Shop All DNA⁄RNA Labeling Kits

Pierce™ Biotin 3' End DNA Labeling Kit (Thermo Scientific™)

The Thermo Scientific Pierce Biotin 3' End DNA Labeling Kit is for tagging single-stranded DNA primers with biotin for use in non-radioactive electrophoretic mobility shift assays (EMSA) and other nucleic acid detection methods.

The DNA biotinylation procedure uses terminal deoxynucleotidyl transferase (TdT) to catalyze nontemplate-directed nucleotide incorporation onto the 3'-OH end of single-stranded DNA. TdT exhibits a substrate preference of single-stranded DNA, but it will label duplex DNA with 3' overhangs and blunt duplexes, albeit with a lower efficiency.

Features of the Biotin 3' End DNA Labeling Kit:

• Non-isotopic labeling eliminates the hassle of hazardous radioactive materials or difficult-to-dispose-of waste
• 1-3 biotinylated ribonucleotides onto the 3' end of DNA strands for less interference with hybridization or sequence-specific binding of proteins
• Biotin-labeled probes are stable for more than one year
• 30-minute labeling procedure is fast and efficient

The Biotin 3' End DNA Labeling Kit has been optimized to incorporate 1-3 biotinylated ribonucleotides (Biotin-11-UTP) onto the 3' end of DNA strands. This labeling strategy has the advantage of localizing the biotin to the 3' end of the probe where it will be less likely to interfere with hybridization or sequence-specific binding of proteins. Biotin-labeled DNA probes can be used to facilitate non-isotopic detection in a variety of applications including electrophoretic mobility shift assays (EMSA), Northern or Southern blots, colony hybridizations or in situ hybridizations.

mirVana™ Probe & Marker Kit (Invitrogen™)

The Ambion® mirVana™ Probe & Marker Kit is designed for rapid 5' end labeling and cleanup of small RNA or DNA probes. The kit also contains reagents to prepare small, radiolabeled RNA size markers (150, 100, 90, 80, 70, 60, 50, 40, 30, 20, and 10 nt) and single-nucleotide RNA ladders. The kit includes sufficient reagents for 30 sample reactions +10 marker reactions.

Features of the Ambion® mirVana™ Probe & Marker Kit

• 5' end label and purify small RNA and DNA probes
• Includes Decade™ Markers – ideal size markers for gel analysis of small RNAs
• Simple and rapid post-labeling probe clean up procedure
• Ideal for small RNA analysis by Northern blot or with the mirVana™ miRNA Detection Kit
• Compatible with chemically synthesized oligonucleotides -—no need to gel purify after labeling

The mirVana™ Probe & Marker Kit uses an end-labeling procedure. Products from this labeling method typically do not require gel purification for subsequent use in the mirVana™ miRNA Detection Kit or RPA procedures. However, there is usually a need to remove unincorporated label. The kit includes purification columns for this purpose. Radiolabeled probes prepared with the mirVana™ Probe & Marker Kit have been successfully used for the detection of miRNA by Northern blot and by solution hybridization using the mirVana™ miRNA Detection Kit. DNA probes can also be efficiently labeled with the Probe & Marker Kit and used in many downstream applications.

How the Kit Works
Preparation of DNA and RNA probes or RNA markers starts with a phosphorylation reaction using T4 Polynucleotide Kinase and [gamma-32P]ATP followed by a rapid column purification procedure. After elution, the purified RNA is recovered in a concentrated aqueous solution. To prepare the Decade Markers, a phosphorylation reaction is performed with a 150 nt RNA transcript (included), then diluted into a cleavage reagent that generates the molecular weight marker set in a five-minute, room-temperature reaction. For exact determination of RNA size, a single ribonucleotide ladder can also be generated using any purified 5' end labeled RNA probe in a ~10 min alkaline hydrolysis reaction.

Turbo Labeling™ Kit, Cy3 dye (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.

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.

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.

Ulysis™ Alexa Fluor™ 546 Nucleic Acid Labeling Kit (Invitrogen™)

ULYSIS® Nucleic Acid Labeling Kits provide a unique method to attach a fluorescent dye to nucleic acids. The labeling reagent in the kit reacts with the N7 of guanine to form a stable coordination complex, and the reaction is simple and fast—just heat denature DNA (5 minutes), add the label (react for 15 minutes), then purify.

ULYSIS® Nucleic Acid Labeling Specifications:
• Dye (Ex/Em): Alexa Fluor® 546 (555/570 nm)
• Labeling reaction is complete in as little as 15 minutes
• Available in several Alexa Fluor® dye colors


The Resulting Labeled Probe is useful for:
• Dot, northern, and Southern blots
• RNA and DNA in situ hybridization
• Multicolor fluorescence in situ hybridization (mFISH)
• Comparative genome hybridization (CGH)
• Microarray analysis

Reliable Labeling With the Universal Linkage System
We developed this series of ULYSIS® kits to enable rapid and simple coupling of our Alexa Fluor® dyes to purine bases in nucleic acid polymers. The method, the Universal Linkage System (ULS™), is based on the use of a platinum dye complex (owned by KREATECH Diagnostics) that forms a stable adduct with the N7 position of guanine and, to a lesser extent, adenine bases in DNA, RNA, PNA, and oligonucleotides. The result is a reliable nonenzymatic method for nucleic acid labeling.

