Example of eighteen microsatellite loci co-electrophoresed in a single capillary

Variable nucleotide tandem repeats (VNTRs) are repeating sequences of multi-base segments of DNA. If the repeat is equal to or less than 6 bases, NTRs are named microsatellites, also known as short tandem repeats (STRs). One common example of a microsatellite is a (CA)n repeat, where n varies between alleles. Because microsatellites are polymorphic DNA loci present throughout the genome, microsatellite genotyping is a widely accepted tool for a variety of research applications such as linkage mapping studies, association studies, and identification of organisms.

Our five-dye chemistry increases the number of microsatellite markers that can be run in a single capillary, substantially improving the throughput.

Step-by-Step Guide to Microsatellite STR Analysis

DNA Purification kit

DNA extraction is a critical first step in the experimental workflow of DNA Sequencing and Fragment analysis. The overall quality, accuracy and length of the DNA sequence read can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. 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.

Recommended Products: DNA Isolation

PCR Kit

Amplify the DNA region containing the microsatellite of interest.

Recommended Products: Perform PCR

Fragment Analysis sizing graph image.

Add aliquot of PCR product to size standard and Hi-Di Formamide mix; heat denature and proceed with electrophoresis.

Recommended Products: Prepare Sample for Analysis

Sizing Information

To learn more about our GeneScan Size standards used in sizing experiments please see our table below.

When DNA fragments are labeled with: Choose a size standards labeled with: Recommended Size Standard Possible Applications Other Kits and Products
dR110, dR6G, dTAMRA™, dROX (Dye Set DS-02 - Filter E5)LIZ®
GeneScan™ 120 LIZ® Size Standard
GeneScan™ 600 LIZ Size Standard v2.0
SNaPshot®
Microsatellite, LOH, ISSR, Chimerism, ISSR, RFLP, T-RFLP, MSMSA
SNaPshot® primer focus kits
Custom Labeled Primer
5-FAM™, HEX™, NED™ (Dye Set DS-30 - Filter D)ROX™GeneScan™ 500 ROX™ Size StandardCustom Fragment AnalysisCustom Labeled Primer
6-FAM™, VIC®, NED™ (Dye Set DS-31 - Filter D**)ROX™GeneScan™ 500 ROX™ Size Standard

Custom Fragment Analysis

Custom Labeled Primer
5-FAM™, JOE, NED™ (Dye Set DS-32 - Filter F)ROX™GeneScan™ 500 ROX™ Size Standard
Microsatellite (Forensic)
AFLP
AmpFℓSTR® Kits,
Plant/Microbial AFLP Kits®
6-FAM™, VIC®, NED™, PET® (Dye Set DS-33 - Filter G5)LIZ®GeneScan™ 600 LIZ Size Standard v2.0
Microsatellite (Forensic)
Pathogen Detection
Custom Fragment Analysis
AmpFℓSTR® Kits,
TrueScience™ RespiFinder®
Custom Labeled Primer
Capillary Electrophoresis

During capillary electrophoresis, the products of the PCR are injected electrokinetically into capillaries filled with polymer. High voltage is applied so that the fluorescent DNA fragments are separated by size and are detected by a laser/camera system.

Which Electrophoresis Instrument (Genetic Analyzer) Is Right for You?

  Instrument
 3730xl
3730xL
3730
3730
3500xl
3500xL
3500
3500
3130xl
3130xL
3130
3130
310
310
Number of Capillaries96482481641
Compatible Applications:
(S) Supported; (A) AB Demonstrated; (C) Customer Demonstrated; (N) Not Supported
Microsatellite
- GenotypingSSSSSSS
- Analysis for Forensics/HIDNNSSSSS
- Instability/RERAAAAAAA

Analyze the RFLP profile.

Which Data Analysis Software Is Right for You?

Highlighted Products for Microsatellite STR Analysis:

3500 Series Genetic Analyzers

GeneMapper® Software

Verti Thermal Cycler