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Fragment analysis comprises a series of techniques in which DNA fragments are fluorescently labeled, separated by capillary electrophoresis (CE), and sized by comparison to an internal standard. While DNA sequencing by CE is used to determine the specific base sequence of a particular fragment or gene segment, fragment analysis can provide sizing, relative quantitation, and genotyping information for fluorescently labeled DNA fragments produced by PCR using primers designed for a specific DNA target.
From straightforward sample preparation to peak analysis, we offer a wide range of products and services to simplify each step of the fragment analysis workflow.
DNA extraction is a critical first step in the experimental workflow of DNA fragment analysis. The overall efficiency, quality, and size of the PCR product can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction and purification. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction.
Learn more about our extraction kits:
Tissue DNA
Blood DNA
Cellular DNA
Plant DNA
Cell-free DNA
To perform fragment analysis on a CE system, primers must be designed that flank the region of interest. Typically, fluorescent dyes are attached to the primers, and the fragments are amplified by PCR before electrophoresis. We offer Applied Biosystems 5´ fluorescently labeled primers and primer pairs that have been validated for use in fragment analysis.
Cat. No. | Size | HPLC yield | 5' Reporter dye | Quantity | Order |
---|---|---|---|---|---|
450056 | 10,000 pmol | 5´ Labeled/Unlabeled Primer Pairs | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
450059 | 80,000 pmol | 5´ Labeled/Unlabeled Primer Pairs | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
450062 | 300,000 pmol | 5´ Labeled/Unlabeled Primer Pairs | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304976 | 10,000 pmol | 5´ Labeled/Unlabeled Di-Repeats | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304977 | 80,000 pmol | 5´Labeled/Unlabeled Di-Repeats | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304978 | 300,000 pmol | 5´ Labeled/Unlabeled Di-Repeats | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304979 | 10,000 pmol | 5´ Labeled/Unlabeled Di-Repeat + Tail | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304981 | 80,000 pmol | 5´ Labeled/Unlabeled Di-Repeat + Tail | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304982 | 300,000 pmol | 5´ Labeled/Unlabeled Di-Repeat + Tail | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
Invitrogen Platinum II Hot-Start PCR Master Mix helps you get to your fragment analysis run, faster. A unique combination of innovative buffer, high-performance Taq DNA polymerase, and Platinum hot-start technology enables exceptional PCR results, even in the toughest applications.
To prepare for capillary electrophoresis, a spectral calibration with the corresponding matrix standard to the group of dye you select for labeling your DNA fragments must be performed on your genetic analyzer to accurately detect the dyes with which your primers are labeled. Each unknown sample is mixed with the size standard and Hi-Di Formamide before proceeding with electrophoresis. Size standards allow sizing of sample peaks and correct for injection variations.
Refer to the following chart for the recommended Applied Biosystems matrix standard and GeneScan size standard for your workflow.
Dye set used to label DNA fragments | Corresponding matrix standard | Recommended size standard | Possible applications |
Dye set E5: dR110 (blue), dR6G (green), dTAMRA (yellow), dROX (red | DS-02 | GeneScan 120 LIZ Size Standard (orange) | SNaPshot multiplexing |
GeneScan 600 LIZ Size Standard v2.0 (orange) | Microsatellite, LOH, chimerism, inter-simple sequence repeat (ISSR), restriction fragment length polymorphism (RFLP), terminal-RFLP (T-RFLP), methylation-sensitive mobility shift assay (MSMSA) | ||
Dye set D: 6-FAM (blue), HEX (green), NED (yellow) | DS-30 | GeneScan 500 ROX Size Standard (red) | Custom fragment analysis |
Dye set D: 6-FAM (blue), VIC (green), NED (yellow) | DS-31 | GeneScan 500 ROX Size Standard (red) | Custom fragment analysis |
Dye set F: 5-FAM (blue), JOE (green), NED (yellow) | DS-32 | GeneScan 500 ROX Size Standard (red) | Microsatellite |
amplified fragment length polymorphism (AFLP) | |||
Dye set G5: 6-FAM (blue), VIC (green), NED (yellow), PET (red) | DS-33 | GeneScan 600 LIZ Size Standard v2.0 (orange) | Microsatellite |
Custom fragment analysis | |||
Dye set J6: 6-FAM (blue), VIC (green), NED (yellow), SID (violet), TAZ (red) | DS-36 | GeneScan 600 LIZ Size Standard v2.0 (orange) | Custom fragment analysis |
A range of platforms to meet your throughput’s need | |||
---|---|---|---|
![]() | ![]() | ![]() | |
Throughput | Low | Med | High |
Learn more › | Learn more › | Learn more › |
The Applied Biosystems SeqStudio cartridge has an integrated system design that includes a capillary array, POP-1 universal polymer, buffer, and pump. The POP-1 universal polymer allows for flexibility to perform simultaneous Sanger sequencing and fragment analysis with one cartridge on the same plate in a single run. The cartridge is removable and can be stored on the instrument up to six months. Just load your samples, insert the cartridge, and start the run.
Using the right Applied Biosystems polymer can help reduce your re-run rate and enables high-quality reproducible data. We offer different polymer chemistries for different needs:
POP-4: Human identification applications, other fragment analysis applications, short DNA fragments (<500 bp)
POP-6: Mid-sized DNA fragments (500–700 bp)
POP-7: Long DNA fragments (>700 bp)
We offer a wide portfolio of Applied Biosystems software solutions for viewing and analyzing your fragment analysis results. Access, analyze, and share data anytime, anywhere, with Connect, our cloud-based platform.
