Mitochondrial mPNA
Plant Mitochondria 16S rRNA Blocker
Mitochondrial mPNA is a PNA-based PCR blocker designed to bind a conserved region of plant mitochondrial 16S rRNA (sequence: ggcaagtgttcttcgga), preventing its amplification during PCR and NGS workflows. By reducing interference from mitochondrial sequences, it enables more accurate detection of nuclear genes in plant genomic studies. Its PNA backbone provides strong binding affinity, high thermal stability, and resistance to nuclease degradation, making it a reliable tool for PCR optimization, metagenomic analysis, and plant transcriptome enrichment.
Main characteristics
Mitochondrial mPNA targets conserved regions of mitochondrial 16S rRNA in plants, allowing selective suppression of unwanted amplification. Its PNA-based design ensures high specificity, strong binding affinity, and excellent stability. By minimizing off-target mitochondrial signals, it improves the detection of low-copy nuclear genes. It is compatible with standard PCR, qPCR, and amplicon-based NGS workflows, and works efficiently across a wide range of plant DNA extraction methods. 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
- Blocks mitochondrial rRNA amplification in plant PCR workflows
- Improves targeting and sequencing of nuclear DNA
- Supports plant transcriptome enrichment
- Enhances amplicon sequencing from plant tissues
- Enables organelle-free (chloroplast and mitochondrial) profiling
- Applicable to environmental and agricultural genomics
Technical specification
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Sequency : | ggcaagtgttcttcgga-G |
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MW : | 4733.46 g/mol |
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Purity : | > 95% |
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Counter-Ion : | TFA Salts |
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Delivery format : | Lyophilized |
Price
| Product | Size | Price € |
Price $ |
| SB336 - 25nmol | 25 nmol | 399 | 479 |
| SB336 - 50 nmol | 50 nmol | 644 | 772 |
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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.
18 August 2018 Volume 6, article number 144, (2018)
Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies
Abstract
Background
The ability to efficiently characterize microbial communities from host individuals can be limited by co-amplification of host organellar sequences (mitochondrial and/or plastid), which share a common ancestor and thus sequence similarity with extant bacterial lineages. One promising approach is the use of sequence-specific peptide nucleic acid (PNA) clamps, which bind to, and block amplification of, host-derived DNA. Universal PNA clamps have been proposed to block host plant-derived mitochondrial (mPNA) and plastid (pPNA) sequences at the V4 16S rRNA locus, but their efficacy across a wide range of host plant species has not been experimentally tested.
Results
Using the universal PNA clamps, we amplified and sequenced root microbial communities from replicate individuals of 32 plant species with a most recent common ancestor inferred at 140 MYA. We found the average rate of host plastid contamination across plant species was 23%, however, particular lineages exhibited much higher rates (62–94%), with the highest levels of contamination occurring in the Asteraceae. We investigated chloroplast sequence variation at the V4 locus across 500 land plant species (Embryophyta) and found six lineages with mismatches between plastid and the universal pPNA sequence, including all species within the Asteraceae. Using a modified pPNA for the Asteraceae sequence, we found (1) host contamination in Asteraceae species was reduced from 65 to 23%; and (2) host contamination in non-Asteraceae species was increased from 12 to 69%. These results demonstrate that even single nucleotide mismatches can lead to drastic reductions in pPNA efficacy in blocking host amplification. Importantly, we found that pPNA type (universal or modified) had no effect on the detection of individual bacterial taxa, or estimates of within and between sample bacterial diversity, suggesting that our modification did not introduce bias against particular bacterial lineages.
Conclusions
When high similarity exists between host organellar DNA and PCR target sequences, PNA clamps are an important molecular tool to reduce host contamination during amplification. Here, we provide a validated framework to modify universal PNA clamps to accommodate host variation in organellar sequences.
