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Custom-designed DNA, RNA, PNA and affinity-enhanced hybridization probe sets for molecular diagnostics, fluorescence imaging, cytogenetics, mutation detection and spatial biology.
Bio-Synthesis designs and manufactures custom hybridization probe sets for RNA localization, DNA detection, cytogenetics, mutation analysis, molecular diagnostics and spatial biology. Projects may range from a single fluorescent probe to large multiplex panels, PNA probes, branched DNA amplification systems or barcoded spatial transcriptomics sets.
Our scientists optimize target accessibility, probe length, hybridization Tm, probe chemistry, fluorophore selection, purification strategy and panel organization to produce hybridization probe sets tailored to your experimental objectives.
Sequence review, target accessibility, probe length, Tm balance and cross-hybridization screening.
DNA, RNA, LNA/BNA, PNA, ENA/cEt, 2′-O modifications and backbone engineering.
Broad dye portfolio with terminal, internal, dual-label and multiple-fluorophore options.
Tube, plate, pooled, barcoded and project-specific probe-set formats with analytical QC.
Select the application that best matches your experiment to explore recommended probe architectures, chemistries, fluorophore strategies and purification options.
Use multi-probe RNA panels, direct fluorescent probes or amplified architectures depending on target abundance.
Multi-probe panel or amplified system.
DNA first; LNA/BNA or PNA for difficult regions.
HPLC for labeled probes and critical panels.
Transcript abundance and expression profiling.
Use directly labeled probe sets, RNA FISH, smFISH or PNA probes for subcellular localization.
Single probe or multi-probe imaging set.
DNA, LNA/BNA or PNA.
Bright photostable visible or far-red dye.
Cellular localization and single-molecule imaging.
Use DNA, LNA/BNA, PNA or longer oligo panels for genomic targets, loci and repeat regions.
Single locus probe or genomic probe panel.
DNA, PNA or affinity-enhanced DNA.
Direct fluorophore or hapten detection.
Chromosomal loci, repeats and genomic visualization.
Use compact high-affinity probes that maximize matched-versus-mismatched discrimination.
Short allele-specific probe pair.
MGB, LNA/BNA, PNA or ENA/cEt.
Center mutation and balance probe Tm.
SNP genotyping and rare-allele detection.
Use chromosome-targeted probes, telomere probes, PNA FISH or Oligopaint-style probe sets.
Repeat probe, locus set or chromosome panel.
DNA, PNA or mixed affinity chemistry.
Direct fluorophore or multi-color panel.
Chromosome structure, telomeres and cytogenetics.
Use encoding probes, orthogonal readout probes and barcoded panels for MERFISH, seqFISH and related methods.
Encoding and readout probe system.
DNA with project-specific modifications.
Plate-based and panel-level organization.
High-plex spatial biology and transcript mapping.
Flexible, scalable and compatible with a broad range of dyes and probe architectures.
Moderate
High
Lower
General probe sets and large panels.
RNA-like hybridization and strong RNA:RNA duplex formation for selected applications.
Moderate–High
Lower without protection
RNA-focused hybridization systems.
Strategic placement raises Tm and improves mismatch discrimination while allowing shorter probes.
Position-dependent Tm lift
Mutation, FFPE and difficult targets.
Neutral-backbone probes with high affinity and strong specificity for short or structured targets.
Very High
Neutral
Short, difficult and repetitive targets.
Advanced affinity chemistries for compact high-Tm probes and sequence-specific tuning.
Advanced
Short or sequence-constrained probes.
Stability-oriented chemistries for difficult sample matrices and nuclease-sensitive workflows.
Variable
Selective placement
FFPE and stability-sensitive assays.
Choose based on transcript abundance, target accessibility and spatial resolution.
RNA FISH probe set
smFISH panel
PNA or LNA-enhanced probe
Use probe architecture according to target size, repeat content and chromosome coverage.
DNA or LNA-enhanced probe
PNA FISH
Oligopaint-style panel
Use compact probes that maximize matched-versus-mismatched discrimination.
LNA/BNA or MGB
PNA
ENA/cEt
Use amplified architectures when target abundance is too low for direct fluorescence.
bDNA amplification
Multi-probe fluorescent set
Direct probe plus amplified backup
Use encoding and readout systems with orthogonal barcodes and panel-level QC.
MERFISH
seqFISH
Barcoded spatial panel
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Increase Tm, shorten probes or improve mismatch discrimination.
Targets are short, structured or mutation-sensitive.
Excessive stabilization that reduces discrimination.
Select dye family and channel according to imaging hardware, background and multiplex needs.
Direct fluorescence or multiplex imaging is required.
Dyes with overlapping spectra in separate channels.
Increase total signal through probe count, multiple labels, branched architectures or hapten detection.
Target abundance is low.
Adding poorly specific probes simply to increase signal.
Modify charge, stability or affinity through backbone chemistry.
Stability or specialized hybridization behavior is needed.
Assuming every backbone improves every application.
Control steric distance between probe, fluorophore, hapten or conjugation handle.
Labels interfere with hybridization or detection.
Adding long spacers without a specific steric need.
Improve resistance to nucleases or harsh sample environments.
Samples or workflows expose probes to degradation.
Over-modification that changes hybridization behavior.
Increase independent target sites, move probes away from structured regions and use a brighter dye or amplified architecture.
DNA first; add limited LNA/BNA or PNA when affinity is limiting.
Adding more poorly specific probes without checking sequence quality.
Remove repetitive probes, reduce concentration and increase wash stringency.
Use standard DNA or lightly modified probes rather than heavily stabilized designs.
Keeping probes that match related transcripts or genomic repeats.
Shorten probes, redistribute target sites and avoid long GC runs.
DNA may already be sufficient; use affinity chemistry sparingly.
Adding LNA or cEt to an already over-stabilized GC-rich probe.
Select alternative accessible regions or use several shorter probes.
PNA, LNA/BNA, ENA or cEt can improve binding to difficult regions.
Over-modifying one inaccessible sequence instead of redesigning it.
Center the variant, shorten the probe and balance allele-specific Tm.
LNA/BNA, MGB, PNA or ENA/cEt.
Over-stabilization that allows both alleles to bind.
Use shorter target regions, multiple independent sites and far-red dyes.
LNA/BNA, PNA, 2′-OMe or limited PS protection.
Assuming chemistry alone can overcome damaged target material.
Balance probe count, chemistry, concentration and dye assignment across the panel.
Keep affinity profiles comparable unless one target requires specialized chemistry.
Using spectrally similar dyes as independent channels.
Avoid strongly folded or protein-bound sites.
Avoid long GC or homopolymer runs.
Use the shortest sequence that meets Tm and specificity goals.
Match probe Tm to assay conditions and panel design.
Remove strong self-structure and probe-probe interactions.
Screen related transcripts and repetitive regions.
Center SNPs or mutations when possible.
Match dye spectra to filters and sample background.
Use high-resolution purification for labeled or critical probes.
Plan analytical traces, mass confirmation where compatible, OD and COA.
Custom hybridization probes, multiplex panels, PNA probes, FISH sets and spatial probe programs with controlled synthesis, purification, analytical QC, documentation and project-specific packaging.
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