5' Pyrene Cap

5'-Pyrene Cap Oligonucleotide Modification

5'-Pyrene Cap is a fluorescent aromatic modification in which a pyrene moiety is attached to the 5' terminus of a DNA or RNA oligonucleotide. Pyrene is a polycyclic aromatic hydrocarbon well known for its exceptional photophysical properties, including high fluorescence quantum yield, excellent photostability, and the ability to form excimers when two pyrene molecules are brought into close proximity. These characteristics make 5'-Pyrene Cap a powerful tool for fluorescence-based nucleic acid research.

Unlike many conventional fluorophores, pyrene produces both monomer fluorescence and excimer fluorescence. The fluorescence profile changes in response to molecular proximity, conformational changes, or hybridization events, allowing researchers to monitor nucleic acid interactions with high sensitivity. This unique behavior has made pyrene one of the most widely used probes for studying DNA and RNA structure, hybridization dynamics, and molecular recognition.

The 5'-Pyrene Cap modification is commonly incorporated into oligonucleotides for applications including fluorescence spectroscopy, hybridization assays, molecular beacons, aptamer development, biosensor design, DNA nanotechnology, and investigations of nucleic acid folding and conformational changes. The hydrophobic pyrene group can also promote stacking interactions with neighboring nucleobases, providing additional insight into duplex stability and local structural environments.

Typical applications include:

• Fluorescence-based hybridization assays

• DNA and RNA structural studies

• Excimer fluorescence measurements

• Molecular beacon development

• Fluorescent biosensors

• Aptamer labeling

• DNA nanotechnology

• Conformational change detection

• Protein–nucleic acid interaction studies

• Molecular diagnostics

Bio-Synthesis offers 5'-Pyrene Cap-modified DNA, RNA, antisense oligonucleotides, siRNA, aptamers, and other custom oligonucleotides manufactured using optimized solid-phase synthesis. The modification can be combined with additional functional groups, including fluorophores, quenchers, biotin, amino modifiers, PEG linkers, click chemistry handles, peptides, GalNAc conjugates, and lipids, enabling multifunctional probe and conjugate design.

Each pyrene-modified oligonucleotide is available with optional HPLC or PAGE purification and comprehensive analytical characterization by LC-MS, MALDI-TOF, UV spectroscopy, and fluorescence analysis, depending on project requirements. The combination of bright fluorescence, excimer formation, and excellent photostability makes 5'-Pyrene Cap an outstanding modification for advanced nucleic acid research and biosensor development.
 

Product Information

 

Product Name:

5' Pyrene Cap

Alternate Name:

Pyrene Cap

Category:

Terminal Cap

Modification Code:

[5PyCap]

Structure:

Purification:

HPLC

Delivery Format:

Lyophilized

Shipping Conditions:

Room Temperature

Storage Conditions:

-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at 20°C) in a nuclease-free environment should be stable for years.

References/Citations:

1. Wilhelmsson LM. Fluorescent nucleic acid base analogues. Quarterly Reviews of Biophysics. 2010.
2. Okamoto A. Pyrene-labeled oligonucleotides for nucleic acid sensing and hybridization studies. Accounts of Chemical Research.
3. Blackburn GM, Gait MJ, Loakes D, Williams DM. Nucleic Acids in Chemistry and Biology. 3rd ed. Royal Society of Chemistry.
4. Lakowicz JR. Principles of Fluorescence Spectroscopy. 3rd ed. Springer.

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