| 2-O-Methyl (OMe) |
OMe |
Sugar Modification |
Methyl group at the 2-prime hydroxyl of the ribose sugar. Enhances nuclease resistance and binding affinity to complementary RNA. |
Stability enhancement, therapeutic oligos |
| 2-Fluoro (2F) |
2F |
Sugar Modification |
Fluorine substitution at the 2-prime position. Increases thermal stability and nuclease resistance while maintaining A-form helix geometry. |
siRNA, antisense oligos, aptamers |
| Phosphorothioate (PS) |
PS |
Backbone Modification |
Non-bridging oxygen in the phosphodiester backbone replaced with sulfur. Dramatically improves nuclease resistance and protein binding. |
Therapeutic oligos, in vivo applications |
| Locked Nucleic Acid (LNA) |
LNA |
Sugar Modification |
Methylene bridge connecting the 2-prime oxygen and 4-prime carbon of the ribose. Locks the sugar in C3-endo conformation, greatly increasing binding affinity. |
Diagnostic probes, antisense therapeutics |
| Bicyclic Nucleic Acid (BNA) |
BNA |
Sugar Modification |
Conformationally restricted nucleotide analog with enhanced binding affinity and nuclease resistance similar to LNA. |
Gene silencing, diagnostic assays |
| 5-Methylcytosine (5-Me-dC) |
5-Me-dC |
Base Modification |
Methyl group at the 5-position of cytosine. Found naturally in DNA methylation; used to modulate gene expression studies. |
Epigenetics research, gene regulation |
| Inosine |
I |
Base Modification |
Deaminated purine base that can pair with A, C, or U. Used to study wobble base pairing and introduce intentional mismatches. |
Site-directed mutagenesis, RNA structure studies |
| Pseudouridine |
Psi |
Base Modification |
Isomer of uridine with C-C glycosidic bond. Enhances RNA stability and reduces innate immune activation. |
mRNA therapeutics, vaccine development |
| N6-Methyladenosine (m6A) |
m6A |
Base Modification |
Most abundant internal mRNA modification in eukaryotes. Regulates mRNA splicing, export, translation, and decay. |
Epitranscriptomics research |
| Biotin |
Biotin |
Conjugation |
High-affinity binding to streptavidin and avidin. Used for pull-down assays, immobilization, and detection. |
Affinity purification, ELISA, Northern blots |
| Fluorescein (FAM) |
FAM |
Fluorophore |
Green-fluorescent dye (Ex 495nm / Em 520nm). Widely used for labeling oligonucleotides in detection and imaging applications. |
qPCR probes, FISH, in situ hybridization |
| Cyanine-3 (Cy3) |
Cy3 |
Fluorophore |
Orange-fluorescent dye (Ex 550nm / Em 570nm). Commonly used in microarray labeling and multicolor fluorescence experiments. |
Microarrays, FRET, two-color imaging |
| Cyanine-5 (Cy5) |
Cy5 |
Fluorophore |
Red-fluorescent dye (Ex 649nm / Em 670nm). Preferred for far-red detection with low background in biological samples. |
Microarrays, in vivo imaging, FRET |
| Alexa Fluor 488 |
AF488 |
Fluorophore |
Bright green-fluorescent dye with superior photostability. Compatible with standard fluorescein filter sets. |
Imaging, flow cytometry, super-resolution microscopy |
| Black Hole Quencher-1 (BHQ-1) |
BHQ-1 |
Quencher |
Non-fluorescent quencher that absorbs in the 480-580nm range. Used on the 3-prime end of hydrolysis probes to quench reporter fluorescence. |
TaqMan probes, molecular beacons |
| Black Hole Quencher-2 (BHQ-2) |
BHQ-2 |
Quencher |
Non-fluorescent quencher absorbing 560-670nm. Pairs with far-red fluorophores like Cy5 for probe-based detection. |
Dual-labeled probes, multiplex qPCR |
| Cholesterol |
Cholesterol |
Conjugation |
Lipophilic conjugate that enhances cellular uptake and circulation time. Interacts with cell membranes to facilitate delivery. |
siRNA delivery, antisense therapeutics |
| GalNAc |
GalNAc |
Conjugation |
Trivalent ligand that targets the asialoglycoprotein receptor on hepatocytes. Enables liver-targeted delivery. |
Liver-targeted siRNA, antisense drugs |
| Dabcyl |
Dabcyl |
Quencher |
Non-fluorescent quencher absorbing at 475nm. Used as a universal quencher in molecular beacon and FRET probe designs. |
Molecular beacons, Scorpion probes |
| Thiol / Sulfhydryl |
SH |
Conjugation |
Reactive group for gold nanoparticle conjugation and disulfide crosslinking. Enables attachment to gold surfaces and thiol-reactive chemistry. |
Gold nanoparticles, biosensors, surface immobilization |
