Some are—e.g., inosine or 7-deaza-dG can be tolerated in primers, while strong universal bases (5-NI/3-NP) and bulky conjugates can inhibit extension. Validate per polymerase.
DNA Base Analogs are chemically modified nucleobases that mimic or substitute for natural DNA bases while altering hydrogen bonding, stacking, or electronic properties. These analogs expand the chemical diversity of oligonucleotides, enabling applications in probing DNA structure, studying replication and repair, enhancing hybridization, or introducing novel functionalities such as fluorescence, crosslinking, or resistance to enzymatic degradation. By incorporating base analogs, researchers can investigate fundamental molecular mechanisms and create tailored tools for diagnostics, sequencing, and therapeutic development.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Abasic II | Non-informational abasic site analog (stable AP site) | Polymerase stalling/repair studies; blocking extension | Lowers Tm; behaves like a gap | dSpacer/AP II |
| Perylene-dU | Perylene fluor attached at 5‑position of dU | Fluorescent stacking probe; FRET donor | Very hydrophobic; prefers internal positions | Per‑dU |
| Pyrene-dU | Pyrene at 5‑position of dU | Environmental/stacking probe; excimer formation | Strong π‑stacker; can quench nearby dyes | Pyr‑dU |
| 5,6-Dihydro-dU | Saturated 5,6‑double bond in uracil ring (damage mimic) | DNA damage/repair and structural studies | Slight Tm reduction vs dT | dhU |
| dX | 2′‑deoxyxanthosine (deamination product of dG) | Mismatch/repair assays; lesion controls | Pairs preferentially with C; can mispair | dX (X) |
| 5-Hydroxymethyl-dU | 5‑CH2OH substituted dU | Protein–DNA binding modulation; labeling handle | Raises hydrophilicity; mild Tm effect | 5hmU |
| 5-F-dU | 5‑fluoro‑dU | Crystallography/NMR probes; Tm tuning | Small halogen; minor Tm change | 5F‑dU |
| 5-I-dU | 5‑iodo‑dU | Phasing in crystallography; photo‑crosslinking | Heavy halogen; increases X‑ray scattering | 5I‑dU |
| 5-Br-dU | 5‑bromo‑dU | X‑ray phasing; photoinduced cleavage/crosslink | Sensitizes to UV; handle with care | 5Br‑dU |
| 2-F-dI | 2‑fluoro‑2′‑deoxyinosine | Base‑pairing studies; stability tuning | Wobble properties like dI; more hydrophobic | 2F‑dI |
| 5-Me-2'-deoxyZebularine | 5‑methyl deoxy‑zebularine (cytidine analog) | Epigenetic/DNA methyltransferase & deaminase studies | Inhibitory analog; alters enzyme recognition | 5Me‑dZeb |
| 2'-deoxypseudoU | 2′‑deoxy‑pseudouridine (C‑glycosidic isomer) | Structure/recognition studies; stability tuning | Alters glycosidic bond geometry | dΨU |
| pdU | 5‑propynyl‑dU (alkynyl at C5) | Affinity increase in probes/primers | Raises Tm ~1–2 °C/base; increases hydrophobicity | p‑dU |
| 5-OH-dU | 5‑hydroxy‑dU (oxidative lesion) | Damage/repair assays | Can mispair; Tm ↓ | 5OH‑dU |
| 4-Thio-dU | 4‑thio‑dU (S at C4) | Photosensitizer; crosslinking; spectroscopy | Strong thio absorbance; UV‑A reactive | s4‑dU |
| O4-Triazolyl-dU | O4‑triazolyl‑dU (click‑compatible/photolabile variant) | Photo/click chemistry studies; crosslinking | Specialty synthetic handle | O4‑trz‑dU |
| dU | 2′‑deoxyuridine (T analog) | Substitute for dT; enzymology controls | Pairs with A; slightly lower stability than dT | dU |
| dP+dK | Orthogonal artificial base pair P:K | Expanded genetic alphabet; labeling/coding | Requires matched partner; polymerase‑dependent | dP/dK |
| dK | Unnatural base K (pairs with P) | Expanded alphabet systems | Use only with dP counterpart | dK |
| dP | Unnatural base P (pairs with K) | Expanded alphabet systems | Use only with dK counterpart | dP |
| 2-Aminopurine | Fluorescent adenine analog (base‑stacking reporter) | Conformation/kinetics; fluorescence assays | Sensitive to stacking/duplex formation | 2‑AP |
| 5-Formyl dC III | 5‑formyl‑2′‑deoxycytidine variant (epigenetic) | 5fC standards; TET/oxidative pathways | May exist as hydrate; affects binding | 5fC (III) |
| tCnitro | Nitro‑substituted tricyclic cytosine analog (fluorescent) | Internal fluorescent probe with minimal perturbation | High quantum yield; pairs like C | tCnitro |
| 5-Nitroindole | Universal base analog (non‑H‑bonding) | Primers across variable sites | Tm ↓; avoid consecutive placements | 5NI |
| tC° | Tricyclic cytosine analog (fluorescent) | Fluorescent base probe for dynamics | Pairs as C; low perturbation | tC° |
