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Near-Infrared (NIR) Oligonucleotide Imaging Probes

Custom NIR fluorescent probe builds for in vivo optical imaging, low-background fluorescence detection, biodistribution studies, and red-shifted fluorescence workflows.

Near-infrared oligonucleotide probes can be designed with common NIR fluorophores for DNA, RNA, siRNA, ASO, SSO, and PNA constructs with 5', 3', or internal labeling for tissue imaging, hybridization, and optical detection applications.

NIR dye labeling5' / 3' / internal labelingDNA / RNA / siRNA / ASO / PNAin vivo optical imaginglow-background fluorescence
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Overview Key features Advantages Common fluorophores Spectral guide Design considerations Selection guide Labeling positions Dyes we provide Contact

What Are Near-Infrared (NIR) Oligonucleotide Imaging Probes?

Near-infrared (NIR) oligonucleotide imaging probes are synthetic DNA or RNA molecules conjugated with red-shifted fluorescent dyes that emit in the near-infrared spectral region, typically about 650-900 nm. These probes combine sequence-specific nucleic acid recognition with NIR optical reporters to enable low-background fluorescence detection of nucleic acid targets in tissues, cells, and complex biological samples.

Compared with many visible-range fluorophores, NIR dyes can offer lower biological autofluorescence, reduced background signal, and improved optical penetration in tissue. For that reason, NIR-labeled oligonucleotide probes are widely used for in vivo optical imaging, biodistribution studies, fluorescence hybridization assays, tissue imaging, and fluorescence-based detection workflows where red-shifted signal improves contrast.

At Bio-Synthesis, custom NIR oligonucleotide probes can be designed with common near-infrared fluorophores spanning orange-red transition dyes, far-red dyes, deep NIR dyes, and advanced high-performance fluorophores. NIR labeling can be configured at the 5' end, 3' end, or internal position depending on probe architecture, spectral requirements, and imaging objectives.

NIR probe technologies are frequently used alongside broader oligonucleotide imaging probe conjugate platforms that support visible-range, near-infrared, and molecular imaging workflows. Foundational literature describing red-shifted fluorescence and NIR molecular imaging continues to inform probe selection, spectral planning, and application fit [1], [2], [3], [4].

Near-infrared oligonucleotide imaging probe showing DNA probe labeled with NIR fluorescent dye for molecular imaging
Near-Infrared Oligonucleotide Imaging Probe. Synthetic DNA or RNA probes labeled with near-infrared fluorophores enable high-contrast fluorescence imaging with reduced biological autofluorescence and improved tissue penetration compared with visible-range dyes.
NIR oligonucleotide imaging probes combine sequence-selective hybridization with red-shifted optical reporters, enabling sensitive fluorescence detection in biological systems where reduced background and improved tissue contrast are important.

Key Features of NIR Oligonucleotide Imaging Probes

Low Background Signal

Reduced biological autofluorescence can improve signal-to-background ratios in complex samples.

Deeper Optical Penetration

Red-shifted wavelengths generally penetrate tissue better than many visible-range dyes.

Flexible Probe Formats

NIR labels can be configured on DNA, RNA, siRNA, ASO, SSO, PNA, and related probe architectures.

Multiple Label Positions

5', 3', and internal labeling can be matched to hybridization, detection, and imaging goals.

Advantages of Near-Infrared Oligo Imaging Probes

Improved Tissue Contrast

  • Reduced interference from sample autofluorescence
  • Cleaner signal in tissue and whole-animal studies
  • Better contrast in challenging biological matrices

Compatibility with In Vivo Studies

  • Useful for optical biodistribution studies
  • Supports nonradioactive imaging workflows
  • Can complement therapeutic oligo tracking studies

Multiplex Potential

  • Can be combined with visible-range dyes
  • Supports multichannel detection strategies
  • Helpful when red-shifted channels are preferred

Common NIR Fluorophores We Offer

Representative fluorophore classes for NIR oligonucleotide probe builds. Exact dye availability and recommended pairing remain project-dependent.

