Some are—e.g., rI and certain fluorescent bases are tolerated, while bulky intercalators or heavy halogens can inhibit extension. Validate per enzyme.
RNA Base Analogs expand the chemical and functional space of natural ribonucleotides. By altering hydrogen bonding, stacking, or electronic properties, these analogs enable applications in epitranscriptomic research (m6A, m5C, pseudouridine), structural probing (thio- and halogenated bases), fluorescent reporting (2-aminopurine, pyrrolo-C, ribo-tC°), and therapeutic engineering (stability-enhancing 2′-F, 2′-OMe, MOE variants). They are powerful tools for dissecting RNA–protein interactions, mapping modifications, designing diagnostic probes, and developing next-generation RNA medicines.
RNA Base Analogs expand the chemical and functional space of natural ribonucleotides. By altering hydrogen bonding, stacking, or electronic properties, these analogs enable applications in epitranscriptomic research (m6A, m5C, pseudouridine), structural probing (thio- and halogenated bases), fluorescent reporting (2-aminopurine, pyrrolo-C, ribo-tC°), and therapeutic engineering (stability-enhancing 2′-F, 2′-OMe, MOE variants). They are powerful tools for dissecting RNA–protein interactions, mapping modifications, designing diagnostic probes, and developing next-generation RNA medicines.
| Products | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| 1‑Methyl A (RNA) | N1‑methyladenosine | Translation/structure mapping; epitranscriptomics | Watson–Crick edge blocked; protonated at phys. pH; synonym of m1A | [m1A] |
| 1‑Methyl‑PseudoUridine | N1‑methyl‑pseudouridine | mRNA therapeutics; immunogenicity reduction | Enhances translation; synonym of m1‑ψ | [m1ψ] |
| 2,6‑Diaminopurine (2‑amino‑A) | A analog with extra exocyclic amine | Increase A:U pairing strength | Tends to raise Tm ~1–2 °C/base | [DAP] |
| 2′‑O‑Methyl‑C Phosphodithioate | 2′‑OMe‑C with PS2 backbone | Nuclease resistance; affinity tuning | RNase‑H incompatible (2′‑OMe) | [2OMeC-PS2] |
| 2′‑O‑Methyl‑G Phosphodithioate | 2′‑OMe‑G with PS2 backbone | Stability in probes/ASO designs | Increased hydrophobicity vs PO | [2OMeG-PS2] |
| 2′‑O‑Methyl‑U Phosphodithioate | 2′‑OMe‑U with PS2 backbone | Nuclease resistance; duplex tuning | Use for challenging matrices | [2OMeU-PS2] |
| 2‑Amino Purine ribose | Fluorescent A analog (RNA) | Stacking/conformation reporter | Quenched in duplex; environment‑sensitive | [2‑A‑rP] |
| 2‑Aminopurine | Fluorescent A analog | Folding/kinetics assays | Use RNA or DNA version as needed | [2AP] |
| 2′‑F Inosine | 2′‑fluoro‑inosine | Wobble pairing with added stability | Pairs with A/C/G/U (bias I–C) | [fI] |
| 2′‑Fluoro Bases | 2′‑F A/C/G/U set | Stability, nuclease resistance | General 2′‑F family | [fN] |
| 2′‑Fluoro deoxyadenosine | 2′‑F‑A (DNA) | Hybrid stability studies | DNA context | [fA] |
| 2′‑Fluoro deoxycytidine | 2′‑F‑C (DNA) | Affinity/structure probes | DNA context | [fC] |