| 5-Formyl-dC | 5‑formyl‑dC (epigenetic oxidation product) | 5fC controls; protein binding studies | Reactive aldehyde; handle gently | 5fC |
| O6-Phenyl-dI | O6‑phenyl‑2′‑deoxyinosine | Polymerase fidelity/lesion studies | Bulky O6 group; pairing perturbed | O6Ph‑dI |
| Pac-2-Amino-dA | 2,6‑diaminopurine dA analog (often Pac‑protected) | Increase duplex stability vs A:T | Adds extra H‑bond to T; Tm ↑ | 2‑APu (DAP‑dA) |
| tC | Tricyclic cytosine analog (fluorescent) | Minimal‑perturbation fluorescence | Pairs as C; good for FRET donor | tC |
| 5-Hydroxymethyl-dC | 5‑CH2OH‑dC (epigenetic) | 5hmC standards; binding assays | Stability ~C; recognized by readers | 5hmC |
| 2'-DeoxyNebularine | Purine analog lacking exocyclic amine (depurination mimic) | AP/abasic mimic; enzyme studies | Weak H‑bonding; often pairs like A | dNeb |
| 2-Amino-dA | 2‑amino‑dA (2,6‑diaminopurine) | Increase A:T pairing strength | Tm ↑; may alter protein recognition | DAP‑dA |
| dmf-isodG | isoguanosine (iG) analog (DMF‑protected) | Orthogonal pairing with isoC | Use with isodC; polymerase‑specific | iG |
| 5-Carboxy-dC | 5‑carboxy‑dC (end‑stage TET oxidation) | 5caC standards; reader protein assays | Acidic; affects duplex stability | 5caC |
| dI | 2′‑deoxyinosine (wobble base) | Degenerate positions in primers | Pairs with A/C/G/T with biases | dI |
| Pyrrolo-dC | Pyrrolo‑cytidine fluorescent base analog | Local environment reporter | Excitation ~350 nm; sensitive to stacking | pyrrolo‑dC |
| Spermine | Polyamine conjugate (multi‑cationic) | Uptake enhancement; condensation | May increase non‑specific binding | Spm |
| NPOM Caged-dT | o‑Nitrophenyl‑propoxycarbonyl caged dT (photoremovable) | Light‑activated control of base pairing | Uncage with ~365–405 nm | NPOM‑dT |
| N3-Cyanoethyl-dT | N3‑cyanoethylated dT (alkyl at N3) | Polymerase/lesion studies; reactive handle | Affects H‑bonding at N3 | N3‑CE‑dT |
| dmf-5-Me-isodC | 5‑methyl‑isocytidine analog (DMF‑protected) | Pairs with isoG; expanded alphabet | Use with iG; polymerase‑dependent | iC(Me) |
| 2-Thio-dT | 2‑thio‑dT (S at C2) | Photocrosslink; triplet sensitizer | Red‑shifted absorbance; Tm ↑ slightly | s2‑dT |
| TMP-F-dU | Trimethoxyphenyl/fluoro photolabile dU variant | Photo‑cleavable/photocaging studies | Specialty protecting group variant | TMP‑F‑dU |
| Etheno-dA | 1,N6‑etheno‑dA fluorescent lesion | Adduct/repair assays; fluorescence readout | Emits ~410 nm; perturbs pairing | ε‑dA |
| CDPI3 MGB™ | Minor‑groove binder (CDPI3) attached | Short qPCR probes; Tm boosting | Increases specificity; typically 5′/3′ | MGB™ |
| 3'-Propargyl-5-Me-dC | 3′‑terminal alkyne on 5‑methyl‑dC | Click‑handle at 3′ end | Use CuAAC; protects during synthesis | 3′‑alkyne‑5MeC |
| 3'-Amino-dT | 3′‑primary amine on dT | 3′ coupling to dyes/solids; blocking | NHS‑ester compatible; blocks extension | 3′‑NH2‑dT |
| 3'-Uaq Cap | 3′ uracil‑based capping group | 3′ blocking of polymerase/ligation | Non‑extendable terminator | 3′‑U‑cap |
| 2'-F-Ac-C-ANA | 2′‑fluoro‑acyl cytidine on ANA backbone | XNA pairing studies; nuclease resistance | Non‑natural sugar (ANA); RNase‑H incompatible | 2F‑Ac‑C‑ANA |
| 2'-F-A-ANA | 2′‑fluoro‑adenosine on ANA backbone | XNA research; stability tuning | Use with complementary ANA strands | 2F‑A‑ANA |
| 2'-F-A | 2′‑fluoro‑adenosine | Stability enhancement; binding tuning | Raises Tm; affects protein recognition | 2F‑A |
| N4-Et-dC | N4‑ethyl‑dC | Protein recognition/lesion mimic | Modifies H‑bond donor/acceptor pattern | N4Et‑dC |
| 5'-OMe-dT | 5′‑O‑methyl‑dT (end‑cap) | Exonuclease protection; blocking | Prevents phosphorylation/extension at 5′ | 5′‑OMe‑dT |
| 7-deaza-dG | 7‑deaza‑dG (N7→C‑H) | Eliminate Hoogsteen/N7 interactions; structure | Alters metal/Protein contacts | 7dz‑dG |
| 8-oxo-dA | 8‑oxo‑deoxyadenosine lesion | Oxidative damage studies | Mispairs; polymerase block/lesion | 8oxo‑dA |
| 8-oxo-dG | 8‑oxo‑deoxyguanosine lesion | Oxidative damage/repair assays | Pairs with A; mutagenic | 8oxo‑dG |
| 8-Br-dA | 8‑bromo‑dA | Structure/crystallography probes | Bulky at C8; Tm ↓ | 8Br‑dA |
| 3'-dA | 3′‑deoxy‑adenosine (chain terminator) | Enzymology; controlled termination | Non‑extendable 3′ end | 3′‑dA |
| N6-Me-dA | N6‑methyl‑dA (epigenetic mimic) | m6A DNA analog studies | Affects protein recognition | m6dA |
| 7-Deaza-dA | 7‑deaza‑dA | Hoogsteen elimination; structure | Modulates protein/ligand binding | 7dz‑dA |
