What is the Difference Between DNA and RNA Probes

The main difference between DNA and RNA probes is that PCR produces DNA probes, whereas RNA probes are produced by in vitro transcription.

DNA and RNA probes are two nucleic acid-based diagnostic tools that allow the analysis of DNA and RNA molecules. They allow the diagnosis of infectious, inherited, and other diseases.   

Key Areas Covered

1. What are DNA Probes
– Definition, Features, Importance
2. What are RNA Probes
– Definition, Features, Importance
3. Similarities Between DNA and RNA Probes
– Outline of Common Features
4. Difference Between Papillae and Follicles
– Comparison of Key Differences

Key Terms  

DNA Probes, RNA Probes

Difference Between DNA and RNA Probes - Comparison Summary

What are DNA Probes

DNA probes are single-stranded, labeled DNA fragments specific to genes or chromosomal regions. There are two types of DNA probes according to labeling. They are end-labeling probes and continuously-labeling probes. Most labeling techniques are enzyme-mediated techniques that depend on the polymerase activity. They are responsible for the incorporation of labeled nucleotides into the DNA fragment. Further, Taq polymerase and other thermostable DNA polymerases allow the labeling reactions at higher temperatures. PCR can perform labeling reactions. Therefore, PCR is an excellent method for probe synthesis. Also, PCR requires very small quantities of template material.

Compare DNA and RNA Probes

Figure 1: DNA probes

Furthermore, appropriately labeled PCR primers are important in synthesizing labeled probes. Also, random primers are oligonucleotide sequences acting as primers. They anneal to the heat-denatured double-stranded template. Primers also become a part of the probe. The Klenow fragment of the DNA polymerase I is responsible for extending primers in the 3’ direction while incorporating the label. One of the oldest probe labeling techniques includes the nick translation.  

What are RNA Probes

RNA probes are single-stranded RNA that detect the presence of complementary nucleotide sequences. The process of detecting is hybridization. Importantly, in vitro transcription is the most reliable method of labeling RNA probes. It is an economical method as well. Also, a large amount of RNA probes can be produced in uniform length by in vitro transcription. The other important feature of RNA probes is that they anneal next to the RNA promoter. Further, DNA can be cloned between two promoters in opposite orientations. It generates sense and antisense RNA for hybridization. On the other hand, the labeling method of RNA probes is to label the 5’ end of the RNA strand. Kinasing reaction is the method of 5’ end labeling.

DNA vs RNA Probes

Figure 2: RNA Probes

Moreover, 3’ end labeling is another method of labeling RNA probes. Poly(A) polymerase catalyzes the labeling reaction during polyadenylation. 

Similarities Between DNA and RNA Probes

  • DNA and RNA probes are two probes that allow the analysis of nucleic acids in clinical samples.
  • They detect infectious, inherited, and other diseases.

Difference Between DNA and RNA Probes


DNA probes refer to a labeled DNA fragment containing a nucleotide sequence specific to the gene or chromosomal region of interest. In contrast, RNA probes refer to stretches of single-stranded RNA used to detect the presence of complementary nucleic acid sequences (target sequences) by hybridization.


PCR produces DNA probes, while RNA probes are produced by in vitro transcription.


DNA probes anneal to a part of a gene while RNA probes anneal to next to an RNA promoter. 


DNA probes can be labeled by labeling nucleotides, while RNA probes can be labeled by 5’ and 3’ labeling. 


In brief, DNA and RNA probes are important in hybridization reactions. They can recognize specific nucleotide sequences. PCR is the method of producing and labeling DNA probes. The incorporation of labeled nucleotides by PCR is important in labeling DNA probes. Also, DNA probes anneal to the parts of genes. In comparison, In vitro transcription is the method of producing RNA probes. They anneal next to an RNA promoter. 5’ and 3’ labeling are the methods of labeling of RNA probes. Therefore, the main difference between DNA and RNA probes is the synthesis. 

  1. What are the differences between DNA and RNA probes?. Enzo Life Sciences. (2023, August 29). 
Image Courtesy:
  1. DNA methylation probe design” By Philippe Hupé – Own Work (CC-BY SA 3.0) via Commons Wikimedia
  2. Probe used for hybridization experiments” By Ultrabem – Own Work (CC0) via Commons Wikimedia

About the Author: Lakna

Lakna, a graduate in Molecular Biology and Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things. She has a keen interest in writing articles regarding science.

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