Labeling is Fast and Easy
The labeling reaction typically takes only 15 minutes, and separation of the labeled nucleic acids from the unreacted ULS™ complex can be accomplished through the use of a simple spin-column procedure. DNA longer than ~1,000 base pairs requires a 10-minute DNase digestion before labeling, which both optimizes labeling and fragments the probe for efficient hybridization.

More Options for Nucleic Acid Labeling
To review various options for nucleic acid labeling, review Labeling Oligonucleotides and Nucleic Acids—Section 8.2 in the Molecular Probes® Handbook or view a list of our kits.

For Research Use Only. Not intended for human or animal therapeutic or diagnostic use.

Turbo Labeling™ Kit, Cy5 dye (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.

SuperScript™ Indirect cDNA Labeling Module, no purification columns (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.

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 30 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.

Silencer™ siRNA Labeling Kit with FAM dye (Invitrogen™)

For the labeling of siRNA with FAM™. Includes sufficient reagents for labeling 65 µg of siRNA. Ambion® Labeled siRNA can be used to analyze siRNA subcellular localization, stability, and transfection efficiency. In addition, fluorescently labeled siRNA is particularly well-suited for use in double-label experiments (with a labeled antibody) to track cells that receive siRNA during transfection and to correlate transfection with down-regulation of the target protein. Research shows that labeling of siRNAs does not affect their biological function.

Accessory Products:
Also available is the Silencer® Cy™3 siRNA Labeling Kit (SKU# AM1632).

ARES™ Alexa Fluor™ 488 DNA Labeling Kit (Invitrogen™)

The ARES™ Alexa Fluor® DNA Labeling Kit provides a versatile, two-step method for labeling DNA with our Alexa Fluor® dyes. In the first step, an amine-modified nucleotide is incorporated into DNA using conventional enzymatic labeling methods. In the second step, the amine-modified DNA is chemically labeled using our proprietary amine-reactive Alexa Fluor® 488 dye. The labeled probes can be used for fluorescence in situ hybridization (FISH) and microarray techniques. We offer ARES™ Alexa Fluor® DNA Labeling Kits in five fluorescent colors, and each kit provides sufficient reagents for 5 to 10 labeling reactions of 1 to 5 µg DNA each.

ARES™ Alexa Fluor® Labeling Kit Specifications:
• Dye (Ex/Em): Alexa Fluor® 488 (492/520 nm)
• Achieves more uniform, consistent labeling than techniques for enzymatic incorporation of labeled nucleotides
• Typically produces one dye per 12–20 bases
• Optimal for FISH and microarrays


More Uniform Labeling With ARES™ Labeling Kits
ARES™ Alexa Fluor® Labeling Kits employ a two-step labeling technology—nick translation to enzymatically incorporate an amine-modified nucleotide (aminoallyl dUTP) followed by chemical labeling with Alexa Fluor® dyes. This method achieves uniformity and consistency of labeling that is difficult to obtain with conventional enzymatic incorporation of labeled nucleotides.
We also offer this two-step labeling technology in our FISH Tag™ DNA and FISH Tag™ RNA Kits, which provide a complete workflow solution for FISH applications, including all of the reagents for probe synthesis, labeling, purification and an anti-fade reagent to help protect the signal during fluorescence microscopy.

More Options for Nucleic Acid Labeling
To review various options for nucleic acid labeling (including DNA and RNA FISH), review Labeling Oligonucleotides and Nucleic Acids—Section 8.2 in the Molecular Probes® Handbook.

For Research Use Only. Not intended for human or animal therapeutic or diagnostic use.

FlashTag™ Biotin HSR RNA Labeling Kits (Applied Biosystems™)

FlashTag™ Biotin HSR RNA Labeling Kits are high-sensitivity labeling reagents designed to prepare target from RNA samples for GeneChip™ miRNA Arrays.

Features and benefits
Easy-to-use: 45-minute assay—from RNA sample to labeled target—without amplification or purification steps
Low sample input: Requires as little as 130 ng total RNA
Variety of samples: Works with any intact, degraded, or FFPE RNA sample
Built-in controls: Contains RNA spike control oligos for GeneChip miRNA Arrays
Superior performance:
    - Reproducibility: Inter-and intra-lot signal correlation is typically R >0.95
    - Sensitivity: Detects 94% of miRNA transcripts at 1.0 attomole
    - Dynamic range: >3 logs
    - Specificity: 1 nucleotide discrimination

The combination of GeneChip miRNA Arrays and FlashTag Biotin HSR Reagents offers a complete solution for accurate and validated miRNA analysis.

