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Custom PNA Synthesis

High-affinity, nuclease-resistant peptide nucleic acids designed for DNA/RNA targeting, PCR clamping, SNP discrimination, FISH probes, molecular diagnostics, and advanced research workflows.

Neutral PNA Backbone High-Affinity Binding PCR Clamping SNP / Mutation Detection FISH / ISH Probes Peptide-PNA Conjugates HPLC / MS QC RUO to Scale-Up
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Overview

Custom PNA synthesis for high-affinity DNA and RNA targeting

Peptide Nucleic Acids (PNAs) are synthetic DNA analogs where the sugar-phosphate backbone is replaced by a neutral N-(2-aminoethyl)-glycine peptide-like backbone. This neutral chemistry reduces electrostatic repulsion and supports strong, sequence-specific hybridization to complementary DNA or RNA.

PMO, fully modified TMO, and TMO-DNA/RNA chimera backbone structures

PNA Build

Configured around target sequence, assay format, label position, solubility strategy, conjugation partner, and QC requirements.

Typical Length

5-40 mer; many diagnostic probes use shorter high-affinity designs.

Labeling Options

N-terminus, C-terminus, and internal labels using spacer/linker strategies.

QC Support

MALDI-TOF MS, analytical HPLC, and optional Tm or functional testing.

Best-Fit Uses

Designed for projects that require stable, short, high-specificity probes with strong DNA/RNA recognition.

PCR Clamping

Wild-type suppression and mutant allele enrichment workflows.

FISH / ISH

Telomere, pathogen, chromosome, and localization probe applications.

Diagnostics

SNP genotyping, mutation detection, capture, pull-down, and probe assays.

Positioning: PNAs are neutral peptide-like nucleic acid mimics, not standard DNA or RNA oligos.
Project fit: useful for high-affinity hybridization, mismatch discrimination, clamping, imaging, and diagnostic probe workflows.
PNA vs DNA/RNA

DNA/RNA, PNA, and γ-PNA comparison

PNA preserves Watson-Crick base recognition while replacing the negatively charged sugar-phosphate backbone of DNA/RNA with a neutral peptide-like scaffold. γ-PNA, also referred to as rPNA in some workflows, introduces γ-backbone substitution to improve conformational preorganization, binding affinity, mismatch discrimination, and probe performance.

Feature DNA / RNA PNA γ-PNA / rPNA
Backbone Type Natural sugar-phosphate backbone Neutral N-(2-aminoethyl)-glycine peptide-like backbone γ-substituted or modified PNA backbone designed for preorganization
Net Charge Negatively charged Neutral Neutral, with optional side-chain tuning depending on design
Hybridization Behavior Watson-Crick base pairing with charge-dependent duplex formation Watson-Crick base pairing with reduced electrostatic repulsion Preorganized binding geometry can further strengthen target hybridization
Binding Affinity Standard DNA/RNA duplex formation High affinity to complementary DNA or RNA Very high affinity due to conformational preorganization
Mismatch Discrimination Moderate High; useful for SNP and mutation detection Very high; useful for allele-specific and mutation-sensitive designs
Nuclease Resistance Limited unless chemically modified Excellent because the backbone is not recognized like natural DNA/RNA Excellent
Salt Dependence More dependent on ionic strength and buffer conditions Reduced salt dependence Reduced salt dependence
Hybridization Stability Moderate duplex stability Strong duplex stability Very strong duplex stability
Water Solubility Generally good Sequence dependent; may require solubility design Can be improved through γ-substitution or side-chain design
Typical Applications PCR, qPCR, sequencing, cloning, and general molecular biology PCR clamping, FISH, SNP detection, mutation detection, capture probes, and diagnostics Advanced targeting, allele discrimination, antisense research, and next-generation PNA probe platforms
Synthetic Chemistry Standard phosphoramidite synthesis Specialized solid-phase PNA synthesis Specialized γ-PNA or modified PNA synthesis
Thermal Stability (Tm) Standard Higher than many DNA/RNA duplexes Often highest among the three classes
Mechanisms of Action

Mechanisms of action of PNA in diagnostics

PNA probes support molecular diagnostics through strong sequence-specific hybridization, mismatch discrimination, polymerase blocking activity, and stable probe-target duplex formation.

PCR Clamp Blocking

PNA clamps hybridize strongly to complementary wild-type DNA sequences and can block polymerase extension during PCR, improving mutation enrichment and SNP discrimination.

Fluorescent Hybridization Detection

Fluorescent PNA probes support FISH and imaging workflows through stable target hybridization, strong mismatch discrimination, and high signal specificity.

Sequence-Specific Targeting

High-affinity PNA duplex formation supports antisense targeting, capture assays, molecular diagnostics, and sequence-selective RNA or DNA recognition workflows.

Applications

Common custom PNA research and diagnostic applications

PNA probes are useful when high binding affinity, mismatch discrimination, nuclease resistance, and compact probe design are important.