Representative fluorophore Typical emission region Typical applications
Cy5-class dyes ~660-680 nm Far-red microscopy, fluorescence hybridization, multichannel detection, and low-background assay workflows.
Cy5.5-class dyes ~690-710 nm Tissue imaging, optical detection, and biodistribution studies that benefit from deeper red-shifted signal.
Alexa Fluor 680 / 700-class dyes ~700-720 nm Microscopy, whole-sample imaging, and optical workflows matched to established far-red channel sets.
Cy7-class dyes ~760-790 nm Deep NIR imaging, in vivo optical imaging, and whole-animal tracking concepts.
IRDye 800-class concepts ~790-820 nm NIR imaging, multiplex detection, and analytical workflows where longer wavelength emission is preferred.
Project-specific advanced NIR fluorophores Variable Custom probe builds matched to specialized instruments, multiplex experiments, or platform-specific spectral requirements.

Near-Infrared Dye Spectral Reference

Near-infrared fluorophores are typically selected based on excitation and emission wavelength compatibility with the imaging instrument. The table below summarizes representative spectral ranges for commonly used NIR dyes.

Dye Excitation (λex) Emission (λem) Typical Use
Cy5 ~649 nm ~670 nm Fluorescence microscopy and hybridization probes
Cy5.5 ~675 nm ~694 nm Analytical fluorescence detection
Cy7 ~743 nm ~767 nm Deep tissue optical imaging
IRDye 800 ~774 nm ~789–810 nm NIR imaging and multiplex assays

Design Considerations for NIR Probes

Spectral Fit

Choose fluorophores that match excitation sources, emission filters, detector sensitivity, and multiplex channel plans.

  • Plan around real instrument optics
  • Minimize spectral overlap in multicolor builds
  • Balance brightness with channel separation

Probe Architecture

Label position can influence hybridization efficiency, steric accessibility, and signal quality.

  • 5', 3', or internal labeling options
  • Avoid disrupting sequence-critical binding regions
  • Consider scaffold and linker effects when needed

Application Fit

Purification, formulation, and analytical confirmation should align with tissue imaging or in vivo optical requirements.

  • Higher sensitivity workflows may need higher purity
  • Tissue applications benefit from lower background
  • Plan controls for nonspecific retention or bleed-through

Tip: For the most useful NIR probe recommendation, share the sequence, instrument channel set, wavelength preference, target application, and whether the probe will be used in cells, tissue, or whole-animal imaging.

NIR Fluorophore Selection Guide

Selecting an appropriate near-infrared fluorophore depends on the imaging instrument, desired emission range, sample background, and whether the probe will be used for microscopy, hybridization detection, or in vivo optical imaging. In general, shorter-wavelength NIR dyes are often used for microscopy and analytical detection, while longer-wavelength dyes are favored for lower background and deeper tissue imaging.

Fluorophore class Typical range Often selected for Practical considerations
Cy5 / Alexa Fluor 647-class ~650–670 nm Microscopy, hybridization assays, fluorescence detection Good fit for red/far-red channels and common fluorescence instruments.
Cy5.5 / Alexa Fluor 680-class ~690–710 nm Lower-background imaging and analytical fluorescence workflows Useful when moving beyond visible red emission into the NIR region.
Cy7 / Alexa Fluor 750-class ~760–780 nm In vivo imaging and deeper tissue optical studies Often preferred when reduced tissue autofluorescence and stronger contrast are priorities.
IRDye 800-class ~790–820 nm High-sensitivity NIR imaging and multiplex detection Instrument compatibility and filter set should be confirmed before final dye selection.

Practical tip: The best NIR dye is usually determined by your instrument channel set, desired emission window, sample background, and whether the probe is intended for microscopy, hybridization detection, or in vivo imaging.

NIR Oligonucleotide Labeling Positions

Label position Description Typical use patterns
5' NIR labeling NIR dye attached at the 5' terminus of the oligonucleotide. Common for imaging probes, tissue imaging studies, and fluorescence hybridization workflows.
3' NIR labeling NIR dye conjugated to the 3' terminus for optical detection. Useful when sequence design or assay format favors terminal labeling away from the 5' end.
Internal NIR labeling NIR fluorophore incorporated within the oligonucleotide sequence. Useful for specialized probe architectures, structural designs, or application-specific signal placement.

