PNA probes for high-affinity hybridization and single-base discrimination

Overview

Custom PNA probes for fast, tight, and specific target recognition

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, supporting fast, tight, and specific hybridization to DNA or RNA, including lower-salt assay conditions.

12–18 nt

Typical PNA FISH / ISH starting range

PNA

Neutral peptide-like backbone

HPLC + MS

Purification and identity confirmation

mg–g

Flexible scale options

PNA Technology & Benefits

Why PNA probes are useful for FISH, clamp PCR, and capture

PNA probes combine high hybridization affinity with strong mismatch sensitivity, making them valuable for imaging, rare-variant enrichment, and stringent target capture.

Technology

• N-(2-aminoethyl)-glycine backbone linked by amide bonds
• Uncharged peptide-like backbone reduces electrostatic repulsion
• Strong PNA-DNA and PNA-RNA duplex formation at shorter lengths
• Lower ionic-strength compatibility helps suppress genomic reannealing
• Resistant to nucleases and proteases in complex sample matrices

Benefits

• High signal-to-noise in FISH/ISH workflows
• Sharp single-base mismatch discrimination
• Useful for SNP genotyping and mutant enrichment
• Broad compatibility with fluorescent labels and capture tags
• Reproducible manufacturing with purification and analytical QC

PNA Probe Types

Probe formats for imaging, enrichment, and capture workflows

FISH / ISH Probes

Short, dye-labeled PNAs for telomere, centromere, microbial, and gene-specific targets. Lower-salt hybridization can reduce reannealing and background.

PNA Clamp PCR

Unlabeled PNA clamps overlap wild-type sites to block polymerase extension, helping enrich mutant alleles for sensitive downstream detection.

Capture / Pull-Down

Biotin-PNA with PEG or AEEA spacers enables stringent capture of DNA or RNA targets in magnetic streptavidin workflows.

Design Guide

Design considerations that improve specificity and signal

Bio-Synthesis can help tune length, Tm, spacers, labels, and stringency so the probe fits your assay window.

FISH / ISH Design

• Start with 12–18 nt and tune to target Tm
• Use lower salt with optional formamide for stringency
• Avoid strong target secondary structure
• Add spacers to reduce dye quenching

Clamp PCR Design

• Clamp should fully span the wild-type site
• Place the mismatch centrally when possible
• Use primers or probes to detect mutant allele
• Start with 50–200 nM clamp and optimize empirically

Capture Design

• Use 5′ biotin-TEG or equivalent capture tag
• Add PEG/AEEA spacer for accessibility
• Use stringent washes for specificity
• Include scramble, mismatch, and no-probe controls

Labels & Colors

Fluorophores, capture tags, quenchers, and spacers

Labels can be matched to your microscope, camera filters, qPCR instrument, or pull-down workflow. Multiplex panels can be selected for reduced spectral overlap.

Fluorophores

• FAM / FITC for green channels
• HEX / VIC-like dyes for yellow channels
• TAMRA / ROX and Texas Red for orange-red channels
• Cy3, Cy5, and Alexa Fluor family options

Tags & Quenchers

• Biotin-TEG for capture and pull-down
• Dark quenchers for specialized applications
• Dual-function designs on request
• Custom tags can be reviewed for feasibility

Spacers

• PEG and AEEA spacers
• Lys tails for solubility support
• Spacer placement to reduce self-quenching
• Custom linker review available

Use Cases

Where custom PNA probes are commonly used

Use Case	Why PNA Helps	Typical Setup
Telomere / Centromere FISH	High affinity plus low-salt compatibility can reduce reannealing and increase signal-to-noise.	12–18 nt dye-PNA, low-salt hybridization, optional formamide.
PNA Clamp PCR	Blocks wild-type extension to enrich mutant alleles.	Unlabeled PNA clamp with qPCR primers/probe; optimize clamp dose.
SNP Genotyping	Sharp single-base discrimination helps distinguish variant sites.	Short PNA across variant; melt-curve or probe-based readout.
Capture & Pull-Down	Tight binding and nuclease resistance support stringent enrichment.	5′ biotin-PNA with PEG spacer and stringent washes.
In Situ Pathogen ID	Specific probes can work in complex biological matrices.	Multiplex dye-PNAs targeting species-specific markers.

Custom Synthesis Options

Flexible PNA synthesis, labeling, purification, and delivery options

Parameter	Options
Format	FISH/ISH probes, PNA clamps, capture/biotin PNAs, and custom architectures.
Length	10–25 nt typical; FISH commonly starts at 12–18 nt, while clamp and capture lengths are design-dependent.
Labels	FAM/FITC, HEX/VIC-like, TAMRA/ROX, Texas Red, Cy3/Cy5, Alexa Fluor family, biotin, and quenchers.
Spacers / Linkers	PEG/AEEA, Lys tail, and custom linkers for solubility, separation, or functional presentation.
Purification	RP-HPLC standard; PAGE available on request.
Scale	1 mg to grams; tubes or 96-well plate formats.
Deliverables	Lyophilized or buffered material with MS and analytical HPLC report options.

Quality Assurance

Purification, analytical QC, documentation, and timeline support

PNA probe deliverables can be aligned with your project’s assay development, documentation, and timeline needs.

Core QC

• Mass spectrometry identity confirmation
• Analytical HPLC or PAGE purity
• OD or mass-based quantitation
• Certificate of Analysis options

Functional Checks

• Optional Tm testing
• Melt-profile support
• Clamp efficacy checks
• Project-specific QC discussion

Typical Timeline

• Known designs: often 1–2 weeks
• Complex multiplex or special labels: often 2–3 weeks
• Lead time depends on labeling, purification, and QC scope
• Rush options may be available

How to Order

What to include for a faster quote

Ordering Steps

• Share target sequence(s) and application: FISH, clamp PCR, or capture.
• Choose labels, tags, spacers, or linker requirements.
• Select scale, purification, and QC readouts.
• Receive a tailored quote and timeline.

Specs Checklist

• Target coordinates or sequence and desired Tm/stringency
• Application and instrument: microscope, qPCR, or capture platform
• Preferred dyes/tags and required multiplex colors
• Scale, purification, buffer, and documentation needs

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/T_m 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.

More FAQ'sAll FAQ's

Contact & Quote Request

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FISH / ISH & Imaging

PNA Clamp & Capture

HPLC + MS QC

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