| 2′‑Fluoro deoxyguanosine | 2′‑F‑G (DNA) | Stability tuning | DNA context | [fG] |
| 2′‑Fluoro deoxyuridine | 2′‑F‑U (DNA) | Photochem./NMR probes | DNA context | [fU] |
| FANA‑N | 2′‑fluoro‑arabino nucleoside | XNA research; nuclease resistance | Requires FANA pairing rules | [FANA‑N] |
| 2′‑O‑Me‑5‑Me‑C | 5‑methyl‑C on 2′‑OMe sugar | Affinity boost; epitranscriptomic mimic | Raises Tm | [m5mC] |
| 2′‑O‑Methyl‑5‑Fluoro‑U | 5‑F‑U on 2′‑OMe sugar | NMR/structural probes | Small halogen; mild Tm effect | [2OMe-5F-U] |
| 2′‑O‑Methyl adenosine | mA | Stability; nuclease resistance | RNase‑H incompatible | [mA] |
| 2′‑O‑Methyl bases | Set of 2′‑OMe A/C/G/U | ASO wings; probe stabilization | General entry | [mN] |
| 2′‑O‑Methyl cytidine | mC | Affinity/stability | Common in probes | [mC] |
| 2′‑O‑Methyl guanosine | mG | Stability; folding control | Use sparingly near G‑runs | [mG] |
| 2′‑O‑Methyl inosine | mI | Stabilized wobble | Pairs broadly; bias I–C | [mI] |
| 2′‑O‑Methyl uridine | mU | Stability; nuclease resistance | Common in ASO wings | [mU] |
| 2′‑O‑Methyl‑2,6‑Diaminopurine | DAP on 2′‑OMe | Strong A:U pairing | High Tm; use sparingly | [2OMe-DAP] |
| 2′‑O‑Methyl‑5‑Bromo‑U | 5‑Br‑U on 2′‑OMe | Photo‑crosslinking; structure | UV‑sensitive | [2OMe-5Br-U] |
| 2′‑O‑Methyl‑5‑Me‑U | m5U on 2′‑OMe sugar | Epigenetic studies; duplex stability; reader protein assays | Raises Tm modestly | [2OMe-5Me-U] |
| 2′‑O‑Methyl‑5‑Me‑C | m5U on 2′‑OMe sugar | Epigenetic studies; duplex stability; reader protein assays | Raises Tm modestly | [2OMe-5Me-C] |
| 2′‑O‑Methyl‑A Phosphodithioate | mA with PS2 linkage | Nuclease resistance | Backbone sulfur x2 | [2OMeA-PS2] |
| 2′‑MOE‑5‑Me‑C | 5‑mC on 2′‑O‑methoxyethyl sugar | ASO/siRNA‑like stabilization | High affinity; nuclease resistance | [MOE‑mC] |
| 2′‑MOE‑5‑Me‑U | 5‑mU on 2′‑MOE | Affinity/stability | Use for probe robustness | [MOE‑mU] |
| 2′‑MOE‑A | A on 2′‑MOE | ASO wings; nuclease resistance | RNase‑H incompatible | [MOE‑A] |
| 2′‑MOE Bases | 2′‑MOE A/C/G/U set | Stability & PK improvements | General entry | [MOE‑N] |
| 2′‑MOE‑G | G on 2′‑MOE | Stabilize G‑poor regions | Combine with PS backbones | [MOE‑G] |
| 2‑Thio‑U (s2U) | S at C2 of uracil | tRNA decoding; crosslinking | Red‑shifted absorbance | [s2U] |
| 3′‑O‑methyl bases (2′–5′ linked) | 3′‑O‑Me N with 2′–5′ linkage | Block extension; structure probes | Non‑extendable; mapping tools | [3OmN] |
| 3′‑O‑methyl rA (2′–5′) | 3′‑O‑Me‑A, 2′–5′ | RNase footprinting; blocking | Terminates polymerases | [3OmA] |
| 3′‑O‑methyl rC (2′–5′) | 3′‑O‑Me‑C, 2′–5′ | As above | Use internally or at ends | [3OmC] |
| 3′‑O‑methyl rG (2′–5′) | 3′‑O‑Me‑G, 2′–5′ | As above | — | [3OmG] |
| 3′‑O‑methyl rI (2′–5′) | 3′‑O‑Me‑I, 2′–5′ | Wobble with block | — | [3OmI] |
| 3′‑O‑methyl rU (2′–5′) | 3′‑O‑Me‑U, 2′–5′ | Extension block | — | [3OmU] |
| 3′‑rA (2′–5′) | 2′–5′‑linked rA | Structure mapping; ligation studies | Non‑canonical linkage | [3rA2‑5] |
