northern blots, colony/plaque hybridizations, dot/slot blots, and in situ hybridizations.

Principle

Random decamers are annealed to a denatured template DNA molecule, and new strands are synthesized by the Klenow Fragment, exo- in the presence of biotin-dUTP. During this reaction, the biotinylated nucleotides are incorporated into the newly synthesized complementary DNA strand.

Related Products
Biotin DecaLabel DNA Labeling Kit

DECAprime™ II DNA Labeling Kit Invitrogen™

The Ambion® kit is for labeling DNA using a random-priming method, which has technical improvements over existing methods including the use of a high-purity, exonuclease-free Klenow and Random Decamers to produce probes with greater than 109 cpm/µg in 10 min reactions. The kit includes sufficient reagents for 100 reactions.

• Fast, 10 min reaction time
• Elimination of Klenow exonuclease activity maximizes specific activity
• Improved labeling kinetics maximizes yields
• Flexible—both -dATP and -dCTP buffers supplied with each kit
• Decamers produce greater primer-template stability

Don't Trade Specific Activity for Yield

There is a trade-off between probe yield and probe specific activity when using the random-priming method for labeling DNA. Both limiting nucleotide and template mass affect probe yield. Until the labeled nucleotide becomes limiting, the larger the amount of DNA template used, the greater the yield of probe. However, once the labeled nucleotide becomes limiting, additional template will only result in lower specific activity, since the unlabeled template competes with the labeled probe for target. The accompanying figure shows the effect of probe-specific activity on the limits of target detection. Note that probe made with the smallest amount of template DNA (6.25 ng) was able to detect target present at 1/4 to 1/8 the level as the probe made with the largest amount of template (100 ng).

Maximal Yields of High Specific Activity Probes
The DECAprime™ II DNA Labeling Kit produces probes with maximum specific activity even when the DNA template is impure or the quantity is unknown or very low. Data shows that low template amounts require long incubation times to reach maximum specific activity. Under these conditions, extended reaction times will increase both the yield and the specific activity of the probe.

Accessory Products:
The NucAway™ Spin Columns (SKU# AM10070) are recommended for probe purification.
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