PCR Blockers

PNA clamping is a technique that uses peptide nucleic acid (PNA) oligomers in PCR or hybridization assays to selectively suppress amplification or detection of unwanted DNA sequences. It is particularly effective for reducing amplification of wild-type DNA when detecting rare SNP mutations or minimizing background from host DNA, such as chloroplast or mitochondrial 16S rRNA, thereby enhancing the sensitivity of low-abundance microbial target detection. Another example is globin reduction using PNA. A blend of PNAs targeting human gamma globin RNA can suppress globin mRNA amplification during cDNA synthesis, leading to more diverse cDNA libraries for microarray analysis.

Due to its high affinity and specificity, PNA binds tightly to complementary sequences—even with minimal mismatches—and blocks access to primers without being extended by DNA polymerase, making it a highly effective molecular clamp. PNA clamping is effective correcting amplification bias and reduce sequencing errors.

Applications of PNA Clamping

  • SNP and mutation detection
  • Microbial profiling
  • Rare allele enrichment
  • Prey analysis
  • PCR assays with high host DNA contamination

PCR blockers for mutation detection – PNA Bio

We offer catalog PNA clamps targeting plant mitochondrial and chloroplast as well as human globin sequences. For other applications, our team can assist with custom design and synthesis of PNA clamps tailored to your project. Please contact us at info@pnabio.com for more information.

PNA Clamps for Host DNA Suppression in Metagenomic Studies

16S, 18S, and 28S rRNA sequencing are widely used for taxonomic classification in metagenomics. However, a frequent challenge is host-derived contamination, where the majority of sequencing reads originate from the host’s mitochondrial or plastid genomes. This can obscure the detection of low-abundance microbial taxa.

To address this, PNA clamps (PNA PCR blockers) are designed to selectively bind to host rRNA regions, suppressing their amplification and enriching microbial sequences in your dataset.

🔬 PNA PCR Blockers We Offer

Our catalog includes a range of PNA blockers targeting mitochondrial, chloroplast, and ITS DNA from multiple host species.

Product Cat No Sequence Target Available Sizes
mPNA MP01-25/MP01-50 GGCAAGTGTTCTTCGGA mitochondria 25 nmole & 50 nmole
pPNA PP01-25/PP01-50 GGCTCAACCCTGGACAG chloroplast 25 nmole & 50 nmole
Pop mPNA PMP01-25 GGCAAGTCTTCTTCGGA mitochondria 25 nmole
Quercus mPNA QMP01-25 KK-GTGAATTGGTTTCGAGA mitochondria 25 nmole
Asteraceae pPNA APP01-25 GGCTCAACTCTGGACAG chloroplast 25 nmole
ITS PNA IP01-25/IP01-50 CGAGGGCACGTCTGCCTGG ITS2 25 nmole & 50 nmole

All products are usually in stock and available for same-day shipping for next-day delivery.

🧪 How to Use PNA PCR Blockers

  • Add PNA blockers directly to the PCR mix at a final concentration of 0.5 µM to 6 µM. Temperature: 70°C – 80°C
  • Include a PNA clamping step between denaturation and primer annealing.
  • For optimization, tryrange of clamping temperature to 65°C–80°C (about 10°C below to 5°C above the predicted Tm of the PNA).
  • Duration: 10 – 30 seconds
  • Add PNA blockers directly to the PCR mix.

📥 Download the full mPNA and pPNA protocol here. 

🧬 Need a Custom Clamp?

If your host genome is not covered by the above options, we can design and synthesize a custom PNA clamp tailored to your target sequence.

📧 Contact us at info@pnabio.com for assistance, or visit our Custom PNA Oligos page for more information.

📚 Scientific References

PNA Clamp to Suppress Aberrant Vk Transcript

🧬 Overview

A validated PNA clamp that selectively suppresses amplification of the aberrant MOPC-21–derived Vκ transcript in SP2/0- or P3X63Ag8.653-based hybridomas, enabling clean amplification of the functional light-chain Vκ from your hybridoma cDNA.