| 5'-CDPI3 MGB™ | 5′‑attached CDPI3 MGB | Tm boost for short probes | Often paired with dark quencher | 5′‑MGB™ |
| 2'-F-Ac-C | 2′‑fluoro‑acyl cytidine (DNA context) | Stability; recognition studies | Specialty base; vendor‑specific | 2F‑Ac‑C |
| 5'-Pyrene Cap | 5′ pyrene moiety | Stacking/excimer probes; surfaces | Hydrophobic; may need spacer | 5′‑Pyr |
| 5'-Amino-dT | 5′ primary amine on dT | NHS‑ester labeling; coupling | Also used as 5′ blocker | 5′‑NH2‑dT |
| N4-Ac-N4-Et-dC | Dual N4 acyl/ethyl substituted dC | Protein recognition/probing | Alters H‑bonding pattern | N4Ac/Et‑dC |
| 5-aza-5,6-dihydro-dC | Zebularine (5‑aza‑5,6‑dihydro‑dC) | Cytidine deaminase/DNMT inhibitor studies | Epigenetic tool compound | Zeb‑dC |
| 8-Amino-dG | 8‑amino‑dG | Lesion/recognition studies | Alters charge/stacking | 8NH2‑dG |
| 3'-dC | 3′‑deoxy‑cytidine | Chain termination studies | Non‑extendable 3′ | 3′‑dC |
| O4-Me-dT | O4‑methyl‑dT lesion | Alkylation/repair studies | Alters pairing; mutagenic | O4Me‑dT |
| 8-Br-dG | 8‑bromo‑dG | Crystallography; structure probes | Bulky at C8; pairing perturbed | 8Br‑dG |
| pdC | 5‑propynyl‑dC | Raise duplex Tm; short probes | ~1–2 °C/base Tm increase | p‑dC |
| 2',3'-ddA | 2′,3′‑dideoxy‑adenosine | Chain terminator; polymerase mapping | No 3′‑OH; Sanger‑like termination | ddA |
| 2'-F-G-ANA | 2′‑fluoro‑guanosine on ANA backbone | XNA studies; nuclease resistance | Use with ANA complement | 2F‑G‑ANA |
| 2'-F-G | 2′‑fluoro‑guanosine | Stability/affinity tuning | Raises Tm; RNase‑H incompatible | 2F‑G |
| 5'-Trimethoxystilbene Cap | 5′ trimethoxy‑stilbene intercalator | MGB/stacking to boost Tm | Hydrophobic; spacing advised | 5′‑TMS |
| 8-Amino-dA | 8‑amino‑dA | Damage/recognition studies | Perturbs pairing; positive charge at low pH | 8NH2‑dA |
| 5-Br-dC | 5‑bromo‑dC | Crystallography; structural probes | Halogen handle; UV sensitive | 5Br‑dC |
| 3'-dG | 3′‑deoxy‑guanosine | Chain termination | Non‑extendable 3′ | 3′‑dG |
| 7-Deaza-8-aza-dG | 7‑deaza‑8‑aza‑dG analog | Fine‑tune Hoogsteen/stacking | Specialty research analog | 7dz‑8az‑dG |
| O6-Me-dG | O6‑methyl‑dG lesion | Alkylation/repair (MGMT) assays | Pairs with T; mutagenic | O6Me‑dG |
| 4-Thio-dT | 4‑thio‑dT (duplicate entry) | Photosensitizer; crosslinking | See s4‑dU; use UV‑A | s4‑dT |
| 2',3'-ddC | 2′,3′‑dideoxy‑cytidine | Chain terminator | No 3′‑OH | ddC |
| 2'-F-U-ANA | 2′‑fluoro‑uridine on ANA backbone | XNA pairing; nuclease resistance | Use with ANA complement | 2F‑U‑ANA |
| 2'-F-U | 2′‑fluoro‑uridine | Tm ↑; stability for probes | Affects enzyme interactions | 2F‑U |
| 1-Me-dA | 1‑methyl‑dA lesion/mimic | Alkylation/repair | Disrupts Watson‑Crick edge | 1Me‑dA |
| 3'-dT | 3′‑deoxy‑thymidine | Chain terminator | Non‑extendable 3′ | 3′‑dT |
| 5-I-dC | 5‑iodo‑dC | X‑ray phasing; photo reactions | Heavy halogen at C5 | 5I‑dC |
| 5-OH-dC | 5‑hydroxy‑dC (oxidative lesion) | Damage/repair studies | Tm ↓; can deaminate | 5OH‑dC |
| 5-Me-dC | 5‑methyl‑dC (natural epigenetic mark) | Methylation standards; binding | Increases duplex stability | 5mC |
| 2'-F-5-Me-U-ANA | 2′‑F‑5‑methyl‑uridine on ANA | XNA stability; probes | Use with ANA complement | 2F‑5MeU‑ANA |
| 2',3'-ddG | 2′,3′‑dideoxy‑guanosine | Chain terminator | No 3′‑OH | ddG |
| N6-Ac-N6-Me-dA | Dual N6 acyl/methyl‑dA variants | Protein recognition/lesion studies | Alters H‑bond donors | N6Ac/Me‑dA |
| 2',3'-ddT | 2′,3′‑dideoxy‑thymidine | Chain terminator | No 3′‑OH | ddT |
| AP-dC | Abasic cytidine analog (AP at C position) | Repair/polymerase tests | Non‑coding; Tm ↓ | AP‑dC |
| Thymidine Glycol | Thymidine‑glycol oxidative lesion | DNA damage/repair assays | Strongly destabilizing; blocks polymerases | Tg |
| 8,5'-Cyclo-dA | 8,5′‑cyclo‑dA lesion (ring‑closed) | Oxidative/UV lesion studies | Blocks replication; mutagenic | cyc‑dA |
| 6-thio-dG | 6‑thioguanine deoxynucleoside | Photodynamic/lesion studies | Photosensitizer; reactive sulfur | 6s‑dG |
| PC Biotin | Photocleavable biotin tag | Affinity capture with light release | Cleaves at ~365 nm | PC‑Btn |
| 5,6-Dihydro-dT | Saturated 5,6‑double bond in thymine | Damage/repair; structure | Slight Tm ↓ | dhT |
| dW | 2,4‑difluorotoluyl universal base analog | Bypass variable sites; abasic mimic | Non‑H‑bonding; Tm ↓ | dW |
| Cyanine 3 | Cy3 fluorophore (as base/label) | Fluorescent labeling/FRET | Attach via linker; avoid self‑quenching | Cy3 |