Seeds 2025, 4(3), 28; https://doi.org/10.3390/seeds4030028
To Clamp or Not to Clamp: Enhancing Seed Endophyte Metabarcoding Success
Abstract
Seed microbes play crucial roles in plant health, but studying their diversity is challenging due to host DNA contamination. This study aimed to optimise methodologies for investigating seed microbiomes across diverse plant species, focusing on the efficacy of peptide nucleic acid (PNA) clamps to reduce host DNA amplification. We tested PNA clamps on three plant species: Melaleuca quinquenervia (tree), Microlaena stipoides, and Themeda triandra (grasses). The effectiveness of PNA clamps was assessed through in silico analysis, axenic tissue culture, and metabarcoding techniques. In silico analysis confirmed the specificity of PNA clamps to the 16S rRNA gene V4 region of chloroplasts in the grass species. Axenic tissue culture experiments showed that applying PNA clamps at both 1 µM and 0.25 µM concentrations significantly reduced plant DNA amplification. Metabarcoding analyses further confirmed that PNA clamps effectively suppressed host DNA, enhancing microbial diversity estimates across all three species while preserving core microbial taxa. The efficacy of the clamps varied among host species, with T. triandra exhibiting the highest blocking efficacy, and chloroplast clamps outperforming mitochondrial ones. This study demonstrates that PNA clamps are a useful for improving seed endophyte metabarcoding datasets, although they require optimisation for some plant species. This knowledge will contribute to enhancing our understanding of seed microbiome diversity and its ecological implications.
Article number: 17479 (2025)
Generalists and keystone species drive rhizosphere microbial diversity and stability in feral Brassica napus
Abstract
Brassica napus (rapeseed) is a globally important crop, primarily valued for its oil production. However, feral B. napus in non-agricultural areas remains under-researched. This study aims to examine the roles of microbial generalists and network keystone species in shaping microbial diversity and network stability of feral B. napus. We analyzed prokaryotic, fungal, and eukaryotic communities in the rhizosphere and bulk soil from five grassland sites. The rhizosphere microbial communities differed significantly from those in adjacent bulk soil, showing lower diversity and richness. Pseudomonas brassicacearum (bacterium), Olpidium brassicae (fungus), and Glissomonadida (eukaryote) were predominantly found in the rhizosphere. Inter- and intra-kingdom association occurred almost exclusively within the rhizosphere, with low interconnectivity compared to the bulk soil, and network keystone species served to bridge these connections. Furthermore, structural equation modeling highlighted the role of generalists and network keystone species in maintaining microbial diversity and stability. Feral B. napus selectively influenced rhizospheric generalists, which, along with keystone species, played key roles in determining microbial diversity and network stability, controlling community structure and interspecies interactions.
Volume 20, article number 6, (2025)
Microbial generalists as keystone species: constructing core network modules in the anthosphere of twelve diverse wild plant species
Abstract
Background
The anthosphere, also known as the floral microbiome, is a crucial component of the plant reproductive system. Therefore, understanding the anthospheric microbiome is essential to explore the diversity, interactions, and functions of wildflowers that coexist in natural habitats. We aimed to explore microbial interaction mechanisms and key drivers of microbial community structures using 144 flower samples from 12 different wild plant species inhabiting the same natural environment in South Korea.
Results
The microbial diversity of the anthosphere showed plant dependence, with the highest diversity observed in Forsythia koreana, indicating microbial dynamics in relation to plant species. Caulobacter, Sphingomonas, Achromobacter, Epicoccum, Cladosporium, and Alternaria were anthosphere generalists, suggesting that the local plant anthosphere had a similar microbial composition. Ecological network analysis revealed that anthosphere generalists were tightly coupled to each other and constructed core modules in the anthosphere. Functions associated with parasites and pathogens were commonly observed in the anthosphere, particularly in Capsella bursa-pastoris and Brassica juncea.
Conclusion
Overall, the anthosphere depends on the plant species and microbial generalists function as keystone species to support and connect the anthospheric microbiome in natural habitats.
