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PNA probes — high-affinity hybridization and single-base discrimination for FISH, clamp PCR, and capture

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Custom PNA Fish Probes

FISH/ISH • PNA clamp PCR • SNP genotyping • Capture & pull-down

Overview PNA Probe Types Design Guide Labels & Colors Use Cases Synthesis Options QC FAQ Contact

Overview

Bio-Synthesis designs and manufactures **peptide nucleic acid (PNA) probes** for FISH/ISH imaging, **PNA clamp PCR** for rare-variant enrichment, SNP genotyping, and capture workflows. PNA’s **neutral, peptide-like backbone** eliminates charge repulsion, delivering **fast, tight, and specific** hybridization to DNA or RNA—even under lower-salt conditions.

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At-a-Glance

  • Applications: **Telomere/centromere FISH**, pathogens, SNPs, clamp PCR, capture
  • Advantages: **High affinity**, **single-base discrimination**, low background
  • Labels: Fluorescein/FAM, rhodamine/TAMRA, Cy3/Cy5, Alexa Fluor®, biotin, quenchers
  • Purification/QC: HPLC/PAGE; **MS confirmation**; optional functional checks
  • Formats: Tubes or 96-well plates; lyophilized or buffered

PNA Technology & Benefits

Technology

  • Backbone: N-(2-aminoethyl)-glycine units linked by amide bonds (uncharged, peptide-like).
  • Hybridization: Strong PNA•DNA/RNA duplexes with **faster on-rates** and higher Tm at shorter lengths.
  • Stringency control: Works at **lower ionic strength** to suppress genomic reannealing—ideal for repetitive targets in FISH.
  • Mismatch sensitivity: **Single-base mismatches** destabilize PNA hybrids more than DNA/DNA.
  • Enzymatic stability: Resistant to nucleases and proteases; durable in complex matrices.

Benefits

  • High signal-to-noise in FISH/ISH (shorter probes, lower background).
  • Exceptional specificity for SNP discrimination and clamp PCR enrichment.
  • Robust performance under low-salt or formamide stringency.
  • Versatile labeling across broad color sets and capture chemistries.
  • Reproducible manufacturing with HPLC + MS QC.

We optimize length, Tm, spacers, and labels to hit your assay window with clean specificity.

PNA Probe Types

FISH / ISH Probes

Short, dye-labeled PNAs for **telomere**, **centromere**, microbial, and gene-specific targets; low-salt hybridization for reduced reannealing.

PNA Clamp PCR

Unlabeled PNA clamps overlap wild-type sites to **block polymerase extension**, enriching mutant alleles for sensitive detection.

Capture / Pull-Down

**Biotin-PNA** (with PEG spacer) for stringent capture of DNA/RNA targets; compatible with magnetic streptavidin workflows.

Design Guide

  • Length (FISH/ISH): 12–18 nt typical; tune to target Tm.
  • Stringency: Lower salt ± formamide to minimize genomic reannealing.
  • Placement: Avoid strong secondary structure; add spacers to limit dye quenching.
  • PNA Clamp PCR: Clamp fully spans WT site; primers/probe detect mutant allele.
  • Mismatches: Place mismatch centrally for sharper discrimination.
  • Concentration: Start 50–200 nM clamp; optimize empirically.
  • Capture PNAs: 5′ biotin-TEG with PEG/AEEA spacer.
  • Washes: Use elevated stringency for specificity.
  • Controls: Include scramble/mismatch and no-probe/NTC controls.

Labels & Colors

Fluorophores

  • FAM / FITC (green), HEX/VIC-like (yellow), TAMRA/ROX (orange-red)
  • Texas Red, Cy3/Cy5, Alexa Fluor® family (e.g., 488/555/594/647)
  • Multiplex sets selected for minimal spectral overlap

Other Tags

  • Biotin-TEG for capture and pull-down
  • Dark quenchers for specialized applications
  • PEG/AEEA spacers for solubility and reduced self-quenching

We match dyes to your microscope/camera filters or qPCR instrument.

We offer much more than listed! - get in touch   
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Use Cases

Use Case Why PNA Helps Typical Setup
Telomere / Centromere FISH High affinity + low salt reduce reannealing → strong S/N 12–18 nt dye-PNA; low-salt hybridization; optional formamide
PNA Clamp PCR (rare variants) Blocks WT extension to enrich mutants Unlabeled PNA clamp + qPCR primers/probe; optimize clamp dose
SNP Genotyping Sharp single-base discrimination Short PNA across variant; melt-curve or probe-based readout
Capture & Pull-Down Tight binding, nuclease resistance 5′ biotin-PNA with PEG spacer; stringent washes
In situ Pathogen ID Specific probes in complex matrices Multiplex dye-PNAs targeting species markers
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Custom Synthesis Options

Parameter Options
Format FISH/ISH; PNA clamp; capture/biotin; custom architectures
Length 10–25 nt typical (FISH 12–18; clamp/capture per design)
Labels FAM/FITC, HEX/VIC-like, TAMRA/ROX, Texas Red, Cy3/Cy5, Alexa; biotin; quenchers
Spacers/Linkers PEG/AEEA, Lys tail, custom linkers for solubility/separation
Purification RP-HPLC (standard), PAGE on request
Scale 1 mg to grams; tubes or 96-well plates
Deliverables Lyophilized or in buffer; MS & analytical HPLC report

Quality Assurance

  • Mass spectrometry for identity confirmation
  • Analytical HPLC/PAGE for purity
  • Optional functional checks (Tm, melt profiles, clamp efficacy)
  • Documentation: RUO standard; GLP/cGMP support available

Typical Timelines

Known designs: 1–2 weeks. Complex multiplex sets or special labels: 2–3 weeks, depending on dyes and purification.

Lead time varies with labeling, purification, and QC scope. Rush options may be available.

How to Order

  1. Share target sequence(s) and application (FISH, clamp PCR, capture).
  2. Choose labels/tags and any spacers or linkers.
  3. Select scale, purification, and QC readouts.
  4. Receive a same-day quote and timeline.

Specs Checklist

  • Target coordinates/sequence; desired Tm or stringency
  • Application (FISH/ISH, clamp PCR, capture) & instrument (microscope/qPCR)
  • Preferred dyes/tags; required multiplex colors
  • Scale, purification, buffer, and documentation needs
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FAQ

Why choose PNA over DNA probes?

PNA’s neutral backbone removes charge repulsion, yielding **tighter binding**, **faster hybridization**, and **sharper mismatch discrimination**, especially useful in low-salt conditions and repetitive regions.

How long should a PNA FISH probe be?

We typically start at **12–18 nt** and tune length/Tm to your target and stringency. Short PNAs often outperform longer DNA probes.

How does PNA clamp PCR enrich mutant alleles?

An **unlabeled PNA** is designed to perfectly match the wild-type site. When bound, it **blocks polymerase extension** across that site, suppressing WT amplification so mutant alleles are relatively enriched.

Which dyes should I pick for microscopy or multiplex panels?

We select fluorophores to match your filter sets (e.g., **FAM/HEX/Texas Red/Cy5**). For multiplex, we space emissions to reduce crosstalk and balance brightness across channels.

What storage and handling do you recommend?

Store lyophilized at **–20 °C** (desiccated). For working stocks, use nuclease-free buffer; avoid repeated freeze–thaw; include surfactant if needed for longer, dye-rich designs.

Ready to design your PNA FISH probes?

Tell us your sequence, modification, linker requirments - our team will send a tailored plan and quote.

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Ask About a PNA Probe

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