During the development of a probe, the nucleotide sequence must be recognized, isolated and reproduced in enough quantities, along with being tagged to a label which is detectable. Theoretically, any nucleic acid can be deployed as a probe, given it is labelled to allow recognition and quantitation of the hybrid molecules which form between the probe to be recognized and the probe. Broadly, probes can be classified into DNA probes and RNA probes.
The differentiating factor between the DNA and RNA probes is that the DNA probes are DNA fragments complementary to that of the target sequences of nucleotides. On the other hand, the RNA probes are extensions of single-stranded RNA complementary to that of the sequences of nucleic acids of the target sequences.
DNA probes
- These are DNA fragments containing sequences of nucleotides that are gene-specific or specific to the target chromosomal area
- These employ nucleic acid hybridization with particularly labelled sequences to quickly discover the complementary sequences in the testing sample
RNA probes
- These are extensions of the single-stranded RNA, which are utilized in the detection of the presence of complementary nucleic acid sequences through hybridization
- A reliable method to label RNA probes is in vitro degradation
- To enable its detection, these probes are typically labelled. For instance, epitopes, radioisotopes or biotin
- These are widely used as hybridization resources as they offer a range of benefits with their application
- These are synthesized by the in vitro transcription and can be alternatively used in place of DNA probes in almost all the applications
- Riboprobes or high-specific activity RNA probes can be synthesized from the templates of DNA that are cloned in the expression vectors
Key Difference between DNA and RNA probes
The table below depicts the difference between DNA and RNA probes.
| These are short DNA fragments complementary to the target sequence | These are short single-stranded RNA extensions that are complementary to the target sequence |
| A, C, T and G | A, C, G and U |
| Comparatively lesser | Comparatively greater |
| High affinity | Tightly associates with its complementary sequence compared to the DNA probes |
| These are vital tools in diagnostics to ensure sensitivity and high specificity. It finds applications in PCR, qPCR and hybridization techniques to detect pathogens accurately. | RNase protection assays, Northern blotting, Southern blotting, In situ hybridization |
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