Labeling array.

Array-based comparative genomic hybridization (aCGH) has emerged as a powerful tool for detecting gene copy number variants implicated in many disease states. Simple, robust genomic DNA labeling and removal of free dye and nucleotides are two of the most critical components determining aCGH experiment’s performance. Suboptimal labeling and purification can lead to lower signals, channel bias, and greater variation, decreasing your ability to make accurate calls from array data. The BioPrime® Total Genomic Labeling System reduces labeling variability
and increases signal-to-noise ratios on arrays, by using an optimized dye-labeled nucleotide mix with novel, application-specific Alexa Fluor® 3 and Alexa Fluor® 5 dyes, improved dNTP linkers, and new buffer chemistry. You’ll experience consistently higher DNA yields and improved signal-to-background ratios on arrays for more accurate data interpretation.

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Make better calls with precious samples

The BioPrime® Total System gives you more confidence in your aCGH experiments. In addition, the optimized supermix formulation and improved dye and buffer chemistries allow you to efficiently work with lower quantities of input material. Using an optimized labeling module and efficient post-labeling clean-up columns, the BioPrime® Total System produces higher signals without a corresponding increase in background. Higher signal to background enhances your ability to detect smaller changes, enabling you to really see what you’ve been missing in your aCGH experiments.

Optimized, robust dye incorporation

Achieving brighter signal on your CGH array without a corresponding increase in background noise is essential to discriminating amplifications and deletions within the genome. To maximize dye incorporation and increase signal on arrays, the BioPrime® Total System includes dCTP labeled with novel Alexa Fluor® 3 and Alexa Fluor® 5 dyes. These dyes were specially formulated for optimal incorporation by Exo– Klenow DNA polymerase fragment, leading to higher signal sensitivity on arrays. Alexa Fluor® 3 and Alexa Fluor® 5 dyes have excitation and emission spectra compatible with conventional two-color scanners without modification, so you can readily measure results. In addition, the BioPrime® Total Genomic Labeling System reaction chemistry overcomes issues with green channel bias by incorporating optimal quantities of each Alexa Fluor® dye to provide equivalent signals from each dye on the array. The end result is better total dye incorporation, reduced green channel bias, and brighter signals on arrays.



Figure 2. The BioPrime® Total Genomic labeling System provides significantly higher yields of DNA compared to competitive kits. Each labeling reaction started with 1ug of sonicated DNA and followed the standard conditions per manufacture's recommendations. labeling reactions using ENZO Genomic DNA Labeling Kit or the BioPrime® Array CGH Genomic Labeling System with GE Amersham Cy® dyes were purified with QIAQuick® columns (Qiagen). Labeled DNA from the BioPrime® Total Genomic labeling System was purified using the included Purelink® purification columns.

Figure 3. The BioPrime® Total Genomic Labeling Systme provides better dye incorporation for more even signal on arrays. Each labeling reaction started with 1ug of sonicated DNA and followed the standard conditions per manufacture's recommendations. Labeling reactions using the ENZO Genomic DNA Labeling Kit or the BioPrime® Array CGH Genomic Labeling System with GE Amersham Cy® dyes were purified with QIAQuick columns (Qiagen). Labeled DNA from the BioPrime® Total Genomic labeling System was purified using the included Purelink™ purification columns.

Streamlined workflow for improved consistency

The BioPrime® Total Genomic Labeling System includes all the components necessary to complete sample labeling and clean-up of your aCGH samples. There’s no need to qualify reagents sourced from multiple vendors, saving you time, effort, and resources. Each kit manufacturing lot is quality controlled as a complete solution to assure optimal performance in your hands. The labeling module features Alexa Fluor® 3 and Alexa Fluor® 5 supermix formulations that include dye-labeled dNTPs. This streamlines reaction setup, which minimizes any potential variation. Labeling takes just three simple steps. Labeling and clean-up take approximately 2.5 hours from start to finish. For your convenience, BioPrime® Total Genomic Labeling products are available in two formats. The all-inclusive BioPrime® Total Genomic Labeling System contains both labeling and purification modules. The BioPrime® Total Genomic Labeling Module is also sold separately. The labeling module includes Alexa Fluor® 3 and Alexa Fluor® 5 reaction mixes, Exo– Klenow fragment, TE buffer, control DNA, and EDTA. The purification module provides PureLink™ spin columns and collection tubes; binding, wash, and elution buffers; and recovery tubes.

Figure 4. Overview of BioPrime® Total Genomic Labeling System labeling protocol. BioPrime® Total Genomic Labeling System features two dNTP supermix formulations that include dye-labeled nucleotides. This reduces the number of pipetting steps, increase labeling consistency, and simplifies the workflow.