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Inosin
2'deoxyinosin is a "universal" base (it has the ability to bind to each of the 4 standard bases). It can be located anywhere in the oligonucleotide chain.
Degen bases like dK and dP refer to synthetic, non-standard nucleobases used in molecular biology used in oligonucleotide synthesis — to allow degenerate (ambiguous) base pairing. They are alternatives to the classic “N” base, used to encode a mixture of A, T, G, C at a given position, but with greater control and performance in some contexts.
dK and dP are part of a complementary base pair system used to create degenerate positions with less bias than traditional N mixtures.
dK (deoxyK):
- Pairs with dP
- Often used in positions where you want a degenerate base that can pair with more than one counterpart.
- Structurally designed to allow non-standard, but selective, base pairing.
dP (deoxyP):
- Also a degenerate or ambiguous base
- Pairs with dK
- Its use allows for controlled degeneracy, unlike random mixtures.
Why Use dK/dP Instead of N?
| Feature | “N” base (A+C+G+T mix) | dK/dP system |
| Mixture bias | High (due to phosphoramidite differences) | Low (single base, not mixed) |
| Predictability of synthesis | Low | Higher (defined synthetic base) |
| Application in enzymatic reactions | Sometimes unpredictable | Better base pairing control |
Comparison (I) with dK/dP
| Feature | Inosine (I) | dK/dP system |
| Base type | Natural analog | Synthetic analogs |
| Pairing spectrum | Broad (C > A ≈ U > G) | dP: A/C/T; dK: G/T |
| Pairing strength | Weak/moderate | Strong/moderate (more specific) |
| Specificity | Low (can pair with multiple bases) | Higher (defined degenerate logic) |
| Duplex stability (Tm) | Lower Tm due to mismatch-like behavior | More stable, predictable Tm |
| Use in PCR/hybridization | Sometimes problematic (off-targets) | Better tolerated, more precise |
| Polymerase compatibility | Can cause stalling or errors | Often better tolerated |
| Typical usage | Legacy degenerate primers | Modern degenerate oligos |
| Cost | Lower | Higher |
| Common issues | Cross-hybridization, low Tm | Still synthetic; polymerase-dependent |
