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Custom Oligopaint Probes for DNA & RNA FISH

Sequence-defined oligonucleotide probe libraries for DNA FISH, RNA FISH, chromosome imaging, genomic locus visualization, MERFISH-style readouts, DNA-PAINT and multiplex spatial biology workflows.

Oligopaint Probes DNA FISH Multiplex Imaging Spatial Genomics
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Overview Architecture Formats Design Modifications Advanced Workflow QC Related FAQ Contact Reading
Overview

What Are Oligopaint Probes?

Oligopaint probes are synthetic, sequence-defined oligonucleotide libraries designed for highly specific fluorescence in situ hybridization (FISH) applications. Unlike traditional long-probe or clone-based systems, Oligopaint designs use short, computationally selected oligonucleotides that hybridize to defined genomic DNA or RNA targets with modular sequence architecture and scalable synthesis.

At the most basic level, an Oligopaint probe contains a target-binding region that hybridizes to the sequence of interest, and it may also include readout sequences, primer sites, adapter segments, amplification handles, or barcode regions depending on the imaging workflow. This modularity makes Oligopaint libraries useful for chromosome painting, genomic locus imaging, RNA visualization, super-resolution microscopy, and multiplexed sequential imaging strategies.

Because the probes are sequence-defined and synthetically produced, Oligopaint platforms provide strong control over probe density, target specificity, readout structure, and labeling flexibility. This makes them especially attractive when traditional probe sources are too coarse, insufficiently modular, or difficult to scale for high-content imaging experiments.

Oligopaint probes are best understood as a probe design platform: a modular oligonucleotide architecture that can be adapted for DNA FISH, RNA FISH, chromosome painting, barcoded imaging, DNA-PAINT, and more complex hybridization workflows.

Oligopaint probe libraries can be supplied unlabeled or manufactured with fluorescent dyes, haptens, affinity-enhancing modifications, barcode sequences, docking strands, amplification handles, and custom conjugation chemistries to support chromosome painting, DNA FISH, DNA-PAINT, multiplex imaging, super-resolution microscopy, and spatial genomics workflows.

Probe Architecture

Representative Oligopaint Probe Architecture

Oligopaint probes are modular synthetic oligonucleotides. A single probe may contain a genomic target-binding sequence plus optional primer sites, barcode segments, readout domains, spacers, labels, haptens, or docking sequences depending on the experiment.

Representative Oligopaint probe architecture showing primer site, target-binding region, adapter or barcode segment, and readout sequence
Representative Oligopaint Probe Architecture. A typical Oligopaint probe may include a primer site, target-binding region, adapter or barcode segment, and readout sequence. The exact layout depends on whether the probe is used for direct DNA FISH, chromosome painting, readout-probe imaging, MERFISH-ready workflows, or DNA-PAINT.
Architecture Component Purpose When It Is Used
Primer Site Supports amplification, indexing, conversion, or library generation workflows. Probe-pool amplification, custom library preparation, barcoded imaging workflows.
Target-Binding Region Hybridizes to the genomic DNA or RNA target sequence. Core element for DNA FISH, RNA FISH, chromosome imaging, and locus-specific probes.
Adapter / Barcode Segment Encodes target identity or links the probe to a readout strategy. Multiplex DNA imaging, spatial genomics, sequential imaging, MERFISH-ready designs.
Readout Sequence Allows secondary fluorescent readout probes to bind. Sequential imaging, multiplex panels, indirect detection, reusable probe libraries.
Fluorophore Provides direct fluorescent detection. Direct Oligopaint probes, chromosome painting, DNA FISH, readout probes.
Biotin / DIG / Hapten Enables streptavidin or antibody-based detection and signal amplification. Indirect FISH, cytogenetics-style workflows, amplification strategies.
DNA-PAINT Docking Site Recruits transient fluorescent imager strands for super-resolution imaging. DNA-PAINT, Exchange-PAINT, super-resolution genome imaging.
Spacer or Modified Base Improves accessibility, spacing, affinity, or stability. Central labeling, difficult targets, imaging optimization, custom conjugation.

Flexible Architecture, Not One Fixed Design

Not every Oligopaint probe contains every component shown above. A simple direct-labeled DNA FISH probe may only require a target-binding region and fluorophore, while multiplex or MERFISH-ready designs may include primer sites, barcode regions, readout handles, spacers, docking sequences, and optional modified bases.

