Affinity-Enhanced Probe Design | LNA, MGB, PNA & ZNA

Overview

Affinity-Enhanced Probe Chemistry for Difficult Targets

Affinity-enhanced probes use modified nucleic acid chemistries to raise duplex stability, improve mismatch discrimination, shorten probe length and support challenging assay formats.

This page is the central chemistry platform for SNP genotyping, mutation detection, rare allele detection, dPCR, FISH, pathogen variant assays and high-specificity qPCR probes. SNP genotyping is therefore treated as an application of affinity-enhanced probe chemistry, not a separate duplicate page.

Bio-Synthesis supports custom affinity-enhanced probes using LNA/BNA, ENA, cEt, ZNA®, MGB 3′ caps, 2′-O-Me, 2′-F, PNA, fluorophores, dark quenchers, double-quenched formats and advanced modification placement.

Shorter Probes

MGB, LNA/BNA and related chemistries help maintain Tm in compact designs.

Higher Specificity

Strategic modification placement improves SNP and mismatch discrimination.

Avoid Over-Stabilization

Too much affinity chemistry can reduce allele discrimination and increase background.

Design Support

Bio-Synthesis helps evaluate Tm, dye pairing, multiplex layout and manufacturability.

Positioning recommendation: Use this page as the main home for SNP genotyping chemistry. Link SNP-related navigation to this page or to a focused application section instead of creating a mostly duplicate SNP page.

Affinity Chemistry Selection & Optimization Guide

What Probe Design Problem Are You Trying to Solve?

Most customers already know the application. The harder question is which modification will improve the probe without creating new problems. Select the design challenge below to see the recommended chemistry, practical optimization strategy, compatible modifications and common design cautions.

Select a probe design challenge

Probe Tm Is Too Low

When the probe is too short or too AT-rich, add affinity chemistry before simply making the probe much longer. The goal is to reach the desired Tm while preserving specificity.

MGB LNA/BNA ZNA® ENA/cEt

Best first choice

MGB for short hydrolysis probes; LNA/BNA for local Tm lift.

Typical effect

MGB can provide strong Tm lift; LNA/BNA gives position-specific lift.

Design tip

Raise Tm gradually and keep the probe as compact as practical.

Watch out

Too much Tm may increase background or reduce mismatch discrimination.

Specificity Is Poor

If the probe binds related targets or mismatched sequences, use chemistry that improves matched-versus-mismatched discrimination rather than simply increasing total binding strength.

LNA/BNA MGB ENA/cEt Shorter probe

Best first choice

Strategic LNA/BNA or MGB, depending on probe length and target window.

Typical effect

Higher local ΔTm and improved mismatch penalty when placed correctly.

Design tip

Keep the mismatch near the middle third of the probe.

Watch out

Over-stabilized probes can bind both matched and mismatched targets.

SNP or Mutation Discrimination Is Needed

For one-base differences, the probe must be short enough to penalize the mismatch while stable enough to bind the correct allele.

MGB LNA/BNA ENA FAM/HEX pair

Best first choice

NMGB or limited LNA/BNA in paired allele-specific probes.

Typical effect

Improves signal separation between matched and mismatched targets.

Design tip

Center the SNP and balance Tm between allele-specific probes.

Watch out

A terminal SNP or very long probe can weaken discrimination.

The Probe Is Too Long

Long probes can lose mismatch discrimination and increase background. Affinity chemistry can help shorten the probe while keeping enough Tm for the assay.

MGB LNA/BNA ZNA® Short target window

Best first choice

MGB for compact hydrolysis probes or strategic LNA/BNA inserts.

Typical effect

Maintains Tm with fewer bases and a shorter target span.

Design tip

Shorten first, then add the minimum affinity chemistry needed.

Watch out

Do not combine long GC-rich probes with excessive affinity chemistry.

