What is the Difference Between SYBR Green and Taqman

The main difference between STBR Green and Taqman is that SYBR green is a dsDNA binding dye used to detect PCR products accumulated during the PCR reaction whereas Taqman is a fluorogenic probe specific to a target gene, which accumulates during PCR. Furthermore, SYBR Green has a medium specificity while Taqman has high specificity. Moreover, the reproducibility of SYBR Green is also medium while the reproducibility of Taqman is high. 

SYBR Green and Taqman are two chemistries used to detect PCR products in real-time PCR procedures. 

Key Areas Covered 

1. What is SYBR Green
     – Definition, Chemistry, Importance
2. What is Taqman
     – Definition, Chemistry, Importance
3. What are the Similarities Between SYBR Green and Taqman
     – Outline of Common Features
4. What is the Difference Between SYBR Green and Taqman
     – Comparison of Key Differences

Key Terms 

Detection of the Product, Real-Time PCR, SYBR Green, Taqman Probes

What is SYBR Green 

SYBR Green is a dsDNA binding dye used to stain DNA and RNA in molecular biology. Generally, it is also used to detects products of real-time PCR. During the progress of PCR, SYBR green binds to each newly amplifying PCR product. Therefore, at the end of the PCR, the amount of products formed is proportional to the fluorescence intensity of the sample.

Figure 1: SYBR Green Chemistry

Furthermore, the main advantage of SYBR Green is that it enables monitoring of the amplification of any double-stranded DNA sequence. However, this, on the other hand, reduces the specificity of the assay by generating false-positive signals. It reduces the cost of the assay by eliminating the use of a probe. Moreover, the use of SYBR Green is technically an easy process. Meanwhile, the binding of multiple dyes to a single PCR product increases the sensitivity of detection.  

What is Taqman 

Taqman is a probe, which is fluorescence-labelled and specifically binds to a target PCR product in the real-time PCR. Therefore, it is necessary to design a specific probe to detect a specific PCR assay. Thus, the main advantage of Taqman probes is their target-specific hybridization. Moreover, the use of probes labelled with different, distinguishable reporter dyes allows the detection of two distinct sequences in one reaction tube. 

Figure 2: Taqman Probe Chemistry

Generally, Taqman probes are oligonucleotide probes with a fluorescent reporter dye on the 5′ end and a quencher dye on the 3′ end. When the probe is intact, the proximity of the quencher dye greatly reduces the fluorescence emitted by the reporter dye by fluorescence resonance energy transfer (FRET). However, when the probe anneals to the target sequence downstream from one of the primer sites, the 5′ nuclease activity of Taq DNA polymerase cleaves the 5′ end of the probe during primer extension. Hence, this separates the reporter dye from the quencher dye, increasing the reporter dye signal.  

Similarities Between SYBR Green and Taqman 

• SYBR Green and Taqman are two chemistries of the detection of PCR products in real-time PCR. 
• Both bind to the PCR product on a real-time basis. 
• Moreover, they help to quantify the PCR product at each PCR cycle. 
• They are important for gene expression analysis, DNA quantitation, ChiP (chromatin immunoprecipitation), etc. 

Difference Between SYBR Green and Taqman 

Definition 

SYBR Green refers to an asymmetrical cyanine dye used as a nucleic acid stain in molecular biology while Taqman refers to the probes, which are designed to increase the specificity of quantitative PCR.  

Significance 

Moreover, SYBR green is a dsDNA binding dye used to detect PCR products accumulating during the PCR reaction while Taqman is a fluorogenic probe specific to a target gene, which accumulates during PCR. Thus, this is the main difference between SYBR Green and Taqman.

Type of Detection 

Also, while SYBR Green can be used to detect any real-time PCR product without sequence specificity, Taqman probes only detect PCR products in a sequence-specific manner. 

Design 

SYBR Green does not need to predesign while Taqman has to be predesigned for the detection of a particular PCR product. 

Optimization 

Furthermore, SYBR Green has to be optimized for a particular real-time PCR, while Taqman does not need to optimize. 

Specificity 

Another difference between SYBR Green and Taqman is that SYBR Green has a medium specificity while Taqman has high specificity. 

Sensitivity 

The sensitivity of SYBR Green is variable while the sensitivity of Taqman is up to 1-10 copies. 

PCR Inhibition 

SYBR Green can inhibit the PCR reaction to some extent, while Taqman does not inhibit the PCR reaction.  

Reproducibility  

The reproducibility of SYBR Green is also medium while the reproducibility of Taqman is high. 

Multiplexing 

Besides, SYBR Green can not be used in multiplexing while Taqman allows the detection of multiple PCR products in the same sample. 

Applications 

SYBR Green is important for gene expression analysis, DNA quantitation in pathogen detection, etc. while Taqman is important for SNP genotyping, detection of copy number variation such as in mutations, protein analysis, etc. 

Conclusion 

In brief, SYBR Green is a dsDNA binding dye used to detect PCR products in real-time PCR. Generally, it binds to all PCR products in the sample in a non-specific manner. Therefore, its specificity is medium. On the other hand, Taqman is a fluorescence-labelled probe, specifically binding to a particular PCR product in the sample. Therefore, these probes vary with the type of sample. Moreover, this gives a high specificity to the assay. Therefore, the main difference between SYBR Green and Taqman is their chemistries and advantages.   

References:

1. “TaqMan vs SYBR Chemistry.” Thermo Fisher Scientific, Thermo Fisher Scientific – US, Available Here.

Image Courtesy:

1. “PCR with SYBR green” By –Ygonaar 23:09, 7 March 2006 (UTC) – It’s a graph create by Ygonaar with Powerpoint (CC BY-SA 3.0) via Commons Wikimedia   
2. “Taqman” By User:Braindamaged – Own work by the original uploader (Public Domain) via Commons Wikimedia