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RNA Oligonucleotide Purification

Long RNA Oligos and Complex Modifications

Gene Link specializes in the synthesis of RNA modified oligos, RNA fluorescent probes with quenchers, chimeric oligos containing various combinations of DNA, 2'O methyl bases and phosphorothioate linkages.

RNA Oligo Gel Purification

Gel Purified Oligo Gel Electrophoresis

Each oligo is run side by side on a polyacrylamide gel to visually assess quality. A real gel picture is included as part of the oligo report. Polyacrylamide gel electrophoresis of crude and gel purified RNA oligos in adjacent lanes. Lanes 1 & 2: 89 mer; lanes 3 & 4: 84 mer; lanes 5 & 6: 68 mer; lanes 7 & 8: 83 mer.

Recommendation:

At Gene Link we recommend gel purification of all RNA oligos longer than 30mer. Gel purification is the “gold standard” method of purification as the denaturing polyacrylamide gel resolution approaches single base and the major band is clearly visible to be purified.
RNA Purification (price per oligo)
Product 50 nmol scale 200 nmol scale 1 umol scale 2 umol scale 10 umol scale 15 umol scale
Gel Purification 90.00 90.00 210.00 310.00 1900.00 2250.00
Catalog Number 27-6400-77 27-6400-77 27-6400-55 27-6400-88 27-6400-44 27-6400-99
 
Reverse Phase Cartridge 45.00 45.00 135.00 270.00 1080.00 1380.00
Catalog Number 27-6400-11 27-6400-11 27-6400-22 27-6400-23 27-6400-33 27-6400-34


RNA Oligo Scale of Synthesis and Typical Yield*
  Crude Desalted RPC Purified** Gel Purified
20 mer RNA oligo
Typical Yield
20 mer RNA oligo
Typical Yield
20 mer RNA oligo
Typical Yield
50 mer RNA oligo
Typical Yield
100 mer RNA oligo
Typical Yield

Scale

A260 Units

nmols

mg

A260 Units

nmols

mg

A260 Units

nmols

mg

A260 Units

nmols

mg

A260 Units

nmols

mg

50 nmol

~5 ~25 ~0.15 ~1 ~5 ~0.04 NA NA NA NA NA NA NA NA NA

200 nmol

~15 ~75 ~0.5 ~3 ~15 ~0.15 ~1 ~5 ~0.04 NA NA NA NA NA NA

1 umol

~40 ~200 ~1.4 ~15 ~75 ~0.6 ~5 ~25 ~0.2 ~2 ~4 ~0.06 ~1 ~1 ~0.03

2 umol

~72 ~360 ~2.52 ~27 ~135 ~1.08 ~9 ~45 ~0.36 ~4 ~8 ~0.12 ~2 ~2 ~0.06

10 umol

~320 ~1600 ~11.2 ~120 ~60 ~4.8 ~40 ~200 ~1.6 ~30 ~60 ~0.9 ~18 ~18 ~0.54

15 umol

~480 ~2400 ~16.8 ~180 ~900 ~7.2 ~60 ~300 ~2.4 ~40 ~80 ~1.2 ~24 ~24 ~0.72

Purity & Yield

Purity is greater than 75%


depending on oligo sequence and structure. 

Reverse phase purification recommended.

Gel purification recommended to achieve purity above 95%.

Purity 85% to 95%


depending on oligo sequence and structure yield and Purity will be lower for sequences with high GC content

Not recommended for RNA oligos longer than 35 mer.

**RPC is reverse phase purification using a cartridge; a substitue for HPLC.

Purity 98% to ~100%


depending on oligo sequence and structure

Yield will gradually decrease as length of oligo increases. Palindromes, hairpins and high GC content oligos and oligos containing stretches of 3 or more G's induce strong secondary structure and base stacking thus decreasing purity and yield.

*a. Typical yield stated in the table is for unmodified random sequence oligos. Reduction in yield is observed with high GC content oligos and those forming strong secondary structures.

b. Reduced yield is expected with modified oligos. The reduction percentage varies with modification type and number of sites. Typical reduction is 10%-20% per modified site.

c. Yield of 40µg/A260 unit for RNA oligos is calculated for an ~equimolar base composition. Long stretches of a single base or homopolymers will have variable yields. Example for homopolymeric 50 mer: A(50) = ~20/A260 Unit; G(50) = ~28/A260 Unit; U(50) = ~35/A260 Unit and C(50) = ~39/A260 Unit

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