Multiplex Probe Panel Needs Balancing

Multiplex performance depends on Tm balance, channel separation, quencher compatibility and probe concentration. Affinity chemistry should not create one overly dominant probe.

Balanced LNA/BNA Matched dyes Dark quenchers Double quencher

Best first choice

Balance Tm and dye channels before adding additional affinity chemistry.

Typical effect

Improves panel uniformity and reduces channel imbalance.

Design tip

Use spectrally separated reporters and compatible quenchers.

Watch out

Channel overlap and probe concentration issues cannot be fixed by affinity chemistry alone.

Fluorescence Background Is High

If signal-to-background is poor, the best solution may be dye–quencher design rather than more affinity chemistry.

BHQ QSY Internal quencher MGB-NFQ Double quencher

Best first choic

Match quencher absorption to dye emission and probe length.

Typical effect

Lower baseline and improved signal-to-background ratio.

Design tip

Avoid 5′ G next to certain fluorophores and consider internal quenching for longer probes.

Watch out

Wrong dye–quencher pairing can look like a chemistry or Tm problem.

Important design note: Use the minimum affinity enhancement necessary to solve the design challenge. More modification is not always better, especially for SNP, mutation and rare-allele discrimination.

Interactive Applications Selector

Where Affinity-Enhanced Probes Are Most Useful

Select an application to see the recommended chemistry, design focus and common pitfalls.

Select an application

SNP Genotyping — use affinity-enhanced chemistry to distinguish one allele from another.

Chemistry

MGB / LNA/BNA

SNP site

middle third

Length

short-to-moderate

Risk

over-stabilization

Recommended Probe

MGB probe, limited LNA/BNA probe or paired allele-specific hydrolysis probes.

Design Focus

Center the SNP, keep the probe compact and tune Tm without binding the mismatch allele.

Common Problem

Both alleles generate signal when the probe is too long or too heavily modified.

Mutation & Variant Detection — improve discrimination for closely related sequences.

Chemistry

MGB / ENA / cEt

Targets

variant / AMR

Focus

ΔTm

Risk

false positive

Recommended Probe

MGB or affinity-enhanced hydrolysis probe; molecular beacon if low background is critical.

Design Focus

Place the discriminating base where mismatch most strongly destabilizes the probe.

Common Problem

Mutation at the probe end may not create enough signal difference.

Rare Allele Detection — improve signal difference against abundant wild-type sequence.

Chemistry

MGB / limited LNA

Focus

low background

Dye

bright reporter

Risk

WT signal

Recommended Probe

Short MGB probe or carefully positioned LNA/BNA probe with a matched dark quencher.

Design Focus

Maximize mutant signal while minimizing wild-type cross-reactivity.

Common Problem

Affinity chemistry can help, but too much can make the wild-type bind too strongly.

Digital PCR — improve cluster separation and allele-specific signal.

Dyes

FAM / HEX

Chemistry

MGB / LNA

Focus

clean clusters

Risk

rain

Recommended Probe

FAM/HEX allele probes with balanced Tm and minimal crosstalk.

Design Focus

Avoid excessive affinity chemistry that creates intermediate partitions or rain.

Common Problem

Poor cluster separation caused by weak signal, background or over-stabilized probes.

FISH & Hybridization Probes — increase target binding and specificity for imaging or hybridization assays.

Chemistry

PNA / LNA / BNA

Target

hybridization

Focus

specificity

Labels

dye / NIR

Recommended Probe

PNA, LNA/BNA or modified hybridization probe depending on target accessibility.

Design Focus

Balance affinity, stringency, wash conditions and fluorophore selection.

Common Problem

Very high-affinity probes can increase off-target background if stringency is not optimized.

Pharmacogenomics & Genotyping Panels — design allele-specific probe sets for clinically relevant research markers.

Markers

CYP / TPMT / DPYD

Chemistry

MGB / LNA

Format

multiplex

Risk

homologs

Recommended Probe

Allele-specific MGB or LNA/BNA probe panels with instrument-matched dye channels.