| 3′‑rC (2′–5′) | 2′–5′‑linked rC | As above | — | [3rC2‑5] |
| 3′‑rG (2′–5′) | 2′–5′‑linked rG | As above | — | [3rG2‑5] |
| 3′‑rU (2′–5′) | 2′–5′‑linked rU | As above | — | [3rU2‑5] |
| 4‑Thio‑U (s4U) | S at C4 of uracil | Photo‑crosslinking (PAR‑CLIP) | UV‑A reactive | [s4U] |
| 5‑Bromo‑rC | Br at C5 of rC | Photo‑crosslinking; phasing | Heavy atom derivative | [5‑Br‑rC] |
| 5‑Bromo‑rU | Br at C5 of rU | Photo‑crosslinking; RNA structure | UV‑sensitive | [5‑Br‑rU] |
| 5‑Iodo‑rC | I at C5 of rC | Crystallography; crosslinking | Strong X‑ray scatterer | [5‑I‑rC] |
| 5‑Iodo‑rU | I at C5 of rU | Photocrosslinking; phasing | Heavy halogen | [5‑I‑rU] |
| 5‑Methyl‑Cytosine | m5C (RNA) | Epitranscriptomics; reader assays | Alters protein recognition | [5mrC] |
| 5‑Methyl‑U | m5U | Affinity tuning; structural studies | Mild Tm increase | [m5U] |
| 6‑Thio‑rG | S at C6 of G | Crosslinking; metal coordination | Photosensitizer; reactive sulfur | [S6‑rG] |
| 8‑Aza‑7‑deaza‑A | Ring‑modified A | Electronics/stacking tuning | Specialty structural analog | [8A-7dA] |
| 8‑Azanebularine (ribo) | Transition‑state/lesion mimic | Deaminase/repair studies | Potent enzyme probe | [8‑AzaN] |
| 8‑Bromo‑rG | Br at C8 of rG | Structure/crystallography; photo‑chem | Bulky at C8; conformational bias | [8‑Br‑rG] |
| 8‑Oxo‑rG | Oxidized lesion analog | Oxidative damage/repair studies | Mispairs with A | [8‑Oxo‑rG] |
| 5′‑Adenylation (rApp) | Pre‑adenylated RNA 5′ | Adapter ligation without ATP | For Rnl2‑based ligations | [5rApp] |
| Amino C6‑U | Primary amine on U via C6 linker | NHS‑ester labeling; conjugation | Post‑synthetic coupling | [AmC6U] |
| Aminoallyl rU | Allylic amine on U | Dye/hapten labeling | Good for fluorescent tags | [AmAll‑rU] |
| Dihydrouracil (ribo) | Reduced 5,6‑double bond | tRNA flexibility/structure | Destabilizes stacking; Tm↓ | [5‑6‑DHrU] |
| Inosine (ribo) | Wobble base (rI) | Degenerate sites; tRNA mimicry | Pairs A/C/G/U with bias | [rI] |
| Inverted rA | Reverse (3′–3′ or 5′–5′) linkage | Nuclease blocking; end capping | Terminates extension | [Inv‑rA] |
| Inverted rC | Reverse linkage | As above | — | [Inv‑rC] |
| Inverted rG | Reverse linkage | As above | — | [Inv‑rG] |
| Inverted rU | Reverse linkage | As above | — | [Inv‑rU] |
| L‑RNA rA | Mirror‑image rA (L‑form) | Spiegelmer/aptamer work; nuclease resistance | Orthogonal to natural enzymes | [L‑rA] |
| L‑RNA rC | L‑rC | As above | — | [L‑rC] |
| L‑RNA rG | L‑rG | As above | — | [L‑rG] |
| L‑RNA rU | L‑rU | As above | — | [L‑rU] |
| N1‑Methyl‑PseudoUridine | m1‑ψ‑rU | mRNA therapy optimization | Reduces innate immune sensing | [m1‑psi‑rU] |
| N1‑Methyl rA (m1A) | m1A | Translation/structure mapping | Watson–Crick edge blocked | [m1A] |
| N3‑Methyl‑C | N3‑alkylated cytidine | Alkylation/repair studies | Positively charged; pairing disrupted | [m3C] |
| N3‑Methyl‑rU | N3‑methyl‑uridine | Lesion/repair studies | Disrupts U:A pairing | [m3U] |