Direct DNA FISH Chromosome Painting Readout Probes MERFISH-Ready DNA-PAINT Spatial Genomics
Technology Positioning

Oligopaint vs Chromosome Painting vs MERFISH, seqFISH and DNA-PAINT

These terms overlap, but they are not interchangeable. This section keeps your Oligopaint page distinct from chromosome painting, MERFISH, seqFISH and DNA-PAINT pages.

Technology Primary Target Probe Architecture Main Goal Best Page Focus
Chromosome Painting Whole chromosome or chromosome territory BAC, cosmid, chromosome library or oligo-based paint Visualize chromosome identity, territory, translocation or cytogenetic structure Cytogenetics and whole chromosome visualization
Oligopaint DNA genomic loci, regions or chromosomes Sequence-defined synthetic oligo libraries Genome imaging, DNA FISH, chromosome architecture, multiplex imaging Advanced synthetic probe-library platform
DNA FISH DNA sequence or locus Probe set targeting genomic DNA Localize genomic sequences in cells or tissue Broad DNA localization workflow
smFISH RNA transcript Many short RNA-targeting oligos Single-molecule RNA detection RNA transcript counting
MERFISH / seqFISH RNA transcriptome Barcoded sequential FISH readout probes High-plex spatial transcriptomics RNA barcoding and spatial transcriptomics
DNA-PAINT DNA docking sites or labeled targets Docking strands plus transient imager strands Super-resolution localization microscopy Docking/imager architecture and super-resolution
Oligopaint Formats

Build the Library Around the Genomic Imaging Goal

Oligopaint-style libraries can be configured for chromosome painting, locus-specific DNA FISH, dense tiling, multiplex imaging or DNA-PAINT workflows.

Select an Oligopaint format

Oligo-Based Chromosome Painting — sequence-defined alternative to traditional chromosome paints.

Best for
chromosome territories
Target scale
Mb to chromosome
Labels
direct or indirect
Focus
specificity

Use Case

Whole chromosome or large segment visualization in metaphase spreads, nuclei or tissue sections.

Design Focus

Repeat masking, large-region tiling, fluorophore strategy and signal balance.

Internal Link Strategy

Cross-link to Chromosome Painting Probes for cytogenetic applications.

Locus-Specific Libraries — probe pools for genes, enhancers, structural variants or genomic intervals.

Best for
DNA FISH loci
Target scale
kb to Mb
Labels
dye / barcode
Focus
precision

Use Case

Visualize one gene, enhancer cluster, copy-number region or structural variant breakpoint.

Design Focus

Target uniqueness, sufficient probe density, Tm matching and off-target filtering.

Output

Directly labeled or readout-compatible oligo pool for targeted imaging.

Dense Tiling Libraries — high probe density for stronger signal or fine-scale genomic mapping.

Best for
architecture
Target scale
variable
Labels
pool-based
Focus
coverage

Use Case

Genome architecture, TAD-level studies, chromatin tracing and structural organization.

Design Focus

Probe density, balanced Tm, repeat exclusion and region segmentation.

Output

High-complexity tiling pool compatible with direct or indirect detection.

Multiplex Oligopaint Libraries — barcoded targets for sequential or multi-color genome imaging.

Best for
multi-region imaging
Architecture
barcodes
Labels
readout probes
Focus
orthogonality

Use Case

Image multiple loci, chromosome segments or genomic compartments in one experiment.

Design Focus

Orthogonal readout domains, color balance, sequential imaging and code-space planning.

Output

Barcoded Oligopaint pool with readout sequences and optional amplification handles.

DNA-PAINT Compatible Oligopaints — docking-sequence libraries for super-resolution localization microscopy.

Best for
super-resolution
Architecture
docking sites
Labels
imager strands
Focus
kinetics

Use Case

Super-resolution mapping of genomic loci or chromosome structures using transient imager binding.

Design Focus

Docking sequence placement, imager compatibility, density and localization precision.

Output

Oligopaint library carrying DNA-PAINT docking domains for imager-strand readout.

Design Considerations

Design Considerations for Oligopaint Probes

Design is one of the most important parts of an Oligopaint project. Probe performance depends on target selection, probe density, repeat filtering, barcode architecture, fluorophore strategy, and optional affinity or stability modifications.

Select a design topic

Target, Probe Density & Length — define the region and balance signal strength, specificity, and manufacturability.