🧾 Product details

  • Target: MOPC-21 aberrant Vκ (CDR3 region)
  • PNA sequence (antisense to abVκ CDR3): 5’ CGTGTAAGCTCCCTA
  • Validated use: PNA-mediated PCR clamping to prevent abVκ amplification while preserving amplification of functional hybridoma Vκ. In the cited work, PNA clamping eliminated abVκ clones and enriched functional Vκ clones.

🧪 PCR clamping conditions

⚗️ PCR Reaction Mix

  • Primers (e.g., Vκ2Back/Vκ4For): 0.25 µM each
  • PNA clamp: 2.5~10 µM
  • Template: cDNA from hybridoma
  • Volume: 20–50 µL

⏱️ PCR Cycle

  1.    94 °C, 2 min
  2.   30 cycles of:
    •  94 °C, 20 s (denaturation)
    •  65 °C, 30 s (PNA preferential clamping)
    •  50 °C, 30 s (primer annealing)
    •  60 °C, 30 s (extension)
  3.   60 °C, 2 min (final extension)

📚 Reference

Globin mRNA is a majority of total mRNA in blood cells (over 70%) and can potentially reduce the sensitivity of non-globin mRNA.

Globin Reduction PNA is a novel, non-enzymatic technology that removes the majority of alpha and beta globin mRNA from total RNA preparations derived from whole blood. PNA oligomers can be effectively used as a clamp by specifically blocking globin mRNA during the process of reverse transcription and resulting in specific PCR amplification of the target non-globin mRNA for your analysis.

The 3 nmole kit (G2000-3) contains 3 nmole of each PNA and includes sufficient reagents for 250 reactions of 5 ug RNA preps. The larger size G2000-10 contains 10 nmole of each PNA.

Download protocol for Globin Reduction PNA Kit.

High-quality PNA clamp kits for SNP analysis – PNA Bio

Globin reduction PNA is composed of the following 4 PNAs that are specific to alpha and beta globin mRNA. It works for both human and mouse globin mRNA.

    • The sequences of G2001, GR PNA-L;

PNA1: k-TAA CGG TAT TTG GAG-k
PNA2: k-GTA GTT GGA CTT AGG-k
PNA3: k-GCC CTT CAT AAT ATC-k
PNA4: k-ATC CAG ATG CTC AAG-k

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  20. Microbial Turnover and Dispersal Events Occur in Synchrony with Plant Phenology in the Perennial Evergreen Tree Crop Citrus sinensis. Ginnan NA et al. (2022) mBio 13(3):e00343-22.
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Most catalog items are in stock and available for immediate shipping. Please Contact us for more information.

You can download the protocol for mPNA/pPNA

Cat No Item Description Size Price Order
MP01-25 mPNA-S Mitochondria rRNA blocker (ggcaagtgttcttcgga) 25 nmole $395.00 Add to cart
MP01-50 mPNA-L Mitochondria rRNA blocker (ggcaagtgttcttcgga) 50 nmole $550.00 Add to cart
PP01-25 pPNA-S Chloroplast rRNA blocker (ggctcaaccctggacag) 25 nmole $395.00 Add to cart
PP01-50 pPNA-L Chloroplast rRNA blocker (ggctcaaccctggacag) 50 nmole $550.00 Add to cart
IP01-25 ITS-PNA-S ITS rRNA blocker (cgagggcacgtctgcctgg) 25 nmole $425.00 Add to cart
IP01-50 ITS-PNA-L ITS rRNA blocker (cgagggcacgtctgcctgg) 50 nmole $585.00 Add to cart
APP01-25 Asteraceae pPNA Asteraceae chloroplast rRNA blocker (ggctcaactctggacag) 25 nmole $395.00 Add to cart
PMP01-25 Pop mPNA Mitochondria rRNA blocker variant (ggcaagtcttcttcgga) 25 nmole $395.00 Add to cart
QMP01-25 Quercus mPNA Oak mitochondria rRNA blocker (KK-gtgaattggtttcgaga) 25 nmole $415.00 Add to cart
G2001-3 GR PNA-S A set of 4 PNA oligos against human globin 3 nmole $495.00 Add to cart
G2001-10 GR PNA-L A set of 4 PNA oligos against human globin 10 nmole $1150.00 Add to cart
VKP-01 Vk PNA Aberrant Vk PNA Blocker (cgtgtaagctcccta) 50 nmole $510.00 Add to cart