NIR Dye Modifications We Provide

Expand each category to see representative NIR dye classes and common application patterns. Specific dye availability and recommended pairing remain project-dependent.

far-red hybridization multicolor
Representative dye / class Typical spectral region Common use patterns
Cy5-class dyes Far-red transition Microscopy, fluorescence hybridization assays, and low-background optical detection.
Alexa Fluor 647-class concepts Far-red visible/NIR transition Multicolor imaging workflows and instrument channels optimized for far-red signal.
ATTO far-red class concepts Far-red transition High-performance fluorescence builds where brightness or photostability is important.

low background tissue imaging optical detection
Representative dye / class Typical spectral region Common use patterns
Cy5.5-class dyes ~700 nm region Optical biodistribution studies, tissue imaging, and red-shifted fluorescence workflows.
Alexa Fluor 680 / 700-class dyes ~700-720 nm region Instruments and scanners configured for NIR-compatible far-red channels.
IRDye 680-type concepts ~700 nm region Analytical imaging, tissue studies, and fluorescence detection requiring strong red-shifted signal.

deep NIR in vivo imaging biodistribution
Representative dye / class Typical spectral region Common use patterns
Cy7-class dyes ~770-790 nm region Whole-animal optical imaging, deep tissue fluorescence, and biodistribution studies.
IRDye 800-class concepts ~790-820 nm region Near-infrared imaging, multiplex detection, and red-shifted analytical platforms.
Advanced deep NIR dyes Variable Custom studies requiring deeper NIR channels or specialized optical instrument compatibility.

advanced fluorophores bright signal project-dependent
Representative dye / class Typical spectral region Common use patterns
Alexa Fluor advanced NIR series Dye-specific Applications prioritizing brightness, photostability, or compatibility with known microscopy filter sets.
ATTO NIR-class dyes Dye-specific High-performance optical imaging and analytical workflows requiring strong signal and stability.
Project-specific advanced NIR fluorophores Variable Custom builds matched to multiplex experiments, specialized scanners, or demanding optical constraints.

Compatible Imaging Platforms

Near-infrared oligonucleotide probes can be detected using a variety of fluorescence imaging instruments including:

  • Confocal fluorescence microscopes
  • Wide-field fluorescence microscopes
  • Near-infrared optical imaging systems
  • Gel documentation and fluorescence scanners
  • Multiplex fluorescence imaging platforms

Applications of NIR Oligonucleotide Imaging Probes

In Vivo Optical Imaging

  • Whole-animal fluorescence imaging workflows
  • Tracking of probe distribution over time
  • Optical readouts without radioisotopes

Tissue & Biodistribution Studies

  • Low-background tissue imaging concepts
  • Biodistribution studies for therapeutic oligos
  • Ex vivo organ and tissue analysis

Hybridization & Detection

  • NIR fluorescence hybridization assays
  • Low-background analytical detection
  • Multichannel fluorescence workflows

Workflow: from design to delivery

1) Define the probe build

Confirm sequence, oligo type, NIR dye region or preferred fluorophore, label position, and application.

2) Build & purify

Perform NIR labeling with a synthesis strategy aligned to sequence architecture, brightness goals, and purification needs.

3) Confirm & release

Provide analytical confirmation and deliver the final NIR probe for imaging, hybridization, or optical detection use.

Fastest quoting tip: Share your probe sequence, oligo format, preferred NIR dye or wavelength range, labeling position, quantity, purification target, and the instrument or imaging application the probe will be used with.

QC & Deliverables

Analytical Confirmation

  • Analytical HPLC or UPLC profile
  • Mass confirmation when applicable
  • Sequence and modification summary

Fit-for-Purpose Purification

  • Purification aligned to the final imaging workflow
  • Handling matched to NIR fluorescence applications
  • Project-dependent format recommendations

Documentation

  • Certificate of analysis
  • Modification and labeling summary
  • Supporting analytical documentation

Related Imaging Probe Platforms

Fluorescent Oligonucleotide Imaging Probes

Visible-range fluorescent probes for microscopy, hybridization detection, and molecular imaging workflows.