Targets
chromosome, locus, gene
Probe length
~32–60 nt
Density
application dependent
Focus
uniform coverage

Target Selection

Start with chromosome, chromosome arm, genomic interval, gene cluster, enhancer region, structural variant, or RNA target depending on the application.

Probe Density

Higher density can improve signal but may increase off-target risk and library complexity. Density should match target size and imaging goal.

Tm Matching

Candidate probes should be designed within a practical Tm range to support uniform hybridization across the library.

Repetitive Sequence Management — avoid repetitive and low-complexity targets to reduce background.

Remove
LINE/SINE/satellite
Check
genome uniqueness
Focus
off-target control
Risk
background signal

Repeat Masking

Computational filtering helps remove LINEs, SINEs, satellite DNA, low-complexity regions, and repetitive genomic elements.

Cross-Hybridization

Candidate sequences should be screened against the target genome to reduce unwanted binding to related loci.

Control Strategy

No-probe, scrambled, competitor, and non-target controls can help evaluate background and specificity.

Barcode and Readout Architecture — add primer handles, barcodes, readout sequences, and adapters when multiplex or sequential imaging is needed.

Architecture
primer-target-barcode
Use
sequential imaging
Focus
orthogonality
Risk
cross-readout

Primer Handles

Forward and reverse primer sites can support amplification, indexing, and conversion workflows.

Readout Barcodes

Orthogonal readout domains support sequential imaging, multiplex DNA FISH, and MERFISH-ready architectures.

Spacer Placement

Spacer 9, Spacer 18, HEG, or TEG can reduce steric interference between target-binding, barcode, and readout domains.

Affinity, Stability and DNA-PAINT Design — tune the architecture for difficult targets, nuclease-sensitive workflows, or super-resolution imaging.

Chemistry
LNA/BNA/ENA
Protection
PS / 2′ mods
PAINT
docking sites
Focus
balance

Affinity Enhancement

LNA, BNA, ENA, 2′-O-Me, or 2′-F modifications may help difficult targets, short probes, or stability-sensitive workflows.

Stability Optimization

Terminal phosphorothioate protection or stabilized bases can be considered for cell-based or nuclease-exposed workflows.

DNA-PAINT Docking

Docking sequences can be added for transient imager-strand binding in DNA-PAINT and Exchange-PAINT experiments.

Important design principle: Oligopaint probes should be optimized as a complete architecture, not only as individual oligo sequences. Target-binding regions, barcodes, dyes, spacers, readouts, and modifications all affect final imaging performance.

Labeling & Modification Options

Oligopaint Probe Labeling, Barcode & Modification Options

Oligopaint-style libraries are programmable imaging architectures. Bio-Synthesis can incorporate terminal labels, internal modifications, haptens, readout domains, barcode sequences, docking strands, amplification handles, spacers, and affinity-enhancing chemistries depending on the final imaging workflow.

Select a modification class

Direct Fluorescent Oligopaints — incorporate common and specialty fluorophores for direct DNA FISH, chromosome imaging, and multiplex microscopy.

Dye families
FAM, Cy, Alexa, ATTO
Position
5′ / 3′ / internal
Use
direct FISH
Focus
brightness + channel fit

Common Fluorophores

FAM, HEX, TET, TAMRA, ROX, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, Alexa Fluor, ATTO, IRDye and NIR dye options can be considered.

Terminal Labeling

5′ or 3′ dye placement supports direct Oligopaint, DNA FISH, chromosome painting, and readout probe strategies.

Multiplex Planning

Choose dye sets around microscope filters, laser lines, camera sensitivity, bleed-through risk, and sample autofluorescence.

Internal Labels and Conjugation Handles — use modified bases and handles when central labeling or post-synthesis conjugation is needed.

Handles
5′ amino / internal amino-dT
Use
conjugation
Partner
NHS ester / dye
Focus
position + spacing

Internal Amino-dT

Supports central dye placement, hapten attachment, nanoparticle coupling, surface immobilization, and custom post-synthesis conjugation.

Internal Fluorophores

Internal Cy3-dT, Cy5-dT, fluorescein-dT, or other dye-linked bases may support signal placement and architecture-specific imaging.

Spacer Modifications

C6, TEG, HEG, Spacer 9, and Spacer 18 can reduce steric hindrance between target-binding, barcode, and readout regions.

Biotin, DIG and Hapten Labels — amplify or detect Oligopaint probes using streptavidin or antibody-based readout strategies.