| 8-Aza-7-deaza-A | 8‑aza‑7‑deaza‑adenine analog | Fine‑tune electronics/stacking | Specialty research base | 8az‑7dz‑A |
| 8,5'-Cyclo-dG | 8,5′‑cyclo‑dG lesion | Oxidative/UV lesion studies | Replication blocking; mutagenic | cyc‑dG |
| Ac-5-Me-dC | Acetylated 5‑methyl‑dC (N4‑acyl) | Protein recognition/epigenetic mimic | Alters H‑bonding; stability ~5mC | Ac‑5mC |
| 7-deaza-8-aza-dA | 7‑deaza‑8‑aza‑adenine | Electronic/stacking tuning | Specialty analog | 7dz‑8az‑A |
| Pyrrolidine | Pyrrolidine‑bearing nucleobase analog | Conformational constraint; ligand display | Specialty synthetic handle | Pyrrolidine‑base |
| 3-deaza-dA | 3‑deaza‑deoxyadenosine | Probe Hoogsteen/recognition | Removes N3; alters H‑bonding | 3dz‑dA |
| Cis-syn Thymine Dimer | Cyclobutane pyrimidine dimer (T=T) | UV lesion/NER studies | Strong replication block; distorts helix | CPD (cis‑syn) |
Degenerate bases mean more than one base can occur at a given position. This is common when DNA sequences are derived from amino acid codons. Oligos can be synthesized with mixtures of bases at a site, often called a wobble or mixed base position.
The IUB (International Union of Biochemistry) defines single-letter pills for all degenerate options. For example, R = A+G means 50% A and 50% G. Positions may include two, three, or four bases.
During synthesis, programmed delivery adds the defined base ratios. For example, N = A+C+G+T (25% each). Base coupling is not perfectly efficient, so expect about 10% variation.
IUB degenerate pills:
Custom spiking means deliberately setting non-equal base ratios (e.g. 10% A, 75% G, 5% C, 10% T).
Custom columns are required for spiking at the 3′ end. Pricing applies per 3′ site or up to 8 internal sites per oligo.
Degenerate bases can pair with more than one natural base, such as purines (A/G) or pyrimidines (C/T). Common examples are deoxyinosine (dI) and 5-nitroindole, which can pair with all four bases. These modifications are useful when imprecise or random pairing is needed but duplex stability must be retained. Applications include reverse-translating protein sequences for primer/probe design, creating probes that hybridize across related genes or viral variants (SNPs, indels), and supporting site-directed mutagenesis or motif cloning.
| Product | Description | Typical Use | Notes | pill |
|---|---|---|---|---|
| 2′-O methyl Inosine | Inosine analog with 2′-O-methyl ribose | Stabilizes wobble pairing; used in RNA/DNA hybrids | Improves nuclease resistance; slightly lowers polymerase efficiency | mI |
| 2-Amino Purine deoxyribose | Fluorescent adenine analog (DNA form) | Base-stacking probe; monitor conformational changes | Fluorescence quenched in duplex; sensitive to local environment | 2-AP |
| 2-Amino Purine ribose | Fluorescent adenine analog (RNA form) | RNA folding/interaction studies | Emission sensitive to stacking; reports RNA dynamics | 2-A-rP |
| 5-methyl isodeoxycytosine (Me iso dC) | Methylated isocytidine analog | Pairs with isoG; expanded alphabet experiments | Provides higher duplex stability than unmodified isoC | 5-Me-isodC |
| 5-nitroindole | Universal base analog (non-H-bonding) | Primers across variable sequences | Lowers duplex Tm; avoid multiple adjacent placements | 5NitInd |
| Degenerate Base (Mixed Base)/ Custom Column | Mixture of standard bases at one position | Library synthesis; polymorphism coverage | IUB pills define ratio; requires custom synthesis column for 3′ sites | CC |
| deoxyXanthosine | dX, deamination product of guanosine | DNA repair/lesion studies; mispairing assays | Pairs with C but prone to mismatch | dX |
| dK degenerate base | Artificial base K | Pairs with dP in expanded alphabet systems | Not functional without partner base dP | dK |
| dP degenerate base | Artificial base P | Pairs with dK in expanded alphabet systems | Not functional without partner base dK | dP |
| Inosine deoxy (dI) | Universal wobble base in DNA | Primers with polymorphic sites | Pairs with A, C, G, or T with bias | dI |
| Inosine ribo (rI) | Universal wobble base in RNA | tRNA wobble base; RNA structure studies | Recognized variably by polymerases | rI |
| iso deoxyguanosine dG (iso dG) | Isoguanosine analog | Pairs with isoC; expanded genetic alphabet | Requires isoC counterpart for correct pairing | iso dG |
Note: ESI-MS is not performed on mixed-base oligos due to sequence ambiguity.