PCR Clamping

Suppress wild-type amplification and enrich mutant allele detection in mutation-specific PCR workflows.

SNP & Mutation Detection

High mismatch discrimination for genotyping, rare variant detection, and molecular diagnostic assay development.

FISH / ISH Probes

Fluorescent PNA probes for telomeres, pathogens, chromosomes, transcripts, and localization assays.

Antisense / Antigene Research

Sequence-specific targeting of RNA or DNA for gene regulation and target validation studies.

Capture & Pull-Down

Biotinylated or affinity-tagged PNA probes for target capture and enrichment workflows.

Conjugate Development

Peptide-PNA, dye-PNA, linker-PNA, and solubility-enhanced PNA constructs for specialized assays.

Synthesis Options

Custom PNA synthesis specifications

PNA projects can be configured around probe length, label placement, solubility, purification, analytical requirements, and final application.

Parameter Available Options
Length 5-40 mer; shorter designs are common for high-affinity probes and clamps
Scale Research scale through larger project quantities
Purification HPLC standard; additional purification options by project need
Labels FAM, TAMRA, Cy3, Cy5, biotin, Dabcyl, quencher, and custom labels
Conjugation Peptide, linker, spacer, solubility enhancer, affinity tag, and custom bioconjugates
QC MALDI-TOF or ESI MS identity confirmation and analytical HPLC
Delivery Format Lyophilized or buffered format by request
Modifications & Conjugation

PNA labels, linkers, solubility groups, and conjugates

Bio-Synthesis supports custom PNA designs for detection, capture, uptake, spacing, solubility, and assay-specific performance.

Labels & Functional Handles

detection, capture, and assay readout

PNA probes can be configured with fluorophores, quenchers, affinity tags, reactive handles, and spacer systems.

Fluorescent Dyes
FAM, TAMRA, Cy3, Cy5, ATTO, Alexa Fluor, and other dye options.
Affinity Tags
Biotin, digoxigenin, and custom capture handles.
Reactive Handles
Amine, thiol, azide, alkyne, maleimide, and related coupling groups.

Conjugates & Solubility Design

delivery, spacing, and performance support

PNA properties can be tuned using peptide conjugation, charged residues, spacers, and application-specific linkers.

Peptide-PNA
CPP, targeting peptide, and functional peptide conjugation options.
Spacer Systems
AEEA, PEG, and custom linkers for steric spacing and signal performance.
Solubility Support
Lysine tails, charged residues, and design review for difficult sequences.
Quality & Documentation

Analytical QC and project documentation support

PNA deliverables can be configured for research-use assays, diagnostic development, imaging, or scale-up programs.

Identity Confirmation

  • MALDI-TOF or ESI mass spectrometry
  • Molecular weight confirmation
  • Lot-linked analytical review

Purity Assessment

  • Analytical HPLC chromatogram
  • Purity reporting
  • Additional testing by request

Documentation

  • Certificate of Analysis
  • Optional Tm or assay support
  • Project-specific records available

FAQ

How does PNA block polymerase extension?
PNA binds complementary DNA with high affinity through Watson-Crick base pairing while its neutral backbone creates a highly stable duplex. During PCR clamping workflows, the bound PNA can physically block polymerase progression or primer extension on wild-type sequences, helping enrich low-frequency mutations or improve mismatch discrimination.
Why use PNA instead of DNA probes?
PNA can provide stronger binding, sharper mismatch discrimination, nuclease resistance, and excellent performance in clamping, FISH, and diagnostic probe workflows.
Can PNA be fluorescently labeled?
Yes. Common dye options include FAM, TAMRA, Cy3, Cy5, ATTO dyes, Alexa Fluor options, and quenchers depending on assay needs.
What is a PNA?
Peptide Nucleic Acid is a synthetic nucleic acid analog with a neutral peptide-like backbone that binds complementary DNA or RNA through standard base pairing.
Why are PNA probes resistant to degradation?
 Unlike DNA or RNA oligonucleotides, PNA contains a synthetic peptide-like backbone rather than a natural sugar-phosphate structure. Because nucleases and many proteases do not efficiently recognize this backbone, PNA probes show excellent resistance to enzymatic degradation and maintain stability in challenging biological environments.
Can PNA improve SNP or mutation discrimination?
 Yes. PNA duplexes often show sharper mismatch discrimination compared to standard DNA probes. Even single-base mismatches can significantly destabilize PNA binding, making PNA useful for SNP genotyping, mutation enrichment, rare variant detection, and molecular diagnostic workflows.
More FAQ'sAll FAQ's
Contact & Quote Request

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For the fastest technical review, share your PNA sequence or target region, application, label or conjugation needs, scale, purification preference, solubility concerns, and QC documentation requirements.
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Need help before quoting?

Email: Info@Biosyn.com Phone: +001-972-420-8505 (INT)
Phone: 800-227-0627 (US/CAN) FAX: 972-420-0442

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