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 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 Oligo Size, Scale of Synthesis & Purification Guidelines
Product	50 nmol scale	200 nmol scale	1 umol scale	2 umol scale	10 umol scale	15 umol scale
Maximum Size	30 mer	60 mer	80 mer	150 mer	150 mer	150 mer
Purification Grade	PAGE or RPC	PAGE	PAGE	PAGE	PAGE	PAGE
All Gene Link RNA oligos shorter than 18 mer usually do not require any further purification.

RNA Purification (price per oligo in USD)
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

Rush Oligo Purification Service

Certain experiments cannot wait for an extra day. When such is the case, order "Rush Oligo Purification Service". The custom oligo will be on fast track to be gel purified as soon as the oligos are synthesized and processed. This typically will save 2-3 days.

Rush Purification Service (Additional charge per DNA oligo, all prices in USD)
Product 50 nmol scale 200 nmol scale 1 umol scale 2 umol scale 10 umol scale 15 umol scale

Catalog No. (PAGE) 27-6400-77R 27-6400-77R 27-6400-55R 27-6400-88R 27-6400-44R 27-6400-99R

Rush PAGE Service Charge 35.00 35.00 50.00 65.00 250.00 250.00

Catalog No. (RPC) 27-6400-11R 27-6400-11R 27-6400-22R 27-6400-23R 27-6400-33R 27-6400-34R

Rush Reverse Phase Purification (RPC) Service Charge 10.00 10.00 15.00 20.00 40.00 60.00

Click here for DNA Oligos scale of synthesis and yield.

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

	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