Learn more about capillary electrophoresis,a powerful technique that allows for very reliable detection of your target sequence using either fragment analysis or Sanger sequencing.
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Fragment analysis workflow
Fragment analysis uses fluorescent fragments of DNA (produced by PCR using primers designed for a specific interrogation task) separated using capillary electrophoresis and sized by comparison to a size standard.. It is ideal for genotyping and microsatellite marker analysis.
Run and analysis—our genetic analysis systems are trusted for Sanger sequencing and fragment analysis, and backed by decades of results. These robust instruments can help you obtain excellent performance and reliability, with world-class support.
PCR amplification—amplify the DNA fragment of interest by PCR using a 5'-labeled fluorescent primer
Prepare sample for analysis—add an aliquot of PCR product to size standard and Applied Biosystems Hi-Di Formamide mix; heat, denature, and proceed with electrophoresis
Hi-Di Formamide—highly deionized formamide used to resuspend samples before electrokinetic injection on capillary electrophoresis systems
Applied Biosystems GeneScan 120 LIZ Size Standard—five dye–labeled size standard that is designed for reproducible sizing analysis of small fragments
Run and analysis—our genetic analysis systems are trusted for Sanger sequencing and fragment analysis, and backed by decades of results. These robust instruments can help you obtain excellent performance and reliability, with world-class support.
Applied Biosystems genetic analyzers—Regardless of your requirements for throughput, ease of use, and regulatory compliance, we have an instrument suitable for your needs. Validating your assay on Applied Biosystems capillary electrophoresis instruments enables you to leverage the expansive, global installed base in end-user laboratories. We also offer instrument placement and reagent rental programs that allow you to provide our instruments to your customers who do not have access to the instrument, or who need an additional instrument to ramp up capacity. Private labeling of our instruments is an option; if you would like to integrate an Applied Biosystems instrument into your workflow, you can deliver it to your customers with your own label attached. Your customers will also gain access to our validation and IQ/OQ (Installation Qualification/Operational Qualification) services at no additional cost.
| Easy-to-use, flexible system | Meets the needs of validation and process-controlled environments | |
|---|---|---|
 SeqStudio Genetic Analyzer |  3500 Series Genetic Analyzers* | |
| Dx version available? | No | Yes |
| Number of capillaries | 4 | 8 (3500), 24 (3500xL) |
| Ease of use | Very simple | Somewhat manual |
| Number of dyes | 6 | 6 |
| Capillary array length (cm) | Integrated into click-in cartridge | 36, 50 |
| Sample capacity | 12 standard 8-strip tubes 1 standard 96-well plate | 2 sample plates (96- or 384-well) |
| Applications | Sequencing and fragment analysis on same run | Sequencing and fragment analysis |
* IVD-labeled instrument available in some regions.
PCR amplification—amplify the DNA fragment of interest by PCR using a 5'-labeled fluorescent primer
Prepare sample for analysis—add an aliquot of PCR product to size standard and Applied Biosystems Hi-Di Formamide mix; heat, denature, and proceed with electrophoresis
Hi-Di Formamide—highly deionized formamide used to resuspend samples before electrokinetic injection on capillary electrophoresis systems
Applied Biosystems GeneScan 120 LIZ Size Standard—five dye–labeled size standard that is designed for reproducible sizing analysis of small fragments
Run and analysis—our genetic analysis systems are trusted for Sanger sequencing and fragment analysis, and backed by decades of results. These robust instruments can help you obtain excellent performance and reliability, with world-class support.
Applied Biosystems genetic analyzers—Regardless of your requirements for throughput, ease of use, and regulatory compliance, we have an instrument suitable for your needs. Validating your assay on Applied Biosystems capillary electrophoresis instruments enables you to leverage the expansive, global installed base in end-user laboratories. We also offer instrument placement and reagent rental programs that allow you to provide our instruments to your customers who do not have access to the instrument, or who need an additional instrument to ramp up capacity. Private labeling of our instruments is an option; if you would like to integrate an Applied Biosystems instrument into your workflow, you can deliver it to your customers with your own label attached. Your customers will also gain access to our validation and IQ/OQ (Installation Qualification/Operational Qualification) services at no additional cost.
| Easy-to-use, flexible system | Meets the needs of validation and process-controlled environments | |
|---|---|---|
SeqStudio Genetic Analyzer | 3500 Series Genetic Analyzers* | |
| Dx version available? | No | Yes |
| Number of capillaries | 4 | 8 (3500), 24 (3500xL) |
| Ease of use | Very simple | Somewhat manual |
| Number of dyes | 6 | 6 |
| Capillary array length (cm) | Integrated into click-in cartridge | 36, 50 |
| Sample capacity | 12 standard 8-strip tubes 1 standard 96-well plate | 2 sample plates (96- or 384-well) |
| Applications | Sequencing and fragment analysis on same run | Sequencing and fragment analysis |
* IVD-labeled instrument available in some regions.