Design Focus

Check homologous genes, pseudogenes, allelic variants and multiplex dye compatibility.

Common Problem

Pseudogene cross-reactivity or poor multiplex balance can affect genotype calls.

Advanced Chemistry Platform

Choose the Right Affinity-Enhancing Chemistry

The best chemistry depends on whether the assay needs local Tm boost, shortest probe length, native sequence preservation, nuclease stability or specialized hybridization behavior.

Select a probe design challenge

LNA/BNA, ENA and cEt for Local Affinity Boost

Locked and bridged nucleic acid chemistries increase duplex stability and can improve mismatch discrimination when placed strategically near weak regions or discriminating bases.

LNA BNA ENA cEt 2–6 inserts typical Avoid long runs

Best for

SNP genotyping, mutation detection, GC-poor targets and compact qPCR/dPCR probes.

Design value

Local Tm lift and mismatch discrimination.

Use caution

Avoid excessive LNA/cEt density and 5′ reporter-adjacent placement.

BSI support

Modification placement, dye pairing and probe manufacturability review.

MGB for the Shortest High-Tm Probe Span

Minor groove binder chemistry stabilizes short probes and is especially useful for allele discrimination, short target windows and high-specificity hydrolysis probe formats.

3′ MGB NFQ options Short probes SNP assays Variant detection

Best for

Short high-specificity probes and allele discrimination.

Design value

Maintains high Tm without making the probe longer.

Use caution

Keep amplicon design and probe location optimized around the discriminating base.

BSI support

MGB probe synthesis and reporter/quencher selection.

ZNA® for Uniform Tm Lift Without Base Substitution

ZNA® polycation chemistry can raise Tm more uniformly while preserving the native probe sequence, which can be useful when the sequence cannot be easily modified.

ZNA® +2 to +6 charge Native bases preserved Salt tolerance Uniform Tm lift

Best for

Designs where base substitution is not preferred.

Design value

Electrostatic Tm boost without changing A/T/G/C sequence.

Use caution

Charge selection should be matched to target, buffer and assay format.

BSI support

ZNA® design and custom synthesis feasibility review.

PNA for Specialized High-Affinity Hybridization

PNA offers a neutral backbone and very strong binding behavior, making it useful for hybridization probes, FISH and PCR clamp-style applications.

PNA Neutral backbone PCR clamp FISH probes Custom labeling

Best for

FISH, PCR clamping, hybridization probes and difficult recognition challenges.

Design value

High affinity and strong mismatch discrimination.

Use caution

Not a direct replacement for all standard qPCR hydrolysis probe formats.

BSI support

PNA probe feasibility, labeling and conjugation review.

2′-O-Me and 2′-F for Stability and Hybridization Control

Sugar modifications can improve nuclease resistance, hybridization behavior and stability in demanding sample matrices, but should be balanced to avoid excessive affinity.

2′-O-Me 2′-F Stability Hybridization control Balanced kinetics

Best for

Harsh matrices, stability-sensitive assays and hybridization control.

Design value

Improves nuclease resistance and adjusts hybridization behavior.

Use caution

Combine sparingly with LNA/cEt to avoid over-stabilization.

BSI support

Patterning review and custom modified probe synthesis.

Dye–Quencher Pairing for Signal and Background Control

Reporter and quencher choice can determine signal-to-background ratio, multiplex compatibility and assay readability. Affinity-enhanced probes must be paired with compatible fluorophores and quenchers.

FAM HEX Cy3 ROX Cy5 BHQ QSY Iowa Black

Best for

qPCR/dPCR readout, multiplex panels and signal optimization.

Design value

Controls background and channel separation.

Use caution

Avoid 5′ G next to certain dyes and match quencher to emission range.

BSI support

Reporter, quencher and double-quenched layout support.

Chemistry Decision Tool

Which Affinity-Enhancing Chemistry Fits Your Design?