DNA extraction is a critical first step in the experimental workflow of DNA fragment analysis. The overall efficiency, quality, and size of the PCR product can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction and purification. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction.
Learn more about our extraction kits:
Tissue DNA
Blood DNA
Cellular DNA
Plant DNA
Cell-free DNA
To perform fragment analysis on a CE system, primers must be designed that flank the region of interest. Typically, fluorescent dyes are attached to the primers, and the fragments are amplified by PCR before electrophoresis. We offer Applied Biosystems 5´ fluorescently labeled primers and primer pairs that have been validated for use in fragment analysis.
Cat. No. | Size | HPLC yield | 5' Reporter dye | Quantity | Order |
---|---|---|---|---|---|
450056 | 10,000 pmol | 5´ Labeled/Unlabeled Primer Pairs | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
450059 | 80,000 pmol | 5´ Labeled/Unlabeled Primer Pairs | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
450062 | 300,000 pmol | 5´ Labeled/Unlabeled Primer Pairs | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304976 | 10,000 pmol | 5´ Labeled/Unlabeled Di-Repeats | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304977 | 80,000 pmol | 5´Labeled/Unlabeled Di-Repeats | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304978 | 300,000 pmol | 5´ Labeled/Unlabeled Di-Repeats | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304979 | 10,000 pmol | 5´ Labeled/Unlabeled Di-Repeat + Tail | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304981 | 80,000 pmol | 5´ Labeled/Unlabeled Di-Repeat + Tail | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
4304982 | 300,000 pmol | 5´ Labeled/Unlabeled Di-Repeat + Tail | 6-FAM, TET, VIC, HEX, NED, PET | 2 tubes | Order |
Invitrogen Platinum II Hot-Start PCR Master Mix helps you get to your fragment analysis run, faster. A unique combination of innovative buffer, high-performance Taq DNA polymerase, and Platinum hot-start technology enables exceptional PCR results, even in the toughest applications.
To prepare for capillary electrophoresis, a spectral calibration with the corresponding matrix standard to the group of dye you select for labeling your DNA fragments must be performed on your genetic analyzer to accurately detect the dyes with which your primers are labeled. Each unknown sample is mixed with the size standard and Hi-Di Formamide before proceeding with electrophoresis. Size standards allow sizing of sample peaks and correct for injection variations.
Refer to the following chart for the recommended Applied Biosystems matrix standard and GeneScan size standard for your workflow.
Dye set used to label DNA fragments | Corresponding matrix standard | Recommended size standard | Possible applications |
Dye set E5: dR110 (blue), dR6G (green), dTAMRA (yellow), dROX (red | DS-02 | GeneScan 120 LIZ Size Standard (orange) | SNaPshot multiplexing |
GeneScan 600 LIZ Size Standard v2.0 (orange) | Microsatellite, LOH, chimerism, inter-simple sequence repeat (ISSR), restriction fragment length polymorphism (RFLP), terminal-RFLP (T-RFLP), methylation-sensitive mobility shift assay (MSMSA) | ||
Dye set D: 6-FAM (blue), HEX (green), NED (yellow) | DS-30 | GeneScan 500 ROX Size Standard (red) | Custom fragment analysis |
Dye set D: 6-FAM (blue), VIC (green), NED (yellow) | DS-31 | GeneScan 500 ROX Size Standard (red) | Custom fragment analysis |
Dye set F: 5-FAM (blue), JOE (green), NED (yellow) | DS-32 | GeneScan 500 ROX Size Standard (red) | Microsatellite |
amplified fragment length polymorphism (AFLP) | |||
Dye set G5: 6-FAM (blue), VIC (green), NED (yellow), PET (red) | DS-33 | GeneScan 600 LIZ Size Standard v2.0 (orange) | Microsatellite |
Custom fragment analysis | |||
Dye set J6: 6-FAM (blue), VIC (green), NED (yellow), SID (violet), TAZ (red) | DS-36 | GeneScan 600 LIZ Size Standard v2.0 (orange) | Custom fragment analysis |
A range of platforms to meet your throughput’s need | |||
---|---|---|---|
![]() | ![]() | ![]() | |
Throughput | Low | Med | High |
Learn more › | Learn more › | Learn more › |
The Applied Biosystems SeqStudio cartridge has an integrated system design that includes a capillary array, POP-1 universal polymer, buffer, and pump. The POP-1 universal polymer allows for flexibility to perform simultaneous Sanger sequencing and fragment analysis with one cartridge on the same plate in a single run. The cartridge is removable and can be stored on the instrument up to six months. Just load your samples, insert the cartridge, and start the run.
Using the right Applied Biosystems polymer can help reduce your re-run rate and enables high-quality reproducible data. We offer different polymer chemistries for different needs:
POP-4: Human identification applications, other fragment analysis applications, short DNA fragments (<500 bp)
POP-6: Mid-sized DNA fragments (500–700 bp)
POP-7: Long DNA fragments (>700 bp)
We offer a wide portfolio of Applied Biosystems software solutions for viewing and analyzing your fragment analysis results. Access, analyze, and share data anytime, anywhere, with Connect, our cloud-based platform.
Learn about our comprehensive solutions for each step of your fragment analysis workflow.
Get bite-sized answers to your everyday Sanger sequencing and fragment analysis questions
Learn about the history of sequencing and how to pick the right platform for your research needs