PNA FISH Probes

PNA FISH probes offer exceptional sensitivity and specificity for hybridization due to the electrically neutral PNA backbone, which offers benefits over the negatively charged backbones of DNA or RNA. This unique property enables PNA probes to bind effectively at low concentrations, reduce background signals, and achieve fast hybridization—typically within a few hours—making them ideal for fluorescent in situ hybridization (FISH) applications.

PNA Bio provides a range of catalog probes, including telomere, centromere, and CAG repeat probes. They can be used for cells or tissue sections. For other targets such as microorganisms or gene specific probes, we offer them as custom PNA. please visit our Custom PNA Oligos page for more information.

PNA FISH probes can also be designed as molecular beacons, functioning similarly to DNA molecular beacons. In the unbound state, the flexible and unstructured PNA backbone keeps the fluorophore and quencher in close proximity, effectively quenching fluorescence. When the probe hybridizes to its complementary DNA or RNA target, the structural change separates the fluorophore and quencher, resulting in a fluorescent signal.

Unlike DNA-based beacons, PNA molecular beacons do not require a stem-loop structure, simplifying probe design and enabling the use of shorter sequences. Combined with PNA’s high binding affinity, specificity, and chemical stability, these MB probes are ideal for real-time detection, mutation analysis, live-cell imaging, and clinical diagnostics.

For the recommended PNA FISH protocol, please download the following file. 

If you would like assistance designing a PNA FISH probe specific to your target, please feel free to contact us

PNA FISH Probes and Reagents

PNA Bio offers a range of high-quality PNA FISH probes and buffers to support your fluorescence in situ hybridization (FISH) workflows. Our product line includes telomere, centromere, and DM1 repeat probes, along with optimized Hybridization and Blocking Buffers to streamline your experiments.

Our FISH probes and reagents are usually in stock and ship the same day if the order is received by 5 pm ET.

🔬 Telomere PNA FISH Probes

We provide two telomeric probes for detecting repetitive sequences at chromosome ends:

  • TelC (C-rich): Binds the leading strand containing 3 repeats of TAACCC
  • TelG (G-rich): Binds the lagging strand containing 3 repeats of TTAGGG

These probes are compatible with human, mouse, rat, and most vertebrate chromosomes.

🧬PNA FISH Reagents

  • PFB01: PNA FISH Hybridization Buffer (20 mM Tris, 60% formamide, pH 7.4 final), 30 ml
  • PFB05: PNA FISH Blocking Buffer, 1.5 ml

🧬 Centromere PNA FISH Probes

  • CENPB Probe: Targets the CENP-B binding site
    Sequence: ATTCGTTGGAAACGGGA
    Stains all human and mouse centromeres except the Y chromosome
  • CENT Probe: Targets the human alpha satellite sequence
    Sequence: AAACTAGACAGAAGCAT
    Selectively stains human centromeres; not compatible with mouse chromosomes, and hybridization intensity may vary by chromosome

🧬 DM1 (CAG Repeat) PNA Probe

Our CAG repeat probe is designed to detect expanded CTG/CAG repeats in the DMPK gene, associated with Myotonic Dystrophy type 1 (DM1).

🧪 Sample Compatibility

All PNA FISH probes are suitable for use with:

  • FFPE tissues
  • Fixed cell preparations

🎨 Custom Fluorophores & Sequences

If you require a different fluorophore than those listed, please contact us at order@pnabio.com

For gene-specific targets not listed above, please visit our Custom PNA Oligos page.

You can download the recommended PNA FISH protocol here. 

 

PNA FISH probes for telomere analysis – PNA Bio Fluorescent PNA FISH probes for centromere detection – PNA Bio High-purity PNA FISH probes for molecular diagnostics – PNA Bio
F1002 (TelC-Cy3) F1008 (TelG-A488) F1002 & F3001
Custom PNA FISH probes for research applications – PNA Bio F1006 & F3006 F5001 (CAG-Cy3)
F3004 (CENPB-A488) F1006 & F3006 F5001 (CAG-Cy3)

 