Select a chemistry to compare practical strengths, typical Tm effect, compatible modifications and design cautions. This replaces a wide scrolling table with a focused decision-support view.

MGB Performance

SNP discrimination ●●●●●

Mutation detection ●●●●●

qPCR ●●●●●

dPCR ●●●●●

Multiplex ●●●●●

FISH / imaging ●●●●●

MGB Design Guidance

Typical Tm increase

Often +8 to +15°C, sequence and format dependent.

Best for

Short hydrolysis probes, SNP assays, mutation detection and difficult qPCR targets.

Compatible Chemistries

BHQ, NFQ, FAM, HEX, Cy dyes and compact probe designs.

Design considerations

Already high-Tm probes, very GC-rich probes and excessive LNA additions.

Typical Design Strategy

Keep the probe short, center the SNP or mutation, and avoid extending the probe length unnecessarily.

5′ Reporter Probe + 3′ MGB-NFQ

LNA/BNA Performance

SNP discrimination ●●●●●

Mutation detection ●●●●●

qPCR ●●●●●

dPCR ●●●●●

Multiplex ●●●●●

FISH / imaging ●●●●●

LNA/BNA Design Guidance

Typical Tm increase

Often about +2 to +8°C per insert, depending on sequence context.

Best for

Local Tm boost, SNP discrimination, GC-poor regions and compact probes.

Compatible Chemistries

BHQ, Cy5, FAM, molecular beacons and selected multiplex designs.

Design considerations

Too many LNA bases, long LNA runs and very high final probe Tm.

Typical Design Strategy

Use 1–3 strategic insertions first, avoid consecutive LNA bases, and increase affinity gradually.

5′ Dye DNA + strategic LNA/BNA inserts + quencher

ZNA® Performance

SNP discrimination ●●●●●

Mutation detection ●●●●●

qPCR ●●●●●

dPCR ●●●●●

Multiplex ●●●●●

FISH / imaging ●●●●●

ZNA® Design Guidance

Typical Tm increase

Progressive, charge-dependent Tm increase without changing base identity.

Best for

Native-sequence probes that need a uniform affinity increase.

Compatible Chemistries

Standard reporters, dark quenchers and qPCR probe formats.

Design considerations

Unreviewed charge selection and designs where local mismatch control is needed.

Typical Design Strategy

Use when the native sequence should be preserved while Tm is lifted through charge-dependent stabilization.

ZNA® tail Native DNA probe + reporter/quencher

PNA Performance

SNP discrimination ●●●●●

Mutation detection ●●●●●

qPCR ●●●●●

dPCR ●●●●●

Multiplex ●●●●●

FISH / imaging ●●●●●

PNA Design Guidance

Typical Tm effect

Very high affinity and strong hybridization behavior.

Best for

FISH, hybridization probes, imaging, clamp PCR and specialty recognition.

Compatible Chemistries

Fluorophores, linkers, peptide-style conjugation and imaging labels.

Design considerations

Assuming PNA is a direct replacement for standard qPCR hydrolysis probes.

Typical Design Strategy

Use for hybridization, FISH, imaging or clamp designs rather than as a universal qPCR substitute.

PNA probe Fluorophore / linker / conjugate

2′-OMe / 2′-F Performance

SNP discrimination ●●●●●

Mutation detection ●●●●●

qPCR ●●●●●

dPCR ●●●●●

Multiplex ●●●●●

FISH / imaging ●●●●●

2′-OMe / 2′-F Design Guidance

Typical Tm effect

Modest to moderate increase with improved stability and hybridization control.

Best for

Stability-sensitive probes, difficult matrices and hybridization tuning.

Compatible Chemistries

LNA/BNA, dyes, quenchers and selected backbone strategies.

Design considerations

Combining too many stabilizing modifications without checking final Tm.

Typical Design Strategy

Use to improve stability or hybridization behavior while monitoring total Tm contribution.