Labels
biotin / DIG / DNP
Detection
streptavidin / antibody
Use
amplification
Focus
background

Biotin

Supports streptavidin-fluorophore detection and optional signal amplification for chromosome painting and DNA FISH.

Digoxigenin / DNP

Hapten labels support antibody-based detection when direct fluorescent labeling is not preferred.

Dual Labeling

Combine haptens and dyes where multiplex imaging, signal amplification, or confirmatory readouts require it.

Readout Barcodes and DNA-PAINT Docking Sites — extend Oligopaint libraries into sequential imaging and super-resolution workflows.

Elements
readout / docking
Use
multiplex imaging
Architecture
primer-target-barcode
Focus
orthogonality

Readout Domains

Barcoded readout sequences enable sequential imaging and multiplex genome mapping.

DNA-PAINT Docking

Docking sequences recruit transient fluorescent imager strands for super-resolution microscopy.

Primer Handles

Amplification handles support probe pool generation, labeling, indexing, and library workflow compatibility.

Affinity and Stability Modifications — tune hybridization, nuclease resistance, and difficult target performance.

Chemistry
LNA/BNA/ENA
Stability
2′-OMe / 2′-F / PS
Use
difficult targets
Focus
balance

LNA / BNA / ENA

Can raise Tm, improve affinity, and support shorter or more specific probes where standard DNA probes are insufficient.

2′-OMe / 2′-F

May improve stability and hybridization behavior in specialized DNA/RNA imaging workflows.

Phosphorothioate

Terminal PS protection can support nuclease resistance for cell-based, crude-sample, or stability-sensitive workflows.

Common Fluorophores for Oligopaint Probe Labeling

These are common fluorophore choices for Oligopaint probe libraries, DNA FISH, chromosome painting, DNA-PAINT readout probes, and multiplex imaging. Availability depends on sequence, scale, position, purification, and conjugation strategy.

Fluorophore Approx. Emission Typical Color Common Oligopaint / FISH Applications
FAM ~520 nm Green Single-color DNA FISH, locus imaging, green-channel readout probes
HEX ~556 nm Yellow-Green Multiplex DNA FISH and secondary readout channels
TET ~538 nm Green-Yellow Legacy FISH workflows and green-yellow channel imaging
TAMRA ~580 nm Orange DNA imaging, readout probes, and orange-channel fluorescence
ROX ~610 nm Orange-Red Multiplex chromosome imaging and red-orange channel workflows
Cy3 ~570 nm Orange Oligopaint probes, chromosome painting, DNA FISH and imaging panels
Cy3.5 ~596 nm Orange-Red Expanded multiplex imaging and spectral separation
Cy5 ~670 nm Far-Red High-sensitivity Oligopaint, DNA FISH and lower-background imaging
Cy5.5 ~694 nm Near-IR Reduced autofluorescence workflows and advanced multiplex imaging
Cy7 ~767 nm Near-IR NIR imaging and advanced multi-channel workflows
Alexa Fluor 488 ~519 nm Green High-brightness DNA FISH and fluorescent readout probes
Alexa Fluor 555 ~565 nm Orange Multi-color FISH and Oligopaint imaging panels
Alexa Fluor 594 ~617 nm Red DNA FISH, chromosome imaging and multiplex fluorescence
Alexa Fluor 647 ~668 nm Far-Red Super-resolution imaging, DNA-PAINT-compatible readouts and far-red channels
ATTO 488 ~520 nm Green High-photostability imaging and green-channel probe detection
ATTO 550 ~575 nm Orange Multiplex fluorescence imaging and orange-channel readout probes
ATTO 647N ~669 nm Far-Red DNA-PAINT, super-resolution microscopy and high-photostability far-red imaging
IRDye 680RD ~694 nm Near-IR Low-background imaging and NIR-compatible workflows
IRDye 800CW ~794 nm Near-IR Advanced near-infrared imaging and multiplex fluorescence applications

Looking for a Different Fluorophore?

The fluorophores listed above represent common choices for Oligopaint probe libraries. Bio-Synthesis supports a much broader selection of fluorescent dyes, near-infrared dyes, specialty imaging fluorophores, quenchers, and custom conjugation chemistries.

Available categories include FAM, HEX, TET, TAMRA, ROX, Cy dyes, Alexa Fluor dyes, ATTO dyes, IRDye dyes, NIR fluorophores, specialty imaging dyes, internal dye modifications, and dual-label configurations.