| N4‑Ethyl‑rC | N4‑ethyl cytidine | Protein recognition studies | Alters H‑bond donor pattern | [N4‑Et‑rC] |
| N6‑Benzyl‑A | N6‑benzyl adenosine | Reader/ligand screening | Bulky N6; pairing perturbed | [bn6A] |
| N6‑dimethyl rA | m6,6A | Translation/structure effects | Positively charged tendency | [m6‑6A] |
| N6‑isopentenyl‑rA (i6A) | Isopentenyl A (tRNA‑like) | tRNA modification studies | Hydrophobic isoprenoid at N6 | [N6‑i6A] |
| N6‑Methyl rA (m6A) | m6A | Epitranscriptomics | Reader/writer/eraser assays | [m6A] |
| Pseudouridine (ribo) | Ψ (C‑glycosidic isomer) | Stability/translation enhancement | Improves folding; lowers innate sensing | [psi‑rU] |
| Pyrrolo‑C | Fluorescent C analog | RNA folding/hybridization reporter | Excitation ~350 nm; environment‑sensitive | [Pyrrolo-C] |
| rAbasic Site (abasic furan) | Stable AP site (RNA) | Block extension; lesion mimic | Behaves like a gap | [rABS] |
| riboadenosine | rA (natural) | Controls; standards | Reference ribonucleoside | [rA] |
| ribocytidine | rC (natural) | Controls; standards | — | [rC] |
| riboguanosine | rG (natural) | Controls; standards | — | [rG] |
| ribouridine | rU (natural) | Controls; standards | — | [rU] |
| Thymidine Ribo | rT (ribothymidine) | tRNA motif studies | Natural in tRNA T‑loop | [rT] |
| Zebularine (RNA) | C analog lacking 4‑amino | Deaminase/DNMT studies | Epigenetic tool; lesion mimic | [rZ] |
Bio-Synthesis offers advanced synthesis of RNA oligonucleotides with a wide range of chemical modifications, including fluorescent probes with quenchers, DNA/RNA chimeric constructs, and combinations of 2′-O-methyl bases, 2′-fluoro bases, and phosphorothioate linkages.
Using state-of-the-art synthesizers and proprietary long-coupling protocols based on β-cyanoethyl phosphoramidite chemistry, Gene Link produces ultra-clean oligos with high fidelity. Because native RNA is highly susceptible to nuclease degradation, incorporation of 2′-O-methyl or 2′-fluoro bases provides enhanced resistance while maintaining RNA-like hydrogen bonding. 2′-O-methyl phosphoramidites also couple more efficiently than standard RNA monomers, yielding longer, more stable oligos.
Bio-Synthesis also customizes DNA/RNA chimeric oligos with user-defined ribo, deoxy, or 2′-O-methyl residues, and can substitute standard phosphodiester bonds with phosphorothioate linkages. Full or partial substitution delivers greater nuclease resistance—particularly valuable for antisense studies.
2′-Fluoro nucleosides adopt an RNA-like C3′-endo conformation, supporting the A-form helix upon hybridization. These modifications raise duplex stability and are applied in diverse settings:
Degenerate bases allow multiple nucleotides at a position; in RNA, inosine (rI) is the classic wobble base. IUB pills (R,Y,M,K,S,W,H,B,D,V,N) define mixtures used for libraries or variant coverage. Programmed delivery sets base ratios (e.g., N = A+C+G+U).
