Quercus mPNA

Quercus mitochondrial 16S rRNA blocker

Quercus mPNA is a species-specific PNA PCR blocker developed to reduce mitochondrial 16S rRNA amplification in oak (Quercus) samples. It targets the conserved sequence gtgaattggtttggagtt, helping to limit background signal from organellar DNA and improve the detection of nuclear genes in PCR and qPCR analyses. This tool is particularly useful in ecological genomics, forest research, and transcriptomic studies on oak, where accurate nuclear DNA amplification is essential.

Main characteristics

Quercus mPNA PCR blocker is designed to target mitochondrial rRNA in Quercus, allowing selective suppression of unwanted organellar amplification. By reducing non-target signals, it enhances the sensitivity and detection of nuclear gene targets. It is fully compatible with standard PCR and qPCR workflows, and its PNA backbone provides high stability and resistance to nuclease degradation. This makes it particularly useful for forest genetics and tree biodiversity studies. A terminal glycine is added to the PNA structure to improve flexibility and reduce steric hindrance, which can help optimize binding efficiency without affecting specificity.

Applications

Suitable for PCR workflows using Quercus DNA and RNA samples
Reduces mitochondrial rRNA amplification in oak tissues
Supports high-resolution genomics and transcriptomics in oak
Applicable to environmental and conservation DNA studies
Useful for studying fungal–plant interactions in forest ecosystems
Enables biodiversity and population genetics research in Quercus species

Technical specification

	Sequency :	gtgaattggtttggagtt-G
	MW :	5069.76 g/mol
	Purity :	> 95%
	Counter-Ion :	TFA Salts
	Delivery format :	Lyophilized

Price

Product	Size	Price €	Price $
SB338 - 25nmol	25 nmol	416	499
SB338 - 50 nmol	50 nmol	674	809

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If your target is not listed, we offer custom PNA design and synthesis. Whether you require sequence optimization, specific modifications, or larger production quantities, our team can support your project. Submit your project details and we will provide a personalized proposal.

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References

2025 Jan 28;20:14. doi: 10.1186/s40793-025-00674-w

Peptide nucleic acid (PNA) clamps reduce amplification of host chloroplast and mitochondria rRNA gene sequences and increase detected diversity in 16S rRNA gene profiling analysis of oak-associated microbiota

Abstract

Background

Acquiring representative bacterial 16S rRNA gene community profiles in plant microbiome studies can be challenging due to the excessive co-amplification of host chloroplast and mitochondrial rRNA gene sequences that reduce counts of plant-associated bacterial sequences. Peptide Nucleic Acid (PNA) clamps prevent this by blocking PCR primer binding or binding within the amplified region of non-target DNA to stop the function of DNA polymerase. Here, we applied a universal chloroplast (p)PNA clamp and a newly designed mitochondria (m)PNA clamp to minimise host chloroplast and mitochondria amplification in 16S rRNA gene amplicon profiles of leaf, bark and root tissue of two oak species (Quercus robur and Q. petraea).

Results

Adding PNA clamps to PCR led to an overall reduction of host chloroplast and mitochondrial 16S rRNA gene sequences of 79%, 46% and 99% in leaf, bark and root tissues, respectively. This resulted in an average increase in bacterial sequencing reads of 72%, 35%, and 17% in leaf, bark, and root tissue, respectively. Moreover, the bacterial diversity in the leaf and bark increased, with the number of ASVs rising by 105 in the leaf samples and 218 in the bark samples, respectively. In root tissues, where host oak chloroplast and mitochondria contamination were low, alpha and beta diversity did not change, suggesting the PNA clamps did not bias the bacterial community.

Conclusion

In conclusion, this study shows that PNA clamps can effectively reduce host chloroplast and mitochondria PCR amplification and improve assessment of the detected bacterial diversity in Quercus petraea and Quercus robur bacterial 16S rRNA gene sequencing studies.

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