View Complete Fluorescent Dye & Labeling Catalog →

Advanced Architecture

Advanced Architecture Considerations, Optional Functional Modifications & MERFISH-Ready Design

These advanced options are worth keeping because they separate Oligopaint as a flexible probe design platform from basic chromosome painting or simple fluorescent oligo pools.

Arch

Advanced Architecture Considerations

Oligopaint probes can include target-binding domains, primer handles, adapter segments, readout sequences, barcode regions, spacers, and docking sites. The final architecture should match whether the library is direct-labeled, readout-based, amplified, barcoded, or DNA-PAINT compatible.

Mod

Optional Functional Modifications

Fluorophores, internal amino-dT, biotin, DIG, DNP, spacers, LNA/BNA/ENA, 2′-O-Me, 2′-F, phosphorothioate protection, and custom conjugation handles can be incorporated depending on sequence, scale, and feasibility.

MER

MERFISH-Ready Design

Although Oligopaint usually targets genomic DNA and MERFISH usually targets RNA, both can use synthetic oligo libraries, barcode domains, and sequential readout logic. MERFISH-ready Oligopaint designs can include orthogonal readout sequences and adapter domains for multiplex spatial imaging workflows.

Recommended positioning: Keep MERFISH-ready content concise and clearly state that Oligopaint is primarily a DNA/genome imaging platform, while MERFISH is primarily an RNA spatial transcriptomics platform. This avoids content conflict while still capturing related search intent.

Applications

Application-Centered Oligopaint Probe Design

Oligopaint-style probe libraries support DNA imaging workflows from chromosome territories to super-resolution spatial genomics.

Select an application goal

Genome Architecture — visualize chromatin organization, locus positioning and structural relationships.

Best for
loci / TADs
Library
tiling
Readout
DNA FISH
Focus
specificity

Design

Tile selected intervals with repeat-filtered, Tm-matched oligos.

Use

Study locus position, chromatin domain organization and nuclear architecture.

Labeling

Direct dye, indirect hapten or readout probe architecture can be used.

Chromosome Territory Imaging — use oligo-based chromosome paints for whole-chromosome visualization.

Best for
chromosome paint
Library
large region
Readout
fluorescence
Focus
coverage

Design

Large-scale probe pools with repeat filtering and balanced signal.

Use

Chromosome territory mapping, translocation research and cytogenetic-style imaging.

Positioning

Link to chromosome painting content rather than duplicating cytogenetics content.

Super-Resolution Imaging — integrate docking sequences for DNA-PAINT and high-resolution localization.

Best for
DNA-PAINT
Library
docking probes
Readout
imager strands
Focus
kinetics

Design

Attach docking domains to genome-targeting oligos while preserving hybridization specificity.

Use

Super-resolution mapping of genomic loci, chromatin regions or chromosome structures.

Labeling

Fluorescence is typically delivered by transient imager strands rather than permanent dye labels.

Spatial Genomics — encode multiple genomic targets for multiplex imaging and spatial mapping.

Best for
multi-target DNA
Library
barcoded
Readout
sequential imaging
Focus
code design

Design

Use orthogonal readout domains and target-specific probe pools.

Use

Map multiple genomic features in the same cells or tissue context.

Connection

Distinct from MERFISH/seqFISH, which generally target RNA transcriptomes.

Spectral Panel Design

Example Spectral Panel Design for Multiplexed Oligopaint Imaging

Spectral panel design helps translate fluorophore availability into practical multiplex imaging. The examples below organize panel type, fluorophore, laser compatibility, and notes without creating a long scrolling table.

Select a representative spectral panel

3-Color Oligopaint Panel — practical starting point for many confocal or widefield multiplex imaging workflows.

Best for
3 targets
Lasers
488 / 561 / 647
Risk
channel bleed
Focus
separation
Panel Type Fluorophore Typical Laser Compatibility Notes
3-Color Alexa Fluor 488 or FAM 488 nm Bright green signal for locus or chromosome target 1.
3-Color Cy3 or Alexa Fluor 555 532–561 nm Orange channel with good separation from green and far-red.
3-Color Cy5 or Alexa Fluor 647 633–647 nm Far-red channel with lower autofluorescence in many samples.

4-Color Oligopaint Panel — useful for chromosome painting, locus panels, and multi-target DNA FISH.