Sanger sequencing workflow
Sanger sequencing is the gold standardin sequencing, used to interrogate a small subset of genes linked to a defined phenotype. Sanger sequencing can detect minor-allele fractions down to 5%, and read contiguous sequences of up to 1,000 bases.
Applied Biosystems Primer Designer Tool—Choose from our database of over 650,000 primer pairs to select the target of interest for your assay.
Applied Biosystems AmpliTaq Gold 360 Master Mix—this master mix is for the amplification of a broad range of targets—even the most challenging. AmpliTaq Gold 360 DNA Polymerase is purified by an additional proprietary separation process that reduces residual bacterial DNA sequences from the enzyme separation. AmpliTaq Gold 360 DNA Polymerase efficiently amplifies targets present in low copy numbers, even in the presence of high concentrations of complex DNA, making it especially suited for low-copy pathogen detection and amplification of targets from degraded DNA samples. The extreme purity of the enzyme contributes to its unmatched sensitivity. AmpliTaq Gold 360 DNA Polymerase efficiently and reproducibly amplifies long sequences, up to 5 kb.
PCR cleanup—Complete this step prior to sequencing in order to remove primers and dNTPs from the PCR reaction. Note: This is not required if you select the Applied Biosystems BigDye Direct Cycle Sequencing Kit for your sequencing.
Applied Biosystems ExoSAP-IT Express reagent—one-tube, one-step protocol to clean up PCR reactions prior to sequencing. This reagent hydrolyzes excess primers and nucleotides into nucleosides and inorganic phosphate, combining exonuclease I and alkaline phosphatase activity in one tube.
Cycle sequencing—depending on your assay, you can choose from a menu of sequencing kits. The Applied Biosystems BigDye Terminator v3.1 kit is ideal for de novo sequencing and resequencing, while the BigDye Terminator v1.1 kit is best for applications that require optimal base calling adjacent to the primer, or to sequence short templates rapidly. The BigDye Direct Cycle kit simplifies the workflow by combining post-PCR cleanup and cycle sequencing, eliminating the need for separate cleanup kits such as ExoSAP-IT Express reagent.
Sequencing cleanup—removes unincorporated BigDye terminators and salts prior to capillary electrophoresis. The Applied Biosystems BigDye XTerminator Purification Kit provides a fast, simple purification method for DNA sequencing reactions to remove unincorporated BigDye terminators and salts. No more dye blobs. Cleanup is complete in under 40 minutes and typically requires less than 10 minutes of labor.
Run and analysis—our genetic analysis systems are trusted for Sanger sequencing and fragment analysis, and backed by decades of results. These robust instruments can help you obtain excellent performance and reliability, with world-class support.
Applied Biosystems genetic analyzers—Regardless of your requirements for throughput, ease of use, and regulatory compliance, we have an instrument suitable for your needs. Validating your assay on Applied Biosystems capillary electrophoresis instruments enables you to leverage the expansive, global installed base in end-user laboratories. We also offer instrument placement and reagent rental programs that allow you to provide our instruments to your customers who do not have access to the instrument, or who need an additional instrument to ramp up capacity. Private labeling of our instruments is an option; if you would like to integrate an Applied Biosystems instrument into your workflow, you can deliver it to your customers with your own label attached. Your customers will also gain access to our validation and IQ/OQ (Installation Qualification/Operational Qualification) services at no additional cost.
| Easy-to-use, flexible system | Meets the needs of validation and process-controlled environments | |
|---|---|---|
SeqStudio Genetic Analyzer | 3500 Series Genetic Analyzers* | |
| Dx version available? | No | Yes |
| Number of capillaries | 4 | 8 (3500), 24 (3500xL) |
| Ease of use | Very simple | Somewhat manual |
| Number of dyes | 6 | 6 |
| Capillary array length (cm) | Integrated into click-in cartridge | 36, 50 |
| Sample capacity | 12 standard 8-strip tubes 1 standard 96-well plate | 2 sample plates (96- or 384-well) |
| Applications | Sequencing and fragment analysis on same run | Sequencing and fragment analysis |
* IVD-labeled instrument available in some regions.