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Inosine (rI) | Universal wobble base in RNA | tRNA wobble; degenerate primer/probe sites | Pairs with A/C/G/U with bias | rI |
| 2′‑O‑methyl Inosine | Inosine with 2′‑OMe ribose | Stabilized wobble positions | Improved nuclease resistance | mI |
| 5‑nitroindole (ribo) | Non‑H‑bonding universal analog | Bypass variable sites in RNA constructs | Tm↓; avoid adjacent placements | 5NI‑r |
| Degenerate Base (Mixed Base) | Mixture of A/C/G/U at one position | Library synthesis; polymorphism coverage | IUB pills define ratio | Mix |
Note: ESI‑MS is not performed on mixed‑base oligos due to sequence ambiguity.
Convertible RNA base analogs are designed with built-in reactive handles or temporary groups that can be selectively transformed after synthesis to introduce dyes, haptens, crosslinkers, or other conjugates. These bases streamline probe design by allowing post-synthetic functionalization at precise positions without compromising oligo yield. Popular examples include 5-ethynyl-U (EU), 5-azidomethyl-U, and O4-triazolyl-U, which enable versatile click-chemistry ligations, while amino-modified uridines support NHS-ester labeling for fluorescent and affinity tags.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| 5-Ethynyl-Uridine (EU) | Alkyne substitution at C5 of uridine | Click chemistry labeling of nascent RNA | Compatible with CuAAC & SPAAC; minimal steric effect | EU |
| 5-Azidomethyl-Uridine | Azide handle at U C5-CH2 | Copper-free click ligation; bio-orthogonal conjugation | Ideal for dye or biotin conjugation; avoids Cu toxicity | AzM-U |
| O4-Triazolyl-Uridine | O4 position linked to triazole | Post-synthetic functionalization; crosslinking | Versatile reactive handle for dyes & ligands | O4-trz-rU |
| Amino-C6-Uridine (AmC6-U) | Primary amine at C6 via flexible linker | Conjugation with NHS-esters (dyes, peptides, haptens) | Commonly used for labeling with long spacer arm | AmC6U |
| Aminoallyl-Uridine (AmAll-rU) | Allylic amine at U | Dye/hapten coupling | Smaller, less flexible than AmC6-U | AmAll-rU |
| 5-Iodo-Uridine | Iodine substitution at C5 of uridine | Photo-crosslinking; halogen substitution chemistry | Activatable convertible handle for derivatization | 5I-rU |
| 5-Bromo-Uridine | Bromine substitution at C5 of uridine | X-ray phasing; substitution to other reactive groups | Useful for structural and crystallography studies | 5Br-rU |
Epitranscriptomic bases such as m6A, m1A, m5C, hm5C, f5C, ca5C, Ψ, and m7G modulate RNA stability, processing, and translation. Synthetic incorporation enables mechanistic studies with defined placements.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| N6‑Methyl‑A | m6A | Reader/writer/eraser assays | Dynamic RNA mark | m6A |
| N1‑Methyl‑A | m1A | Translation/structure mapping | Watson–Crick edge blocked | m1A |
| 5‑Methyl‑C | m5C | Epigenetics, binding modulation; | Tm↑; context‑dependent | m5C |
| 5‑Methyl‑U | m5U | Epigenetic studies, altered binding assays | Tm↑; tolerated by polymerases with a minor efficiency changes | m5U |