Best for
4 targets
Lasers
488 / 561 / 594 / 647
Risk
orange-red overlap
Focus
filters
Panel Type Fluorophore Typical Laser Compatibility Notes
4-Color Alexa Fluor 488 488 nm High-brightness green channel.
4-Color Cy3 532–561 nm Reliable orange signal for Oligopaint or readout probes.
4-Color Alexa Fluor 594 or ROX 561–594 nm Red-orange channel; confirm filter separation from Cy3.
4-Color Cy5 / Alexa Fluor 647 633–647 nm Far-red channel for reduced background and strong separation.

5-Color Oligopaint Panel— advanced panel using visible and near-infrared channels.

Best for
high multiplex
Lasers
visible + NIR
Risk
spectral overlap
Focus
controls
Panel Type Fluorophore Typical Laser Compatibility Notes
5-Color Alexa Fluor 488 / FAM 488 nm Green channel for bright targets.
5-Color Cy3 / Alexa Fluor 555 532–561 nm Orange channel for moderate-to-bright targets.
5-Color Alexa Fluor 594 / ROX 561–594 nm Red-orange channel; validate separation from Cy3.
5-Color Cy5 / Alexa Fluor 647 633–647 nm Far-red channel for low-background detection.
5-Color Cy7 / IRDye 800CW 730–750+ nm NIR channel for advanced imaging systems with compatible optics.

DNA-PAINT Spectral Panel — high-photostability imager strands for super-resolution localization.

Best for
DNA-PAINT
Dyes
ATTO family
Risk
kinetics
Focus
imager design
Panel Type Fluorophore Typical Laser Compatibility Notes
DNA-PAINT ATTO 488 488 nm Green imager option with high photostability.
DNA-PAINT ATTO 550 532–561 nm Bright orange imager strand option.
DNA-PAINT ATTO 647N 633–647 nm Common far-red DNA-PAINT dye for super-resolution imaging.
DNA-PAINT Cy5 / Alexa Fluor 647 633–647 nm Alternative far-red options depending on imager kinetics and microscope configuration.

Panel design note: These are representative examples only. Final fluorophore selection should be optimized based on microscope configuration, laser lines, filter sets, detector sensitivity, sample autofluorescence, spectral overlap, imaging buffer, multiplex complexity, and experimental goals.

Workflow

Custom Oligopaint Probe Library Workflow

A successful Oligopaint project connects computational design, library synthesis, optional amplification, labeling/readout architecture, hybridization and imaging.

01
Target Region

Define chromosome, locus, interval, structural feature or genome-scale panel.

02
Probe Design

Use repeat masking, uniqueness filtering, Tm matching and density planning.

03
Architecture

Add primer handles, barcodes, docking sites, spacers or modification positions.

04
Synthesis

Manufacture oligo pools, modified oligos or fluorescent probe libraries.

05
Label / Amplify

Support direct dyes, amino conjugation, biotin/DIG or readout probe workflows.

06
QC & Delivery

Deliver with yield, concentration, documentation and custom packaging.

Manufacturing & QC

QC Strategy for Oligopaint-Style Probe Libraries

Oligopaint libraries may be delivered as sequence-defined oligo pools, modified probe sets, labeled oligonucleotides or workflow-ready components depending on project requirements.

Manufacturing & Analytical Control Matrix

QC packages may include pool yield, OD260 concentration, analytical traces for modified components, mass confirmation where compatible, library documentation, plate maps, barcodes, custom packaging and project-specific release documentation.

Pool Synthesis

High-complexity oligo pools for genome-targeted probe libraries and tiling designs.

Modification QC

HPLC, UPLC or MS confirmation for labeled or modified oligo components where applicable.

Documentation

Sequence files, plate maps, modification maps, CoA and custom project records.

Delivery Formats

Dried pools, normalized aliquots, plates, barcoded vials and project-specific packaging.

Design Review

Review target architecture, modification placement, barcode strategy and manufacturability.

Labeling Support

Direct fluorescent dyes, amino handles, biotin, DIG and indirect readout workflows.

Scale

Research-scale pools through larger custom probe-library programs.