Applied Biosystems Primer Designer Tool—Choose from our database of over 650,000 primer pairs to select the target of interest for your assay.
Applied Biosystems AmpliTaq Gold 360 Master Mix—this master mix is for the amplification of a broad range of targets—even the most challenging. AmpliTaq Gold 360 DNA Polymerase is purified by an additional proprietary separation process that reduces residual bacterial DNA sequences from the enzyme separation. AmpliTaq Gold 360 DNA Polymerase efficiently amplifies targets present in low copy numbers, even in the presence of high concentrations of complex DNA, making it especially suited for low-copy pathogen detection and amplification of targets from degraded DNA samples. The extreme purity of the enzyme contributes to its unmatched sensitivity. AmpliTaq Gold 360 DNA Polymerase efficiently and reproducibly amplifies long sequences, up to 5 kb.
PCR cleanup—Complete this step prior to sequencing in order to remove primers and dNTPs from the PCR reaction. Note: This is not required if you select the Applied Biosystems BigDye Direct Cycle Sequencing Kit for your sequencing.
Applied Biosystems ExoSAP-IT Express reagent—one-tube, one-step protocol to clean up PCR reactions prior to sequencing. This reagent hydrolyzes excess primers and nucleotides into nucleosides and inorganic phosphate, combining exonuclease I and alkaline phosphatase activity in one tube.
Cycle sequencing—depending on your assay, you can choose from a menu of sequencing kits. The Applied Biosystems BigDye Terminator v3.1 kit is ideal for de novo sequencing and resequencing, while the BigDye Terminator v1.1 kit is best for applications that require optimal base calling adjacent to the primer, or to sequence short templates rapidly. The BigDye Direct Cycle kit simplifies the workflow by combining post-PCR cleanup and cycle sequencing, eliminating the need for separate cleanup kits such as ExoSAP-IT Express reagent.
Sequencing cleanup—removes unincorporated BigDye terminators and salts prior to capillary electrophoresis. The Applied Biosystems BigDye XTerminator Purification Kit provides a fast, simple purification method for DNA sequencing reactions to remove unincorporated BigDye terminators and salts. No more dye blobs. Cleanup is complete in under 40 minutes and typically requires less than 10 minutes of labor.
Run and analysis—our genetic analysis systems are trusted for Sanger sequencing and fragment analysis, and backed by decades of results. These robust instruments can help you obtain excellent performance and reliability, with world-class support.
Applied Biosystems genetic analyzers—Regardless of your requirements for throughput, ease of use, and regulatory compliance, we have an instrument suitable for your needs. Validating your assay on Applied Biosystems capillary electrophoresis instruments enables you to leverage the expansive, global installed base in end-user laboratories. We also offer instrument placement and reagent rental programs that allow you to provide our instruments to your customers who do not have access to the instrument, or who need an additional instrument to ramp up capacity. Private labeling of our instruments is an option; if you would like to integrate an Applied Biosystems instrument into your workflow, you can deliver it to your customers with your own label attached. Your customers will also gain access to our validation and IQ/OQ (Installation Qualification/Operational Qualification) services at no additional cost.
| Easy-to-use, flexible system | Meets the needs of validation and process-controlled environments | |
|---|---|---|
SeqStudio Genetic Analyzer | 3500 Series Genetic Analyzers* | |
| Dx version available? | No | Yes |
| Number of capillaries | 4 | 8 (3500), 24 (3500xL) |
| Ease of use | Very simple | Somewhat manual |
| Number of dyes | 6 | 6 |
| Capillary array length (cm) | Integrated into click-in cartridge | 36, 50 |
| Sample capacity | 12 standard 8-strip tubes 1 standard 96-well plate | 2 sample plates (96- or 384-well) |
| Applications | Sequencing and fragment analysis on same run | Sequencing and fragment analysis |
* IVD-labeled instrument available in some regions.
For Research Use Only. Not for use in diagnostic procedures.