Deoxyinosine (dI) is the most widely used degenerate base. It acts as a “universal” nucleotide, able to pair with all four natural bases (preference order: I–C > I–A > I–T ≈ I–G). Despite unequal affinities, inosine is effective in primers and probes where wobble pairing is needed to recognize related sequences.
Other degenerate bases are useful in specific contexts. 5-nitroindole, for example, pairs indiscriminately with all four bases by stacking rather than hydrogen bonding. Its effectiveness depends on placement within a primer or probe, but it has been used in probe sets targeting conserved rRNA regions across different microorganisms. Additional analogs such as 2-aminopurine, iso-dG, and 5-methyliso-dC each have specialized applications described in their respective technical sheets.
Convertible bases are modified nucleotides that carry temporary substituents or reactive handles. After oligo synthesis, these groups can be selectively transformed or displaced to introduce dyes, haptens, cross-linkers, or other functional moieties. This strategy allows precise placement of labels or reactive sites without disrupting synthesis efficiency.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Convertible 5-F-dC (TMP-5-F-dU) | Fluoro-substituted cytidine analog with removable protecting group | Convertible handle for post-synthetic labeling or conjugation | Useful for generating reactive intermediates; mild effect on Tm | 5-F-dC |
| Convertible dA (O6-Phenyl-deoxyinosine) | Purine analog with bulky O6-phenyl group | Polymerase fidelity and lesion bypass studies | Perturbs hydrogen bonding; good for mutagenesis assays | O6-Phenyl-dI |
| Convertible dG (2-Fluoro-deoxyinosine) | Fluorinated guanine/inosine analog | Stability and recognition studies; reactive convertible base | Alters wobble pairing; adds hydrophobicity | 2-FdI |
| Convertible dU & dC (O4-Triazolyl-dU) | O4-linked triazole-modified uracil | Click chemistry and cross-linking applications | Versatile reactive handle; requires CuAAC or strain-promoted click | O4-Tri-dU |
| N6-Methyl rA (m6A) | N6-methyladenosine, natural epigenetic RNA modification | Epitranscriptomics studies; RNA–protein binding assays | Common in mRNA; regulates translation and splicing | m6A |
Epigenetic and methylation mimics include cytosine and adenine derivatives that model natural DNA and RNA modifications such as 5mC, 5hmC, 5fC, 5caC, and m6A. These bases are valuable for studying gene regulation, chromatin structure, DNA repair, and RNA processing. They allow researchers to replicate or interrogate natural marks in synthetic oligos for binding, enzymatic, or structural assays.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| 5-Carboxy dC | Oxidized form of 5-methylcytosine (5mC) | Epigenetic studies; mapping DNA demethylation intermediates | Weakens duplex stability; recognized by TET proteins | 5-ca-dC |
| 5-formyl dC | Formylated derivative of cytosine | Epigenetic and DNA repair studies | Reactive aldehyde group; can cross-link or modify proteins | 5-for-dC |
| 5-hm dC (5-Hydroxymethyl-dC) | Oxidized 5mC derivative | Epigenetic modification mapping; 5hmC detection assays | Intermediate in active demethylation; alters protein recognition | 5hm-dC |
| 5-Hydroxymethyl-dU | Thymidine analog with hydroxymethyl group | DNA-protein binding studies; labeling handle | Increases hydrophilicity; mild effect on duplex Tm | 5-hm-dU |
| 5-methyl deoxycytosine (5mdC) | Methylated cytidine | Model for CpG methylation; gene regulation studies | Raises duplex stability; affects protein binding | 5mdC |
| 5-methyl-Cytosine (5mrC) | Methylated cytosine (RNA form) | Epitranscriptomics research; RNA modification studies | Alters RNA structure and protein interactions | 5mrC |
| N6-Methyl dA (m6dA) | Methylated adenine in DNA | DNA epigenetics; methylation mapping | Rare in higher eukaryotes; important in prokaryotes | m6dA |
| N6-Methyl rA (m6A) | Methylated adenosine in RNA | Epitranscriptomics; regulation of mRNA translation and splicing | Most abundant internal RNA modification; reversible | m6A |
| rZebularine | Cytidine analog lacking amino group at C4 (RNA form) | DNA methyltransferase inhibitor studies | Acts as a cytidine mimic; reduces methylation activity | rZ |
| Zebularine- deoxy-5 methyl (dZ-5me) | Deoxycytidine analog with methyl substitution | Epigenetic research; DNMT inhibition | Stabilizes duplexes; commonly used as methylation mimic | dZ-5me |
Engineered base pairs can pair selectively outside A/T/G/C rules, enabling specialized labeling, storage, or molecular computing workflows. Availability is platform-specific; reach out to discuss current options.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| IsoC | Isocytosine analog designed to pair specifically with isoguanine (isoG) | One of the earliest orthogonal base pairs | Requires isoG partner; prone to mispairing if isoG tautomerizes | isoC |
| IsoG | Isoguanine analog that pairs specifically with isocytosine (isoC) | One of the earliest orthogonal base pairs | Tautomerization can cause mispairing with C | isoG |
| 5-Me-iso-dC | 5-Methyl-isodeoxycytidine, methylated isoC analog | Expanded alphabet systems; improves isoC–isoG stability | Methyl group reduces tautomeric shifts and increases polymerase compatibility | 5-Me-iso-dC |