FAQ

Are Oligopaint probes and chromosome painting probes the same?
No. Chromosome painting is an application focused on visualizing whole chromosomes or chromosome territories. Oligopaint is a synthetic oligonucleotide probe-library technology that can be used for chromosome painting, locus-specific DNA FISH, genome architecture and multiplex imaging.
What modifications can be incorporated into Oligopaint-style probes?
Options include 5′, 3′ or internal fluorophores, amino modifiers, biotin, digoxigenin, spacers, readout barcodes, DNA-PAINT docking sequences, amplification handles, LNA/BNA/ENA, 2′-OMe and terminal phosphorothioate protection.
Can Bio-Synthesis incorporate central/internal modifications?
Yes. Internal modifications such as amino-dT, biotin-dT, internal fluorophore-dT and spacer modifications can be incorporated depending on sequence, scale, design and manufacturing feasibility.
How are Oligopaint probes different from MERFISH or seqFISH probes?
Oligopaint generally targets genomic DNA. MERFISH and seqFISH usually target RNA transcripts for spatial transcriptomics, although all three use programmable oligonucleotide and readout architectures.
Can Oligopaint probes be directly fluorescently labeled?
Yes. Direct dye labels such as FAM, Cy3, Cy5, ATTO-family dyes and other fluorophores can be considered. Indirect detection using biotin or DIG is also possible.
What information is needed for a quote?
Provide target species, genome build, target region, desired probe density, labeling strategy, barcode/readout design, modification needs, scale, QC requirements and delivery format.
Can Oligopaint probes support DNA-PAINT?
Yes. Oligopaint-style probes can include docking sequences that recruit transient fluorescent imager strands for DNA-PAINT and super-resolution microscopy.
Can Bio-Synthesis help review the design?
Yes. Bio-Synthesis can review modification placement, labeling strategy, barcode architecture, dye compatibility, manufacturability and delivery format for custom Oligopaint-style libraries.
More FAQ'sAll FAQ's
Before Requesting a Quote

Information Helpful for Oligopaint Library Design

Species
genome build
Target
chromosome, locus, region
Design
density, length, Tm
Labels
dye, biotin, DIG, barcode
Workflow
DNA FISH, PAINT, spatial
QC
pool, HPLC, MS, docs
Contact & Quote Request

Need help planning an Oligopaint probe library?

Share your species, genome build, genomic target region, probe density, desired labeling strategy, barcodes or docking sequences, modification requirements, scale, purification, QC and delivery format. Bio-Synthesis can help translate your design into a manufacturable probe-library workflow.
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)
OP

Library Strategy

Review genomic target, design density, repeat filtering, readout architecture and labeling strategy.

DNA FISH DNA-PAINT Barcodes Dyes
QC

Project Support

Support pool synthesis, modified oligos, documentation, plate maps and custom packaging.

Pools HPLC MS CoA
Quality Systems

Quality Support for Oligopaint Probe Library Programs

Oligopaint libraries require coordinated control of sequence files, pool synthesis, modifications, labeling strategy, packaging and documentation.

QMS

ISO-Supported Oligonucleotide Library Platform

Bio-Synthesis supports design review, oligo pool synthesis, modified oligos, fluorescent labels, readout components, custom packaging and documentation for genome imaging and spatial biology workflows.

ISO 9001:2015 Quality management system
ISO 13485:2016 Medical-device quality framework
Analytical QC Pool yield, HPLC/UPLC, MS where compatible and CoA
Custom Programs Oligopaint, DNA FISH, DNA-PAINT, multiplex imaging and spatial genomics
Recommended Reading

Oligopaint Literature & Design Resources

Use these references to support scientific background for Oligopaint-style probe libraries, genome imaging, DNA-PAINT and computational design.

  1. Beliveau BJ, Joyce EF, Apostolopoulos N, et al. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proceedings of the National Academy of Sciences. 2012.
  2. Beliveau BJ, et al. Visualizing genomes with Oligopaint FISH probes. Current Protocols in Molecular Biology. 2014.
  3. Beliveau BJ, Boettiger AN, Avendaño MS, et al. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nature Communications. 2015.
  4. Beliveau BJ, Kishi JY, Nir G, et al. OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proceedings of the National Academy of Sciences. 2018.
  5. Hershberg EA, et al. PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments. Nature Methods. 2021.
  6. Jungmann R, et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nature Methods. 2014.

Technical note: Oligopaint designs should be evaluated within the target genome build, repeat-masking strategy, probe density, barcode architecture, modification plan, hybridization conditions and imaging platform.

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Greetings, Researchers,

Please be advised that any information, guidelines, write-ups, and oral/video/graphic content on our website are intended solely as general guidelines.
It is the researcher's sole responsibility to conduct thorough research on the design of products intended for their experiments before submitting
their designs to Biosynthesis for production feasibility review.
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