Modified sugar pattern Probe + reporter/quencher

ENA/cEt Performance

SNP discrimination ●●●●●

Mutation detection ●●●●●

qPCR ●●●●●

dPCR ●●●●●

Multiplex ●●●●●

FISH / imaging ●●●●●

ENA/cEt Design Guidance

Typical Tm effect

Strong local affinity increase, often similar to or greater than LNA depending on context.

Best for

Advanced affinity tuning, difficult SNPs and compact mutation probes.

Compatible Chemistries

Standard dyes, dark quenchers and selected LNA/BNA-style designs.

Design considerations

High-density placement without checking over-stabilization risk.

Typical Design Strategy

Use as an advanced affinity-tuning option and avoid dense placement without Tm review.

DNA + ENA/cEt inserts Affinity-tuned reporter probe

Best for SNP

MGB / LNA

Highest affinity

PNA

Native sequence

ZNA®

Best for qPCR

MGB

Best stability

2′-OMe / 2′-F

Fine tuning

ENA / cEt

Interpretation note: Filled circles are relative design guidance, not absolute performance ratings. Final selection depends on sequence, target, assay format and validation conditions.

Best-practice principle: Use the minimum affinity enhancement necessary to solve the design challenge. More modification is not always better, especially for SNP, mutation and rare-allele discrimination.

Combination Chemistry

Common Affinity Chemistry Combinations

Yes, many probe chemistries can be combined, but the design should avoid unnecessary over-stabilization. These examples show common combinations and caution points.

Need more than one modification?

Many high-performance probes combine affinity enhancers, fluorophores, dark quenchers, internal quenchers, spacers or specialty handles. Bio-Synthesis can help balance multi-modification designs so the final probe is specific without becoming over-stabilized.

MGB + BHQ / NFQ

Excellent

Standard qPCR and RT-qPCR pathogen detection probes with 5′ fluorophore and 3′ quencher chemistry.

LNA/BNA + BHQ

Excellent

Useful for local Tm boost and mismatch discrimination in qPCR or dPCR probes.

LNA/BNA + MGB

Use sparingly

Can be useful for difficult assays, but too much combined affinity may reduce specificity.

ZNA® + FAM / HEX

Good fit

Helps raise Tm while preserving the native probe sequence and standard reporter layout.

PNA + Fluorophore

Common

Frequently used in hybridization, FISH, clamp-style and imaging probe formats.

2′-OMe / 2′-F + LNA

Balance needed

Can combine stability and affinity, but modification patterning must be controlled.

Internal Q + Long probe

Useful

Internal or double-quenched formats can improve background for longer probe designs.

Many LNA + High GC

Avoid excess

May over-stabilize the probe and reduce SNP or mutation discrimination.

Design Caution

When Not to Add More Affinity Chemistry

Affinity-enhancing modifications are powerful, but some probe problems are better solved by sequence redesign, primer repositioning, dye–quencher changes or assay optimization.

Probe Tm is already high

If the probe is already above the desired Tm window, more LNA, MGB or cEt may increase background.

Probe is already long and GC-rich

High-GC long probes may bind mismatched targets too well. Shorten or reposition before adding chemistry.

SNP is near the probe end

Terminal mismatches are often tolerated. Reposition the probe or amplicon before increasing affinity.

Secondary structure is strong

Hairpins, dimers or target folding should be addressed before adding more modifications.

Multiplex channels overlap

More affinity chemistry will not fix poor dye spacing, wrong quenchers or spectral bleed-through.

Probe already binds both alleles

Reduce probe length, remove affinity modifications or rebalance Tm instead of adding more stabilization.

Practical Troubleshooting

Common Affinity-Enhanced Probe Problems

Most issues come from too much Tm increase, over-modification, poor dye-quencher matching or unfavorable sequence placement.

Tm

Tm Increased Too Much

What happens

Matched and mismatched targets both generate signal.

