Backbone Modification using Sulfurisation Reagents (Phosphorothioate Synthesis)

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Applicable Products

0023 Sulphurising Reagent
2171 EDITH

Physical & Dilution Data

Dilution volumes (in ml) are for 0.05M solutions in dry acetonitrile (4050). Adjust accordingly for other concentrations.

Item

Mol. Formula

Mol. Wt.

Pack Size

Dilute With

0023-C001 C7H4O3S2 200.23  1g 100ml
0023-C002 C7H4O3S2 200.23 2g 200ml
2171-G005 C4H5NO2S2 163.21 5mmol 100ml
2171-G010 C4H5NO2S2 163.21  10mmol 200ml
2171-G023 C4H5NO2S2 163.21 22.5mmol 450ml

Dissolution

Beaucage Reagent (0023) is supplied in solid form in 1g and 2g packs, together with a silanised bottle suitable for direct attachment to an automated DNA synthesiser. Simply pour the reagent into the silanised bottle and add anhydrous acetonitrile (100ml/g) to obtain a 0.05M solution. For smaller scale syntheses, smaller quantities can be prepared (e.g. 0.5g/50ml). After use, the silanised bottle may be rinsed with acetonitrile, dried and stored for future use. EDITH (2171) is available in millimolar pack sizes ready for dilution with convenient amounts of anhydrous acetonitrile to a 0.05M concentration, according to the table above.

Sulphurisation

Routinely sulphurisation reagents are used on an automated DNA synthesiser, utilising the dedicated thio port where available, following the instrument manufacturer’s recommendations for sulphurisation cycles. Depending on the type of synthesiser, there may be a cycle for sulphurising reagent available. If a dedicated port and line is not available, the oxidiser port and line may be used. In this case, the line must first be flushed extensively with acetonitrile followed by liberal flushing with the sulphurising reagent. After use, remove the reagent immediately from the instrument and flush the line with acetonitrile.

When using EDITH (2171) a sulphurisation time of 30s is recommended, although longer times will not have any adverse affect on the oligo if reducing the sulphurisation time in the cycle is not possible.

For optimum results, it is recommended that the sulphurisation is carried out prior to the capping step in order to minimise competitive oxidation.

Some deleterious G modification has been observed when using EDITH with certain labile (fast) deprotection chemistry.1 This can be eliminated by using a modified coupling-cap- thio-cap cycle, thus allowing preparation of phosphorothioate oligos without the need for prolonged ammonium hydroxide deprotection. The cap-thio-cap cycle is possible using EDITH due to the short sulphurisation time required.

Cleavage & Deprotection

Phosphorothioate oligos can be cleaved from the support and deprotected using ammonium hydroxide, therefore follow any necessary guidelines according to the nucleobases used.

Purification

Phosphorothioate purification is routinely carried out by RP-HPLC or cartridge methods. SAX2 and WAX3 HPLC has also been described, however the former requires high salt concentrations. FPLC at high pH is not recommended.

Note that high purity or 2’-OMe phosphorothioates are best purified by PAGE.

Analysis

The best means of identifying the presence of oxidised linkages in the oligo is by MS. Either ESI or MALDI are effective for this purpose.

Storage & Stability

2171 - Store the solid in a glass container in the freezer at –10 to –30°C. Although EDITH is reportedly stable in solution for several months, we recommend, as with all other oligonucleotide synthesis reagents, that solutions are freshly prepared as close to use as possible. It can be used on the synthesiser for several days, however, without any drop in performance provided no precipitate is observed.

0023 - Store the solid reagent in a freezer at –10 to –30 ̊C, and dry. In solution in acetonitrile, it must be stored in plastic or silanised glass containers. It will remain stable under these conditions for several months (precipitation will accompany decomposition). Where the solution has been used on an oxidiser port, the reagent will decompose over 1-2 days. Where a spare port is routinely used for this reagent, the solution will be stable for up to a month.

References

  1. Evaluation of 3-ethoxy-1,2,4-dithiazoline- 5-one (EDITH) as a new sulfurizing reagent in combination with labile exocyclic amino protecting groups for solid-phase oligonucleotide synthesis, M.Y.-X. Ma, J.C. Dignam, G.W. Fong, L. Li, S.H. Gray, B. Jacob- Samuel and S.T. George, Nucleic Acids Research, 25, 3590-3593, 1997.
  2. Separation of synthetic phosphorothioate oligonucleotides from phosphodiester-defect species by strong-anion exchange HPLC, B.J. Bergot and G. Zon, Annals of the New York Academy of Sciences, 660, 310-312, 1992.
  3. Ion-exchange high-performance liquid chromatography analysis of oligodeoxyribonucleotide phosphorothioates, V. Metelev and S. Agrawal, Anal. Biochem., 200, 342-346, 1992.

The use of EDITH in the US is protected under US Patent No. 5,852,168 and licence for such use must be sought from The University of Minneapolis.

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