Restriction fragment length polymorphism (RFLP) (pronounced “rif lip”) is one of the earliest molecular markers developed for genetic mapping and one of the first techniques used for analysis in forensic science and several other fields. RFLP is a type of polymorphism that results from variation in the DNA sequence recognized by restriction enzymes. A RFLP probe is a labeled DNA sequence that hybridizes with one or more fragments of the digested DNA sample after they are separated by gel electrophoresis, revealing a unique blotting pattern characteristic to a specific genotype at a specific locus.

What are the benefits of RFLP analysis?

Although RFLP is less widely used now, it still has an important role in enabling mapping of the human genome as well as investigating genetic diseases. RFLP analysis is useful in finding where a specific gene for a disease lies on a chromosome and was one of the first methods used for genetic typing. RFLP analysis also has roles in aiding and understanding the genetic aspects of different breeding patterns in various animals. Research applications for RFLP include:

  • DNA fingerprinting
  • Paternity
  • Genetic diversity

What are the challenges of RFLP analysis?

Compared to some of the newer DNA analysis techniques, such as fragment analysis, RFLP is slow and more tedious, requiring substantially larger sample sizes and a lengthy process, taking up to a month to accomplish. Polymerase chain reaction (PCR) has become a replacement for many of the previous applications of RFLP.

Read how one lab that had been using RFLP switched to fragment analysis and revolutionized the way they could provide results ›

Today, RFLP has variations, such as terminal restriction fragment length polymorphism (T-RFLP), a blend of PCR and RFLP analysis, which has applications in the characterization of bacteria and related communities.


 Application Note: Terminal Fragment Length Polymorphism (T-RFLP) Analysis on Applied Biosystems Capillary Electrophoresis Systems: T-RFLP on the 3130/3730

Data is presented from T-RFLP assays that were performed on microbial communities present in enrichment cultures of Perchlorate Respiring Bacteria (PRB).

Fragment analysis—how can you take your DNA research further?

Fragment analysis is faster and less tedious than RFLP. 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 fragment, fragment analysis can provide sizing, relative quantitation, and genotyping analysis for fluorescently labeled DNA fragments produced by PCR using primers designed for a specific DNA target.

  • Simple—from straightforward sample preparation to peak analysis, fragment analysis applications use simplified workflows
  • Fast turnaround time—data are delivered in hours instead of days
  • Cost effective—fewer steps and less reagent per action compared to sequencing, and multiple loci can be analyzed in a single run

Read how one lab that had been using RFLP switched to fragment analysis and revolutionized the way they could provide results ›
Fragment analysis workflow ›
Adapt fragment analysis applications to broaden the possibilities of your DNA research ›


Brochure: DNA fragment analysis by capillary electrophoresis

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Instruments for fragment analysis

Our capillary electrophoresis genetic analyzers for fragment analysis are more powerful than you may think. This one platform offers a multitude of fragment analysis applications, including cell line authentication, gene editing, microsatellite marker analysis, SNP genotyping, and QF-PCR.


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