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Custom RNA Oligonucleotide Synthesis

Search Modifications
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 & 2' O methyl RNA unmodified Oligonucleotides (price per base)*
Product 50 nmol scale 200 nmol scale 1 umol scale 2 umol scale 10 umol scale 15 umol scale
RNA Oligonucleotides $6.25 $8.25 $14.40 $28.00 $118.00 $192.00
Catalog Number 27-6400-05 27-6400-02 27-6400-01 27-6400-03 27-6400-10 27-6400-15
Maximum Length of Synthesis 30 mer 60 mer 100 mer 150 mer 150 mer 150 mer
 
2' O methyl RNA Oligo $6.00 $8.00 $16.00 $28.00 $102.00 $148.00
Catalog Number 27-6410-05 27-6410-02 27-6410-01 27-6410-03 27-6410-10 27-6410-15
Maximum Length of Synthesis 30 mer 60 mer 160 mer 160 mer 160 mer 160 mer
 
phosphorothioate linkages $3.50 $4.25 $6.50 $9.00 $52.00 $65.00
Catalog Number 27-6401-05 27-6401-02 27-6401-01 27-6401-03 27-6401-10 27-6401-15
 
chimeric linkages $50.00 $50.00 $75.00 $110.00 $425.00 $610.00
Catalog Number 27-6420-05 27-6420-02 27-6420-01 27-6420-03 27-6420-10 27-6420-15
*minimum charge for 15 mer or 15 phosphorothioate linkages apply
RNA Oligo Scale of Synthesis and Typical Yield of Unmodified Oligos*
  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 ~0.25 ~1 ~0.03 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 ~600 ~4.8 ~40 ~200 ~1.6 ~20 ~40 ~0.60 ~10 ~10 ~0.30

15 umol

~480 ~2400 ~16.8 ~180 ~900 ~7.2 ~60 ~300 ~2.4 ~40 ~60 ~0.90 ~15 ~15 ~0.45

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

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 oligonucleotides

RNA and 2’-O-methyl RNA oligonucleotide synthesis is performed at Gene Link using the beta cyanoethyl chemistry and state of the art synthesizers. These involve proprietary software protocols with long coupling times and specialized cycles to obtain ultra clean oligos.

RNA oligos are susceptible to degradation to the same extent as native RNA extracted from various sources. An attractive alternate to prevent degradation from nucleases is the use of 2’-O- methyl RNA bases, when specific 2’OH is not required. The 2’-O- methyl oligonucleotides confer considerable nuclease resistance and are similar in hydrogen bonding properties to RNA/RNA than the lower RNA/DNA binding property. The coupling efficiency of 2’-O- methyl phosphoramidite is also higher than the RNA monomers resulting in higher yield of full length oligos.

Gene Link also offers custom synthesis of RNA and DNA chimeric oligos with investigator specified ribo or deoxy bases or 2’-O-methyl bases. The chimeric oligos can also be synthesized with the regular phoshodiester bonds or substituted with phosphorothioate linkages. The combination of 2’-O- methyl RNA bases with phosphorothioate internucleotide linkages imparts these oligos greater nuclease resistance which is particularly useful for antisense studies (please refer to our technical sheet on Antisense Oligonucleotides for other modifications). Custom phosphorothioate oligonucleotides synthesized by Gene Link can be specified to have all the diester bonds substituted or only some selected diester linkages depending upon the researchers experimental requirement. Substitution of all diester linkage is recommended to provide greater nuclease resistance.

References

1. Goodwin,J.T., Stanick,W.A. and Glick,G.D. (1994) Improved solid phase synthesis of long oligoribonucleotides. Application to tRNA (phe) and tRNA(gly). J. Org. Chem. 59:7941-7943
2. Cotton,M., Oberhauser,B., Burnar, H. et al. (1991) 2'O methyl and 2'O ethyl oligoribonucleotides as inhibitors of the in vitro U7 snRNP-dependent messenger-RNA processing event. NAR 19:2629
3. Milligan, J.F., Matteucci, M.D. and Martin, J.C. (1993) Current concepts in antisense drug design. J. Medicinal Chem. 36:1923-1937.
4. Helene, C., Toulme, J. (1990) Specific regulation of gene expression by antisense, sense and antigene nucleic acids. Biochim. Biophys. Acta. 1049: 99-125.
5. Weintraub, H. M. (1990) Antisense RNA and DNA. Sci. Amer. 262:40-46.
6. Iyer, R.P., Egan. W., Regan, J.B and Beaucage, S.L. (1990) J. Am. Chem. Soc.112; 1253-1254.
7. Wagner, R.W., Matteucci, M.D., Lewis, J.G., Gutierrez, A.J., Moulds, C. and Froehler, B.C. (1993) Antisense gene inhibition by oligonucleotides containing C-5 propyne pyrimidines. Science 260:1510-1513.

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