Catalog Number Item Label Information
F1001 TelC-FAM FAM TelC telomere probe
(CCCTAA repeats)
C-rich / leading strand
Reacts to human, mouse, rat, etc
F1002 TelC-Cy3 Cy3
F1003 TelC-Cy5 Cy5
F1004 TelC-Alexa488 Alexa Fluor 488
F1009 TelC-FITC FITC
F1013 TelC-Alexa647 Alexa Fluor 647
F2001 TelC-Biotin Biotin
F1005 TelG-FAM FAM TelG telomere probe
(TTAGGG repeats)
G-rich / lagging strand
Reacts to human, mouse, rat, etc
F1006 TelG-Cy3 Cy3
F1007 TelG-Cy5 Cy5
F1008 TelG-Alexa488 Alexa Fluor 488
F1010 TelG-FITC FITC
F1014 TelG-Alexa 647 Alexa Fluor 647
F2002 TelG-Biotin Biotin
F3001 CENPB-FAM FAM Pan-centromere probe
(ATTCGTTGGAAACGGGA)
Reacts to human & mouse
F3002 CENPB-Cy3 Cy3
F3004 CENPB-Alexa488 Alexa Fluor 488
F3005 CENPB-Cy5 Cy5
F3008 CENPB-Biotin Biotin
F3009 CENPB-RC-Cy3 Cy3
F3010 CENPB-FITC FITC
F3011 CENPB-Alexa647 Alexa Fluor 647
F3003 CENT-Cy3 Cy3 Human only pan-centromere probe
(AAACTAGACAGAAGCATT)
F3006 CENT-FAM FAM
F3007 CENT-RC-A488 Alexa488
F5001 (CAG)5-Cy3 Cy3 Stains CAG repeats (DM-1)
F5002 (CAG)5-Cy5 Cy5
  • Cy3 is more stable alternative for Texas Red, TRITC, TMR and other red dyes.
  1. Visualization of the three-dimensional structure of the human centromere in mitotic chromosomes by superresolution microscopy. Tommaso ED et al. (2023) Mol Biol Cell 34(6): ar61.
  2. Adjusting the Structure of a Peptide Nucleic Acid (PNA) Molecular Beacon and Promoting Its DNA Detection by a Hybrid with Quencher-Modified DNA. Hajime H et al. (2022) Processes 10(4):722.
  3. Fluorescence spectroscopic detection and measurement of single telomere molecules. Beh CW et al. (2018) Nucleic Acids Res 46(19): e117.
  4. Integrity of the human centromere DNA repeats is protected by CENP-A, CENP-C, & CENP-T . Giunta S & Funabiki H. (2017) Proc Natl Acad Sci USA 114(8):1928-1933.
  5. Comprehensive characterization of neutrophil genome topology. Zhu Y et al. (2017) Genes & Development. 31(2):141–153.
  6. Long telomeres protect against age-dependent cardiac disease caused by NOTCH1 haploinsufficiency. Theodoris CV et al. (2017) J Clinical Investigation 127(5):1683-1688.
  7. Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow. Gunkel M et al (2017) Methods 114:60-73.
  8. Telomere Replication Stress Induced by POT1 Inactivation Accelerates Tumorigenesis. Pinzaru AM et al. (2016) Cell Rep 15(10):2170-2184.
  9. Regulation of the Human Telomerase Gene TERT by Telomere Position Effect—Over Long Distances (TPE-OLD): Implications for Aging and Cancer. Kim W et al (2016) pLoS Biology 2000016.
  10. Dysfunctional telomeres induce p53‐dependent and independent apoptosis to compromise cellular proliferation and inhibit tumor formation. Wang Y et al (2016) Aging Cell 15(4): 646–660.
  11. ATRX loss promotes tumor growth and impairs nonhomologous end joining DNA repair in glioma. Koschmann C et al (2016) Sci Transl Med. 8(328):328.
  12. Oocyte Polarization Is Coupled to the Chromosomal Bouquet, a Conserved Polarized Nuclear Configuration in Meiosis. Elkouby YM et al. (2016) PLoS Biol. 14(1):e1002335.
  13. Cell Death During Crisis Is Mediated by Mitotic Telomere Deprotection. Hayashi MT et al (2015)Nature 522(7557):492–496.
  14. SMARCAL1 maintains telomere integrity during DNA replication. Poole LA et al. (2015) Proc Natl Acad Sci U S A. 112(48):14864-14869.
  15. Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH. Komosa M et al. (2015)Nucleic Acids Res. 43(4):2152–2163.
  16. Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand.Teasley DC et al (2015) J Biol Chem. 290(24):15133-45.
  17. Replication Stress and Telomere Dysfunction Are Present in Cultured Human Embryonic Stem Cells. Janson C et al (2015) Cytogenet Genome Res. 146(4):251-60.
  18. Genomic mosaicism with increased amyloid precursor protein (APP) gene copy number in single neurons from sporadic Alzheimer’s disease brains. Bushman DM et al. (2015) Elife 4:e05116.
  19. Somatic mosaicism of EPAS1 mutations in the syndrome of paraganglioma and somatostatinoma associated with polycythemia. Yang C et al (2015) Hum Genome Var. 2:15053.
  20. Induction of telomere dysfunction mediated by the telomerase substrate precursor 6-thio-2′-deoxyguanosine. Mender I et al (2015) Cancer Discov. 5(1):82-95.
  21. Role of Tet proteins in enhancer activity and telomere elongation. Lu F et al (2014)Genes Dev. 28(19): 2103–2119.
  22. Expression of the genetic suppressor element 24.2 (GSE24.2) decreases DNA damage andoxidative stress in X-linked dyskeratosis congenita cells. Manguan-Garcia C et al. (2014) PLoS One. 9(7):e101424.
  23. Telomerase Protects Werner Syndrome Lineage-Specific Stem Cells from Premature Aging. Cheung HH et al (2014) Stem Cell Reports 2(4):534–546.
  24. Rapid analysis of chromosome aberrations in mouse B lymphocytes by PNA-FISH. Misenko SM & Bunting SF (2014) Journal of visualized experiments 10.3791/51806.
  25. Identification of small juvenile stem cells in aged bone marrow and their therapeutic potential for repair of the ischemic heart. Igura K et al (2013) Am J Physiol Heart Circ Physiol. 305(9): H1354–H1362.
  26. Structure of the human telomeric Stn1-Ten1 capping complex. Bryan C et al (2013) PLoS One 8(6):e66756.
  27. Direct DNA and PNA probe binding to telomeric regions without classical in situ hybridization. Genet MD et al (2013) Molecular Cytogenetics 6:42.
  28. Telomere and microtubule targeting in treatment-sensitive and treatment-resistant human prostate cancer cells. Zhang B et al (2012) Mol Pharmacol. 82(2):310-321.
  29. Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data. Parker M et al (2012) Genome Biol. 13(12):R113.
  30. Dynamic rearrangement of telomeres during spermatogenesis in mice. Tanemura K et al. (2005) Dev Bio 281:196-207.
  31. High-throughput telomere length quantification by FISH and its application to human population studies. Canela A et al (2007) Proc Natl Acad Sci USA 104(13):5300-5. (Q-FISH)
  32. Analysis of repetitive DNA in chromosomes by flow cytometry. Brind-Amour J and Lansdorp PM (2011) Nat Methods 8(6):484-6.(Q-FISH & Flow FISH)
  33. Age-related telomere length dynamics in peripheral blood mononuclear cells of healthy cynomolgus monkeys measured by Flow FISH. Lee WW et al (2002) Immunology 105:458-65. (Q-FISH & Flow FISH)
  34. Single base discrimination of CENP-B repeats on mouse and human Chromosomes with PNA-FISH. Chen C et al (1999) Mammalian Genome 10(1):13–18.