| 2′-O-Methyl-5-Methyl-Uridine | m5U on 2′‑OMe sugar | Epitranscriptomic mimic; affinity tuning; duplex stability | Mild Tm↑; generally well tolerated; 5‑methyl at U behaves like rT analog | [2OMe-5Me-U] |
| 2′-O-Methyl-5-Methyl-Cytidine | m5C on 2′‑OMe sugar | Epigenetic studies; duplex stability; reader protein assays | Tm↑; can alter protein recognition vs C; commonly used in methylation models | [2OMe-5Me-C] |
| 5‑Hydroxymethyl‑C | hm5C | Demethylation intermediates | Hydrophilic handle | hm5C |
| 5‑Formyl‑C | f5C | tRNA modification studies | Reactive aldehyde | f5C |
| 5‑Carboxyl‑C | ca5C | Advanced oxidation product | Tm↓; acidic | ca5C |
| Pseudouridine | Ψ | Stability/translation effects | C‑glycosidic; improves folding | Ψ |
| 7‑Methyl‑G | m7G (cap analog) | 5′ cap modeling | Terminal use typical | m7G |
Engineered base pairs (e.g., isoC/isoG, 5‑Me‑iso‑dC/isoG, dP/dZ) can operate in RNA contexts for labeling or coding with specialized enzymes. Availability is platform‑specific—contact us to review current options.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| isoC | Pairs with isoG | Orthogonal pairing | Requires matched partner | isoC |
| isoG | Pairs with isoC | Orthogonal pairing | Tautomerization risk | isoG |
| 5‑Me‑iso‑dC | Methylated isoC analog | Improved fidelity vs isoC | Stabilizes isoC–isoG | 5‑Me‑iso‑dC |
| dP/dZ system | Orthogonal pair | Expanded genetic alphabet | Polymerase‑dependent | dP/dZ |
Hapten‑tagged bases carry small antigenic tags (biotin, DIG, DNP, fluorescein, rhodamine) for capture or immunodetection in RNA probes and assays.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Biotin‑rU / Biotin‑rC | Biotin hapten on base | Affinity capture/immobilization | High affinity to streptavidin | Bio‑rU |
| DIG‑rU / DIG‑rC | Digoxigenin hapten | ISH/FISH; immunodetection | Anti‑DIG antibody detection | DIG‑rU |
| DNP‑rU | Dinitrophenol hapten | Immunodetection | Anti‑DNP antibodies | DNP‑rU |
| FITC‑rU / Rhodamine‑rU | Fluorophore haptens on base | Fluorescence + immuno workflows | Beware self‑quenching | FITC‑rU |
Structure & blocking bases disrupt canonical pairing, introduce bulky/rigid features, or sterically block enzymatic access to control secondary structure, hybridization, and processing.
| Product | Description | Typical Use | Notes | Category |
|---|---|---|---|---|
| Abasic (rSpacer) | Missing base; structural gap | Blocks extension; lesion mimic | Behaves like a gap | Bulky/Steric Blocking |
| Spacer C3 / C9 / HEG | Non‑nucleosidic spacers | Prevent pairing/extension | Steric block; structure control | Bulky/Steric Blocking |
| Pyrene‑rU / Perylene‑rU | Bulky aromatics | Intercalating block; FRET probes | Strong π‑stackers | Helix‑Distorting |
| Pyrrolo‑rC | Altered geometry | Local structure probing | Fluorescent readout | Helix‑Distorting |
| 4‑Thio‑U | Thio substitution | UV‑trap to lock structure | Photo‑crosslinker | Photo/Crosslinking |
| 5‑Br‑rU / 5‑I‑rU | Halogenated bases | Photo‑induced crosslinking | UV‑sensitive | Photo/Crosslinking |
Cross‑linking & ligation bases include photo‑reactive thio/halo bases, psoralens, and click handles (alkynes/azides) for covalent trapping, structure mapping, and post‑synthetic conjugation.