Explore Fluorescent Probes

Radiolabeled Oligonucleotide Probes

Radioisotope-labeled probes for PET, SPECT, and biodistribution imaging studies.

Explore Radiolabeled Probes

Oligonucleotide Imaging Probe Conjugates

Overview of imaging probe conjugation strategies including fluorescent, NIR, and radiolabeled probe architectures.

Explore Platform

FAQ

What are near-infrared (NIR) oligonucleotide imaging probes?

Near-infrared (NIR) oligonucleotide imaging probes are DNA or RNA molecules labeled with fluorescent dyes that emit light in the ~650–900 nm spectral range. These probes combine sequence-specific hybridization with NIR fluorescence detection, enabling sensitive imaging, nucleic acid localization, and molecular detection in biological samples.

Which oligonucleotide formats can be labeled with NIR dyes?

NIR fluorophores can be incorporated into DNA, RNA, siRNA, antisense oligonucleotides (ASO), splice-switching oligonucleotides (SSO), and peptide nucleic acids (PNA), depending on the probe design and application requirements.

Can NIR probes be labeled at the 5′, 3′, or internal position?

Yes. Near-infrared fluorophores can be attached at the 5′ terminus, 3′ terminus, or internal positions within the oligonucleotide sequence depending on probe architecture, hybridization performance, and imaging objectives.

What fluorophores are commonly used for NIR oligonucleotide probes?

Common near-infrared fluorophores include Cy5, Cy5.5, Cy7, Alexa Fluor 680, Alexa Fluor 750, and IRDye dyes. These fluorophores emit between approximately 650–900 nm and are widely used for fluorescence imaging and hybridization detection workflows.

Why are near-infrared probes preferred for biological imaging?

NIR probes emit fluorescence in a spectral region where biological tissues produce lower autofluorescence and reduced light scattering. This improves signal-to-background ratios and allows deeper tissue imaging compared with visible-range fluorescent probes.

Can DNA or RNA probes be labeled with near-infrared fluorophores?

Yes. Both DNA and RNA oligonucleotides can be conjugated with NIR dyes. These labeled probes are commonly used for fluorescence imaging, nucleic acid hybridization assays, and molecular detection applications.

How should near-infrared oligonucleotide probes be designed?

NIR probe design considers probe length, hybridization specificity, fluorophore brightness, and labeling position. Proper design ensures strong fluorescence signal while maintaining efficient target binding and compatibility with the imaging instrument.

What information is needed to request a quote for custom NIR probes?

Please provide the probe sequence, oligonucleotide format, preferred dye or wavelength range, labeling position (5′, 3′, or internal), quantity, purification requirement, and intended imaging or detection application.

More FAQ'sAll FAQ's

Contact & Quote Request

For the fastest quote on custom NIR oligonucleotide imaging probes, share the sequence, probe type, preferred dye or wavelength range, labeling position, quantity, purification needs, and intended tissue imaging or optical detection workflow.

Fast quote checklist

  • Sequence and oligonucleotide format (DNA, RNA, siRNA, ASO, SSO, PNA)
  • Preferred NIR dye or wavelength range
  • 5', 3', or internal labeling preference
  • Quantity, purification target, and intended application

Fastest path

Request a Quote Speak to a Chemist

Recommended Reading & Literature References

Selected peer-reviewed literature supporting NIR fluorescence imaging, red-shifted probe design, and optical molecular imaging strategies.

  • Weissleder, R. A clearer vision for in vivo imaging. Nature Biotechnology 2001. DOI
  • Frangioni, J.V. In vivo near-infrared fluorescence imaging. Current Opinion in Chemical Biology 2003. DOI
  • Ntziachristos, V.; Ripoll, J.; Wang, L.V.; Weissleder, R. Looking and listening to light: the evolution of whole-body photonic imaging. Nature Biotechnology 2005. DOI
  • Hong, G.; Antaris, A.L.; Dai, H. Near-infrared fluorophores for biomedical imaging. Nature Biomedical Engineering 2017. DOI

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