Related Links
FlashTag™ Biotin HSR RNA Labeling Kits
GeneChip™ miRNA 4.1 24-Array Plate and Trays
GeneChip™ miRNA 4.1 96-Array Plate and Trays
GeneChip™ miRNA 3.1 24-Array Plate and Trays
GeneChip™ miRNA 3.1 96-Array Plate and Trays

BioPrime™ DNA Labeling System (Invitrogen™)

The BioPrime® DNA Labeling System is specifically designed for use in the preparation of biotinylated probes. Random primers (octamers) are annealed to the denatured DNA template and extended by Klenow fragment in the presence of biotin-14-dCTP to produce sensitive biotinylated-DNA probes for use in the nonradioactive detection of DNA and RNA. With the BioPrime® DNA Labeling System, considerable net DNA synthesis occurs resulting in a 10–40 fold amplification of the probe. This product is particularly well suited for situations in which the DNA is limited. Probes made with this product have been used for hybridization to Southern and northern blots, plaque and colony lifts, and for in situ hybridization to chromosome spreads. The BioPrime® DNA Labeling System:

• Requires less template DNA than nick translation
• Amplifies template to provide an increased amount of biotinylated probe
• Labels 50 to 500 ng of template DNA in one reaction

Pierce™ RNA 3' End Desthiobiotinylation Kit (Thermo Scientific™)

The Thermo Scientific Pierce RNA 3'-End Desthiobiotinylation Kit contains reagents for easy and efficient desthiobiotin labeling of RNA for use as probes or as antibody alternatives for enrichment of RNA binding proteins.

Features of the RNA 3'-End Desthiobiotinylation Kit:

Non-radioactive – a single biotin labels has similar detection sensitivity as radioactivity
Easy to use – RNA ligase and optimized reaction buffer are included
Economical – only a fraction of the cost purchasing synthetic biotinylated RNA probes
End-labeled – results in minimal disturbance of RNA secondary structure
Flexible – desthiobiotin label may be used for detection or as an affinity handle for streptavidin resin

The Pierce RNA 3'-End Desthiobiotinylation Kit is optimized for labeling the 3'-end of single-stranded RNA using T4 RNA ligase. Once labeled, the RNA can be used as a probe or target for gel-shift EMSA reactions, Northern blots and protein-RNA interaction experiments. The desthiobiotinylated RNA also can be used to enrich for RNA binding proteins (RBP) using streptavidin affinity resin, because the desthiobiotin tag binds to streptavidin in a manner which allows gentle elution of the ribonucleoprotein complex. The labeling kit is also included as a component of the Thermo Scientific Pierce Magnetic RNA-Protein Pull-Down Kit.

Includes:
Desthiobiotinylated cytidine bisphosphate, T4 RNA ligase and buffer, unlabeled RNA oligonucleotide for use as a positive control, a biotinylated RNA probe standard, RNase inhibitor, glycogen, and ligation enhancing reagents

Applications:
• Northern blotting
• EMSA
• Enrichment of RNA binding proteins (RBP)

This RNA labeling kit uses T4 RNA ligase to attach a single desthiobiotinylated cytidine bisphosphate to the 3-'end of single-stranded RNA. Each labeling reaction was designed for 50 pmol of RNA; however, reactions may be scaled (1 pmol to 1nmol have been tested), if necessary. The reaction uses a 20-fold excess of desthiobiotinylated nucleotide and requires incubation times from 30 minutes at 37°C (for less complex RNA) to overnight at 4 to 16°C (for longer or more complex RNA). Optimization of the labeling efficiency for complex RNA structures is achieved by altering the RNA:nucleotide ratio, increasing the incubation time, or by adding DMSO to relax the RNA structure. After organic extraction and precipitation with ethanol, the desthiobiotin-labeled RNA is ready for use in downstream applications.

Example experiments with different RNA molecules demonstrate the robustness of the ligation reaction. Synthetic RNA and in vitro transcribed RNA were evaluated, and ligations efficiencies were determined by semi-quantitative dot blot using a synthetic biotinylated RNA as the 100% labeled control (Table). Ligation efficiencies were all greater than 50%, with many greater than 70%. The kit control RNA had greater than 90% efficiency, and serves as an indicator of the overall reaction conditions and reagents. Further optimization was necessary for RNA having significant secondary structure, and refolding was required for in vitro transcribed RNA after ligation.

A pull-down assay involving the let-7 miRNA:Lin28 interaction demonstrates the experimental functionality of desthiobiotinylated-labeled RNA. The developmentally regulated Lin28 protein is a selective inhibitor of let-7 miRNA processing through binding to a loop region of let-7 pre-miRNA. To test this interaction, the loop portion of let-7 miRNA was end-labeled with desthiobiotinylated cytidine and attached to streptavidin magnetic beads. Beads were subsequently incubated with embryonal carcinoma cell lysate (NCCIT) in Protein-RNA binding buffer. Samples were eluted and assayed by Western blotting. The results indicate that the labeled let-7 miRNA specifically enriched Lin28 protein from NCCIT lysate, while an unrelated RNA did not.

This kit is also included in The Pierce Magnetic RNA-Protein Pull-Down Kit and utilizes the labeling kit in conjunction with optimized binding, wash, and elution buffers to enrich RNA binding proteins.

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.