| Product | Description | Typical Use | Notes | Category |
|---|---|---|---|---|
| Psoralen‑rU (C2/C6) | Psoralen linked to U | UV‑induced interstrand crosslinks | 320–365 nm activation | Intercalator/Photoadduct |
| 4‑Thio‑U | Thiolated U | Photo‑crosslinking; PAR‑CLIP | UV‑A reactive | Photoreactive |
| 6‑Thio‑G | Thiolated G | Metal coordination; crosslinking | Sulfur reactivity | Reactive |
| 5‑Ethynyl‑U (EU) | Alkyne handle | Click ligation/labeling | CuAAC/SPAAC compatible | Clickable |
| 5‑Azidomethyl‑U | Azide handle | Strain‑promoted click | Copper‑free | Clickable |
| 5‑I‑rU / 5‑Br‑rU | Halogenated bases | Photocrosslink; crystallography | Strong scatterers | Photoreactive |
Bromine, iodine, or fluorine substitutions provide photo‑reactivity and strong X‑ray scattering, enabling cross‑linking, structural probing, and phase determination in RNA structural biology.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| 5‑Bromo‑rU | Brominated uridine | Crystallography; photocrosslinking | UV‑inducible | 5Br‑rU |
| 5‑Bromo‑rC | Brominated cytidine | RNA structural probes | Heavy atom derivative | 5Br‑rC |
| 5‑Iodo‑rU | Iodinated uridine | Photocrosslinking; phasing | Strong scatterer | 5I‑rU |
| 5‑Iodo‑rC | Iodinated cytidine | RNA crystallography | Heavy halogen | 5I‑rC |
| 5‑Fluoro‑rU | Fluorinated uridine | NMR probes; Tm tuning | Small halogen; mild effects | 5F‑rU |
Intercalator‑modified bases carry bulky aromatic groups that insert between stacked base pairs, enhancing duplex stability and enabling fluorescence/FRET or photo‑induced crosslinking.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Psoralen‑rU (C2/C6) | Psoralen on U | UV interstrand crosslinking | 320–365 nm activation | Psor‑rU |
| Ethidium‑rU | Ethidium dye on U | Fluorescent intercalator | Strong emission upon binding | Et‑rU |
| Acridine‑rC / Acridine‑rU | Acridine linked bases | Stabilize duplex; probes | Tm↑; strong intercalator | Acr‑rC/rU |
| Pyrene‑rU | Pyrene at U C5 | Excimer/exciplex studies | Environment‑sensitive | Pyr‑rU |
| Perylene‑rU | Perylene at U C5 | FRET donor/acceptor | Hydrophobic; internal sites | Per‑rU |
| Anthraquinone‑rU | AQ group on U | Photoinduced ET | Generates ROS on hv | AQ‑rU |
| Naphthyl‑rC | Naphthyl on C | Stacking probes | Smaller intercalator | Naph‑rC |
Fluorescent base analogs minimally perturb RNA structure while reporting on stacking, pairing, or conformational changes—ideal for FRET, hybridization monitoring, and RNA–protein interaction assays.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Ribo‑tC° | Fluorescent C analog | RNA duplex probe | Pairs like C; bright | ribo‑tC° |
| tC° | Neutral tricyclic C | Environment‑sensitive probe | Minimal perturbation | tC° |
| tCnitro | Nitro‑substituted tricyclic C | Internal fluorescent reporter | High quantum yield | tCnitro |
| Pyrrolo‑C (rC) | Fluorescent cytidine | Hybridization dynamics | Exc. ~350 nm | pyr‑rC |
| 2‑Aminopurine (ribo) | Fluorescent adenine analog | Stacking/conformation | Quenched in duplex | 2‑AP‑r |
| 2′-OMe-2-Aminopurine | Fluorescent adenine analog | folding and kinetics reporter | Quenched in duplex | [2OMe-2AP] |
| Pyrene‑rU / Perylene‑rU | Aromatic fluorophores | FRET/excimer probes | Hydrophobic; spacing advised | Pyr‑rU / Per‑rU |
Custom synthesis and modification of small interfering RNA for gene silencing applications.
Learn MoreASO design with 2′-OMe, 2′-F, LNA and phosphorothioate linkages for stability and potency.
Learn MoreModified RNA aptamers with enhanced nuclease resistance and high affinity binding.
Learn Morem1Ψ, m5C and cap analog incorporation for vaccine and therapeutic development.
Learn MoreTypical research scales range from 0.05–15 µmol; development 1 mg–100 gram; large‑scale multi‑gram available with full documentation. Turnaround depends on analog choice, length, and purification.
Some are—e.g., rI and certain fluorescent bases are tolerated, while bulky intercalators or heavy halogens can inhibit extension. Validate per enzyme.
Yes—contact us with your target base/handle (e.g., special photo‑reactive groups or click handles) and we’ll evaluate feasibility.
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