| dP (P sugar) | 2-amino-8-(1-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one | Strong orthogonal base pairing in expanded genetic systems | Designed by Steven Benner’s group (Foundation for Applied Molecular Evolution) | dP / dS |
| dZ (Z sugar) | 6-amino-3-(2′-deoxyribofuranosyl)-5-nitropyridin-2(1H)-one | Strong orthogonal base pairing in expanded genetic systems | Designed by Steven Benner’s group (Foundation for Applied Molecular Evolution) | dZ / dB |
Hapten-tagged bases are modified nucleotides that carry small antigenic tags such as biotin, digoxigenin (DIG), dinitrophenol (DNP), fluorescein, or rhodamine. These tags enable highly specific detection or capture of oligos via antibody recognition or streptavidin/avidin binding. Hapten modifications are widely used in molecular biology, diagnostics, FISH/ISH assays, ELISAs, and affinity purification workflows.
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Biotin-dU / Biotin-dC / Biotin-dT | Base analogs carrying a biotin hapten | Affinity capture, immobilization, ELISA, blotting | High-affinity binding to streptavidin or avidin | Bio-dU |
| Digoxigenin (DIG)-dU / DIG-dC | Plant steroid hapten attached to pyrimidine base | ISH/FISH probes; immuno-detection assays | Detected with anti-DIG antibodies | DIG-dU |
| Dinitrophenol (DNP)-dU | Small aromatic hapten (dinitrophenol) | Immuno-detection, probe localization | Recognized by anti-DNP antibodies | DNP-dU |
| Fluorescein (FITC)-dU | Fluorescein hapten conjugated to uridine analog | Fluorescence + antibody detection | Recognized by anti-FITC antibodies | FITC-dU |
| Rhodamine-dU | Rhodamine hapten conjugated to uridine analog | Dual immuno-fluorescent detection | Recognized by anti-Rhodamine antibodies | Rho-dU |
| Nitrophenyl / Nitrobenzyl bases | Aromatic nitro hapten or photocleavable group | Specialty probes; cross-reactivity assays | Immunogenic; some variants photocleavable | NP-dU |
| Steroid-hapten bases | Modified bases conjugated with steroid haptens (e.g. cortisol, estradiol) | Aptamer selection, immunogenic probe development | Special order; used in hormone-related assays | Steroid-dU |
structure & blocking modifications are typically bases (or base analogs) that disrupt normal Watson–Crick pairing, introduce bulky or rigid features, or sterically block enzymatic access. These are used to control success structure, hybridization, and nuclease interaction.
Here’s a structured list of common modified bases for structure and blocking:
| Product | Description | Typical Use | Notes | Catagory |
|---|---|---|---|---|
| Abasic (dSpacer, Abasic II) | Lacks a nucleobase; creates a structural gap that interrupts duplex formation. | Blocks polymerase extension; mimics abasic lesions in DNA. | Commonly used as a structural block in assays. | Bulky / Steric Blocking Bases |
| Spacer C3 / C9 / HEG | Non-nucleosidic spacers inserted in place of bases. | Prevent hybridization or extension at specific positions. | Technically spacers, but used as structural/steric blocks. | Bulky/Steric Blocking Bases |
| Pyrene-dU / Perylene-dU | Bulky aromatic base analogs that strongly perturb duplex structure. | Intercalating probe; blocks enzymatic recognition. | Often used in structural or FRET-based studies. | Helix-Distorting / Non-Natural Bases |
| Pyrrolo-dC | Fluorescent cytosine analog with altered geometry. | Local structure probing, blocking normal base-pairing. | Used for fluorescence studies. | Helix-Distorting / Non-Natural Bases |
| Pseudo-Uridine / 2′-deoxypseudoU | Modified uridine that alters hydrogen bonding. | Stabilizes or perturbs structure; blocks recognition. | Common in RNA studies. | Helix-Distorting / Non-Natural Bases |
| 5-Bromo-dU / 5-Iodo-dU | Halogenated bases that can form UV-induced crosslinks. | Crosslinking, blocking, and photoreactive studies. | Photo-activated blockers. | Photoreactive / Crosslinking Bases (block via covalent trapping) |
| 4-Thio-dU | Sulfur substitution at the 4-position of uracil. | UV-activated crosslinker to trap structure. | Used in photo-crosslinking assays. | Photoreactive / Crosslinking Bases (block via covalent trapping) |
| 5-Me-2′-deoxyZebularine | Cytidine analog that disrupts hydrogen bonding. | Blocks polymerase extension; mimics DNA lesions. | Epigenetic and structural blocking applications. | Structure-Mimicking / Artificial Bases |
| Unnatural Bases (dP, dK, X, Y) | Do not pair with natural bases; distort helix. | Blocking, structure probing, artificial base-pair studies. | Useful in studying unnatural base pairs and blocking reactions. | Structure-Mimicking / Artificial Bases |
Cross-Linking and Ligation Bases — Modified nucleoside analogs such as psoralens, halogenated bases, thio-derivatives, and clickable groups (alkyne, amino, convertible bases) provide powerful tools for covalent cross-linking, structural probing, and bioconjugation. These modifications enable UV- or light-induced cross-links, click-chemistry ligation, or post-synthetic functionalization, supporting diverse applications in nucleic acid structural biology, diagnostics, and therapeutic design.
