Universal Bases

Universal Bases

Universal bases can be used to replace degenerate bases. This type of modifier can base pair with all four of the standard bases. Designing primers from protein sequences by backtranslation usually results in degenerate oligonucleotides. Universal bases are used to reduce oligonucleotide degeneracy. The best known of these types of modified bases are 2'-DeoxyInosine and 2'-DeoxyNebularine. Neither of these two bases binds to all four bases evenly, but they are a frequently used method of reducing degeneracy. As an alternative, bases such as 3-Nitropyrrole 2'-deoxynucleoside and 5-Nitroindole 2'-deoxynucleoside can be used to take advantage of duplex stabilization by base stacking effects. The degenerate bases dP and dK can form base pairs with purines and pyrimidines, respectively, and can also be used to reduce the overall degeneracy of an oligonucleotide.

Deoxy Inosine (dI)	Qty.	5'-Mod	Internal	3' -mod
200 nmol	15 OD	$30	$30	$30
1.0 µmol	35 OD	$35	$35	$35
Nitroindole	Qty.	5'-Mod	Internal	3' -mod
200 nmol	15 OD	$150	$150	$50
1.0 µmol	35 OD	$225	$225	$60
2'-DeoxyNebularine	Qty.	5'-Mod	Internal	3' -mod
200 nmol	15 OD	$170	$170	NA
1.0 µmol	35 OD	$225	$225	NA
3-Nitropyrrole	Qty.	5'-Mod	Internal	3' -mod
200 nmol	15 OD	$180	$180	$80
1.0 µmol	35 OD	$290	$290	$95
dP	Qty.	5'-Mod	Internal	3' -mod
200 nmol	15 OD	$195	$195	NA
1.0 µmol	35 OD	$195	$195	NA
dK	Qty.	5'-Mod	Internal	3' -mod
200 nmol	15 OD	$195	$195	NA
1.0 µmol	35 OD	$195	$195	NA
dP + dK	Qty.	5'-Mod	Internal	3' -mod
200 nmol	15 OD	$195	$195	NA
1.0 µmol	35 OD	$195	$195	NA

Purification

Desalt or cartridge (RP1) purification is acceptable for most common phosphoramidite modifiers. However, additional purification is strongly recommended for modifiers that require NHS-ester chemistry to conjugate a dye through an amine linker such as Molecular Probes dyes.

Minimum Guarantee Purified Yield

Due to the chemistry of many modifications, yield will be approximately 40 - 60 % less than a standard oligo.Please see our yield chart for details.

Quality Controls

Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD₂₆₀ In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

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