Why it happens

Too many affinity bases, MGB plus high-GC sequence or probe too long.

How to fix

Remove some modifications, shorten probe, reposition LNA/BNA or consider ZNA® for smoother Tm lift.

LNA

Probe Is Over-Modified

What happens

Probe loses ability to discriminate a one-base mismatch.

Why it happens

LNA/cEt clustered too closely or too many inserts across the probe.

How to fix

Use minimal effective modification density and avoid long LNA/cEt runs.

Dye-Quencher Pairing

Reporter and Quencher Selection

Affinity-enhanced probes need compatible reporter and quencher chemistry, especially for short probes, MGB-NFQ formats, double-quenched probes and multiplex dPCR.

Green Channel

FAM is a common primary channel. Pair with BHQ-1, QSY7 or Iowa Black FQ.

Yellow / Orange Channel

HEX, VIC-compatible dyes, Cy3 and ATTO 550 support duplex or multiplex designs.

Red Channel

ROX, TAMRA and Texas Red typically pair with BHQ-2 or related quenchers.

Far-Red Channel

Cy5 and ATTO 647N can support low bleed-through multiplex designs.

Common Pairing Map

FAM BHQ-1 / QSY7

HEX / VIC BHQ-1 / QSY7

Cy3 / ATTO 550 BHQ-2 / QSY9

ROX / TAMRA BHQ-2 / QSY21

Cy5 / ATTO 647N BHQ-3 / BBQ-650

MGB probes

Often pair with 3′ MGB-NFQ formats for low background and compact probe design.

LNA/ZNA probes

Can pair with BHQ, QSY, BBQ or double-quenched layouts depending on emission range.

Full dye list

Review additional dye options at Fluorescent-Labeled Oligonucleotides.

Beyond Standard Modifications

Bio-Synthesis Can Modify More Than Listed

Affinity-enhanced probe design often requires more than one catalog modification. Bio-Synthesis can evaluate standard, advanced and custom chemistries for research probe engineering when feasible.

Custom Probe Engineering Capabilities

Use this section to invite customers to ask about modifications not shown on the page. Many specialized projects require custom placement, internal labels, unusual dyes, proprietary handles, or customer-specified building blocks.

✔

Modified Bases

LNA/BNA, ENA, cEt, 5-Me-dC, 2,6-DAP and custom base analogs.

✔

Sugar Modifications

2′-O-Me, 2′-F, FANA, UNA and related analogs when compatible.

✔

Backbone Analogs

PNA, PMO, phosphorothioate, PACE and other specialized backbones.

✔

Internal Labels

Internal amino modifiers, internal fluorophores and internal quenchers.

✔

Fluorophores

FAM, HEX, Cy dyes, Alexa Fluor®, ATTO, NIR dyes and specialty reporters.

✔

Quenchers

BHQ, QSY, Iowa Black, BBQ, Dabcyl and double-quenched formats.

✔

Spacers & Handles

HEG, TEG, Spacer 9/18, PEG, amino, azide, alkyne and click handles.

✔

De Novo Chemistry

Custom nucleotides, novel base analogs and feasibility-reviewed probe architectures.

Need something not listed? Send the target sequence, desired modification, assay format and any preferred reagent or structure. Bio-Synthesis can review feasibility, placement and synthesis strategy.

Specs & QC

Build Specifications and Quality Support

Typical Length

14-22 nt, depending on chemistry, GC content and target design.

Chemistries

LNA/cEt, BNA, ZNA®, MGB, 2′-O-Me, 2′-F, PNA and dye/quencher options.

Purification

HPLC standard; dual-HPLC/UPLC available on request.

QC

Analytical HPLC, MS where compatible, UV/OD yield and COA.

Related Services

Related Probe & qPCR Services

MGB

MGB Probes

Minor groove binder probes for short high-Tm spans and tight discrimination.