Here’s a structured list of common modified bases for crosslinking and ligation bases::
| Product | Description | Typical Use | Notes | Catagory |
|---|---|---|---|---|
| Convertible dG (2-Fluoro deoxy inosine) | Convertible base analog that can be derivatized post-synthetically for cross-linking or conjugation | Post-synthetic modification, conjugation, cross-linking | Useful for versatile conjugations | |
| 3-Cyanovinylcarbazole (CNVK) | Photo-reactive base analog enabling UV-induced cross-linking to nucleic acids/proteins | UV-induced cross-linking of oligos with nucleic acids/proteins | Light-activated modification | |
| 3'-Propargyl-5-Me-dC | Alkyne-modified base analog for click chemistry ligation and conjugation | Click chemistry ligation and conjugation | Compatible with azide reagents | |
| 3'-Amino-dT | Amino-modified thymidine enabling conjugation to activated esters (NHS esters) | Cross-linking with NHS-ester activated compounds | Amine allows broad conjugation chemistry | |
| Psoralen C6 | Psoralen derivative with long linker arm for interstrand cross-linking upon UV irradiation | DNA interstrand cross-linking, photobiology studies | Strong interstrand cross-links | |
| Psoralen C2 | Psoralen derivative with shorter linker for interstrand cross-linking studies | Cross-linking for DNA interaction studies | Shorter spacer than C6 | |
| 5-Iodo-dT | Halogenated base analog for photocrosslinking, enhances structural probing | Structural probing, photo-crosslinking | Iodine enhances crosslink yield | 5'-I-dT |
| 5-Iodo-dU | Halogenated uridine analog, used in photocrosslinking and X-ray crystallography | Cross-linking in nucleic acid-protein studies | Facilitates phase determination in crystallography | 5-I-dU |
| 5-Iodo-dC | Halogenated cytidine analog, enhances base pairing studies and photocrosslinking | Crystallography, cross-linking | Stable halogenated cytidine derivative | 5-I-dC |
| 5-Bromo dU | Brominated uridine for cross-linking and crystallography (UV-inducible) | X-ray crystallography, photocrosslinking | Widely used in structural biology | 5-Br-dU |
| 5-Bromo-dC | Brominated cytidine, useful in crystallography and photo-induced cross-linking | Crystallography, nucleic acid structural studies | High efficiency in crystal studies | 5-Br-dC |
| 8-Bromo-dG | Brominated guanosine analog for structural probing and photocrosslinking | Probing DNA structure and dynamics | UV-inducible crosslink base | 8-Br-dG |
| 8-Bromo-dA | Brominated adenosine analog, induces photo-crosslinking | Photo-crosslinking and nucleic acid dynamics | Effective in photo-induced probing | 8-Br-dA |
| 6-thio-dG | Thio-modified guanosine, enhances cross-linking and metal coordination | Metal coordination and cross-linking | Reactive sulfur site | 6-thio-dG |
| 2-Thio-dT | Thio-modified thymidine for structural probing and cross-linking | Cross-linking, structure probing | Forms stable cross-links | 2-Thio-dT |
| 4-Thio-dT | Thio-modified thymidine variant, used in photocrosslinking and probing interactions | Photo-crosslinking | Alternative sulfur-modified analog | 4-Thio-dT |
| 4-Thio-dU | Thio-modified uridine analog with cross-linking capability | Cross-linking and probing studies | Sulfur enables reactivity | 4-Thio-dU |
| 5-Ethynyl-dU | Ethynyl-modified uridine for click chemistry ligation, conjugation, and cross-linking | Click chemistry ligation, labeling, cross-linking | Alkyne enables click ligation |
Halogenated bases — Incorporating bromine, iodine, or fluorine into nucleosides provides photo-reactivity and strong X-ray scattering, enabling cross-linking, structural probing, and phase determination in crystallography. These modifications are widely used in DNA and RNA structural biology, diagnostics, and design of photoreactive probes.