FISH probes and reagents are usually in stock and shipped out the same day for the next day delivery if the order is received by 5 pm EST.

 

Cat No Item Description Size Price
F1001 TelC-FAM C-rich telomere probe, FAM labeled 5 nmole $295.00
F1002 TelC-Cy3 C-rich telomere probe, Cy3 labeled 5 nmole $295.00
F1003 TelC-Cy5 C-rich telomere probe, Cy5 labeled 5 nmole $295.00
F1004 TelC-Alexa488 C-rich telomere probe, Alexa Fluor 488 labeled 5 nmole $375.00
F1005 TelG-FAM G-rich telomere probe, FAM labeled 5 nmole $295.00
F1006 TelG-Cy3 G-rich telomere probe, Cy3 labeled 5 nmole $295.00
F1007 TelG-Cy5 G-rich telomere probe, Cy5 labeled 5 nmole $295.00
F1008 TelG-Alexa488 G-rich telomere probe, Alexa Fluor 488 labeled 5 nmole $375.00
F1009 TelC-FITC C-rich telomere probe, FITC labeled 5 nmole $295.00
F1010 TelG-FITC G-rich telomere probe, Cy3 labeled 5 nmole $295.00
F1013 TelC-Alexa647 C-rich telomere probe, Alexa Fluor 647 labeled 5 nmole $375.00
F1014 TelG-Alexa647 G-rich telomere probe, Alexa Fluor 647 labeled 5 nmole $375.00
F1020 aTelC-Alexa488 TelC probe for arthropods, Alexa Fluor 488 labeled 5 nmole $375.00
F2001 TelC-Biotin C-rich telomere probe, Biotin labeled 5 nmole $295.00
F2002 TelG-Biotin G-rich telomere probe, Biotin labeled 5 nmole $295.00
F3001 CENPB-FAM CENP-B box binding pan-centromere probe, FAM labeled 5 nmole $295.00
F3010 CENPB-FITC CENP-B box binding pan-centromere probe, FITC labeled 5 nmole $295.00
F3002 CENPB-Cy3 CENP-B box binding pan-centromere probe, Cy3 labeled 5 nmole $295.00
F3004 CENPB-Alexa488 CENP-B box binding pan-centromere probe, Alexa Fluor 488 labeled 5 nmole $375.00
F3005 CENPB-Cy5 CENP-B box binding pan-centromere probe, Cy5 labeled 5 nmole $295.00
F3011 CENPB-Alexa647 CENP-B box binding pan-centromere probe, Alexa Fluor 647 labeled 5 nmole $375.00
F3008 CENPB-Biotin CENP-B box binding pan-centromere probe, Biotin labeled 5 nmole $295.00
F3009 CENPBR-Cy3 Reverse complement of CENPB probe, Cy3 labeled 5 nmole $295.00
F3003 CENT-Cy3 Centromere probe, Cy3 labeled 5 nmole $295.00
F3006 CENT-FAM Centromere probe, FAM labeled 5 nmole $295.00
F3007 CENT-RC-A488 Reverse complement of CENT probe, Alexa488 labeled 5 nmole $375.00
F5001 (CAG)5-Cy3 CAG repeats, Cy3 labeled 5 nmole $295.00
F5002 (CAG)-Cy5 CAG repeats, Cy5 labeled 5 nmole $295.00
PFB01 Hybridization Buffer PNA FISH Hybridization Buffer 30 ml $65.00
PFB05 FISH Blocking Buffer PNA FISH Blocking Reagent 1.5 ml $35.00