→

DL

Dual-Labeled Hydrolysis Probes

Standard hydrolysis probes matched to affinity-enhanced designs.

→

MB

Molecular Beacons

Stem-loop probes for low-background mutation and pathogen detection research.

→

Mx

Multiplex qPCR Probes

Balanced dye/quencher panels for multi-target assays.

→

Contact & Quote Request

Need Probe Design Support?

Need help choosing MGB, LNA/BNA, ZNA® or PNA?

Share your target sequence, assay platform, SNP or mutation position, instrument channels, preferred dye/quencher, sample type, scale and QC requirements.

Request a Quote Speak to a Scientist

Need help before quoting?

Email: info@biosyn.com

Phone: 800-227-0627 (US/CAN)

Phone: +001-972-420-8505 (INT)

Tm

Design Review

Probe length, Tm, chemistry placement, SNP position and multiplex channel review.

MGB

Chemistry Selection

MGB, LNA/BNA, ENA, cEt, ZNA®, PNA and dye-quencher options.

Quality Systems

Quality Systems & Manufacturing Support

Affinity-enhanced probe design requires controlled synthesis, labeling, purification, analytical QC, sequence handling and project-specific documentation. Bio-Synthesis supports research probe programs from sequence review through finished probe delivery.

QMS

ISO-Supported Oligonucleotide Manufacturing Platform

Bio-Synthesis supports custom MGB probes, LNA/BNA probes, ZNA® probes, PNA probes, dye–quencher labeled probes, molecular beacons, dPCR probes, multiplex probe panels, advanced base chemistries, purification, analytical QC, documentation and project-specific packaging.

ISO 9001:2015 Quality management system

ISO 13485:2016 Medical-device quality framework

Analytical QC HPLC/UPLC, MS where compatible, OD260, CoA and traces

Custom Programs qPCR, dPCR, SNP, mutation, FISH and advanced probe chemistry

Controlled synthesis

Custom DNA, modified bases, specialty backbones and labeling formats.

Purification options

HPLC, cartridge-based purification and project-specific cleanup strategies.

Analytical documentation

COA, OD yield, analytical traces and MS where compatible with chemistry.

Project packaging

Aliquoting, plates, dry-down, concentration targets and light-protected handling.

Affinity-Enhanced Probe Literature & Technical Background

Obika S, Nanbu D, Hari Y, et al. Novel bicyclic nucleosides having a fixed C3′-endo sugar puckering. Tetrahedron Letters. 1997.
Kutyavin IV, Afonina IA, Mills A, et al. 3′-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Research. 2000.
Letertre C, Perelle S, Dilasser F, Arar K, Fach P. Evaluation of LNA and MGB probes in 5′-nuclease PCR assays. Molecular and Cellular Probes. 2003.
Vester B, Wengel J. LNA: high-affinity targeting of complementary RNA and DNA. Biochemistry. 2004.

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Affinity-Enhanced Probe Synthesis

Affinity-Enhanced Probe Chemistry for Difficult Targets

Shorter Probes

Higher Specificity

Avoid Over-Stabilization

Design Support

What Probe Design Problem Are You Trying to Solve?

Probe Tm Is Too Low

Best first choice

Typical effect

Design tip

Watch out

Specificity Is Poor

Best first choice

Typical effect

Design tip

Watch out

SNP or Mutation Discrimination Is Needed

Best first choice

Typical effect

Design tip

Watch out

The Probe Is Too Long

Best first choice

Typical effect

Design tip

Watch out

Multiplex Probe Panel Needs Balancing

Best first choice

Typical effect

Design tip

Watch out

Fluorescence Background Is High

Best first choic

Typical effect

Design tip

Watch out

Where Affinity-Enhanced Probes Are Most Useful

Recommended Probe

Design Focus

Common Problem

Recommended Probe

Design Focus

Common Problem

Recommended Probe

Design Focus

Common Problem

Recommended Probe

Design Focus

Common Problem

Recommended Probe