Here’s a structured list of common modified bases for crosslinking and ligation bases::
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| 5-Bromo-dC (5-Br dC) | Brominated cytidine analog | X-ray crystallography; photo-induced cross-linking | Heavy atom for phasing; UV-sensitive | 5-Br-dC |
| 5-Bromo-dU (5-Br dU) | Brominated uridine analog | Crystallography; photocrosslinking | UV-inducible; widely used in structural biology | 5-Br-dU |
| 5-Bromo-rC (5-Br rC) | Brominated ribocytidine (RNA form) | RNA structural probing; photo-crosslinking | Introduces heavy atom for RNA crystallography | 5-Br-rC |
| 5-Bromo-rU (5-Br rU) | Brominated ribouridine (RNA form) | RNA structure/dynamics studies | Enhances X-ray scattering | 5-Br-rU |
| 5-Fluoro-deoxyuridine (5-F dU) | Fluorinated uridine analog | NMR probes; duplex stability tuning | Small halogen; mild Tm change | 5-F-dU |
| 5-Iodo-rC (5-I rC) | Iodinated ribocytidine | RNA crystallography; phase determination | Heavy halogen substitution | 5-I-rC |
| 5-Iodo-dC (5-I dC) | Iodinated deoxycytidine | X-ray phasing; cross-linking | Enhances scattering; stable derivative | 5-I-dC |
| 5-Iodo-dU (5-I dU) | Iodinated deoxyuridine | Photocrosslinking; X-ray crystallography | Strong heavy-atom derivative | 5-I-dU |
| 5-Iodo-rU (5-I rU) | Iodinated ribouridine | RNA structural studies; photocrosslinking | UV-activated crosslinker | 5-I-rU |
Intercalator-modified bases are nucleoside analogs carrying bulky aromatic groups that insert between stacked base pairs, enhancing duplex stability, enabling fluorescence or FRET studies, and supporting photo-induced crosslinking for structural biology, diagnostics, and probe design.
Here’s a structured list of common modified bases for crosslinking and ligation bases::
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Psoralen-dU (Psoralen C2 / C6) | Psoralen attached at uridine with short or long linker | UV-induced interstrand crosslinking, photobiology | Forms covalent crosslinks upon 320–365 nm irradiation | Psor-C2 / Psor-C6 |
| Ethidium-dU | Ethidium dye conjugated to deoxyuridine | Fluorescent intercalator, nucleic acid detection | Classic dye; strong fluorescence upon binding | Et-dU |
| Acridine-dC / Acridine-dU | Acridine aromatic moiety linked to cytidine or uridine | Stabilizing duplexes; structural probes | Strong intercalator; raises duplex Tm | Acr-dC / Acr-dU |
| Pyrene-dU | Pyrene ring attached at 5-position of dU | Stacking probe; excimer/exciplex fluorescence | Sensitive to environment; can quench nearby dyes | Pyr-dU |
| Perylene-dU | Perylene fluorophore attached at 5-position of dU | FRET donor/acceptor, stacking probe | Very hydrophobic; prefers internal positions | Per-dU |
| Anthraquinone-dU | Anthraquinone aromatic group linked to uridine | Photoinduced electron transfer, damage studies | Generates reactive oxygen species upon irradiation | AQ-dU |
| Naphthyl-dC | Naphthyl aromatic group conjugated to cytidine | Probing stacking interactions | Smaller intercalator vs pyrene/acridine | Naph-dC |
Fluorescent base analogs are modified nucleosides that emit fluorescence when incorporated into DNA or RNA. Unlike bulky dye labels, they minimally perturb native duplex structure while reporting on stacking, pairing, or conformational changes. These bases are powerful tools for FRET studies, hybridization monitoring, and nucleic acid–protein interaction assays.
Here’s a structured list of common modified bases for crosslinking and ligation bases::
| Product | Description | Typical Use | Notes | Code |
|---|---|---|---|---|
| Ribo-tC° | Tricyclic cytosine analog (RNA version) | Fluorescent reporter for RNA duplexes and structural studies | Pairs like C; minimal perturbation of RNA structure | ribo-tC° |
| 2-Aminopurine (2-AP) | Fluorescent adenine analog | Base-stacking probe; conformational dynamics | Fluorescence quenched in duplex; sensitive to local environment | 2-AP |
| Pyrrolo-C | Fluorescent cytosine analog | Local environment and stacking studies | Emission sensitive to hybridization; minimally disruptive | Pyr-C |
| Perylene-dU | Perylene moiety conjugated at 5-position of dU | FRET donor/acceptor; stacking probe | Hydrophobic; prefers internal positions | Per-dU |
| Pyrene-dU | Pyrene fluorophore linked at 5-position of dU | Excimer/exciplex fluorescence; stacking probe | Sensitive to environment; strong π-stacking | Pyr-dU |
| tCnitro | Nitro-substituted tricyclic cytosine analog | Internal fluorescent reporter; FRET quencher | High quantum yield; pairs as C | tCnitro |
| tC° | Neutral tricyclic cytosine analog | Environment-sensitive fluorescent probe | Pairs as C; minimal structural perturbation | tC° |
| tC | Tricyclic cytosine analog | FRET donor/acceptor; duplex stability studies | Pairs like C; excellent fluorescent reporter | tC |
| Pyrrolo-dC | Fluorescent cytidine analog | Hybridization and conformational studies | Excites ~350 nm; sensitive to stacking | Pyr-dC |
| Etheno-dA (ε-dA) | Fluorescent adenine lesion analog | DNA damage/repair assays; fluorescence reporter | Emits ~410 nm; perturbs base-pairing | ε-dA |
Synthesis of standard and modified DNA oligonucleotides, from discovery to GMP production.
Learn MoreTaqMan®, molecular beacons, FRET probes and custom dual-labeled designs for sensitive assays.
Learn MoreCustom selection and chemical optimization of DNA aptamers for diagnostics and therapeutics.
Learn MoreCodon-optimized synthetic DNA constructs, delivered in vectors, ready for expression or cloning.
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., inosine or 7-deaza-dG can be tolerated in primers, while strong universal bases (5-NI/3-NP) and bulky conjugates can inhibit extension. Validate per polymerase.
Yes—contact us with your target base/handle (e.g., special photo-reactive groups or cross-coupling handles) and we’ll evaluate feasibility.
Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.