dC (Ac) (5-Me) CE-Phosphoramidite
dC (Ac) (5-Me) CE-Phosphoramidite
Key featuresShow Hide
- C-5 Methyl pyrimidine nucleosides are known to stabilise duplexes relative to the non-methylated bases.
- The stabilisation properties of Me-dC make this a suitable modification for stabilisation of triplex strands, where its presence raises the melting temperature of the third strand.
- Acetyl nucleobase protection allows compability with milder deprotection conditions.
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The hybridisation properties of synthetic oligonucleotides are crucial for almost all applications. Optimisation of base pairing, and subsequent duplex stabilisation, is therefore desirable. C-5 Methyl pyrimidine nucleosides are known to stabilise duplexes relative to the non- methylated bases. Therefore the use of 5-Me-dC-CE Phosphoramidite (available either as N-Bz or N-Ac )(1) rather than dC results in enhanced binding (a similar comparison can be made between thymidine and 2'-deoxyuridine). This increase in duplex stabilisation is attributed to the hydrophobic nature of the methyl groups that helps eliminate water molecules from the duplex. We also offer a 5-Me-dC CPG for modification at the 3'-end. The stabilisation properties of Me-dC make this a suitable modification for stabilisation of triplex strands, where its presence raises the melting temperature of the third strand.
- Effect of 5-methylcytosine on the stability of triple-stranded DNA-a thermodynamic study, L.E. Xodo, G. Manzini, F. Quadrifoglio, G.A. van der Marel and J.H. van Boom, Nucleic Acids Research, 19, 5625-5631, 1991.
|LK2287||dU SynBase™ CPG 1000/110|
|LK2293||dI SynBase™ CPG 1000/110|
|LK2323||5-Me-dC SynBase™ CPG 1000/110|
Physical & Dilution Data
Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile (LK4050). Adjust accordingly for other concentrations. For µmol pack sizes, products should be diluted as 100µmol/ml to achieve 0.1M, regardless of molecular weight.
Couple the phosphoramidites LK2013, LK2016 and LK2017 using the standard method as recommended by synthesiser manufacturer with coupling times as per standard bases. 90s is recommended for 2529. A coupling time of 15min is recommended for LK2145. A coupling time of 3min is recommended for LK2164. The solid supports are used as per standard nucleoside supports.
For LK2013, LK2016, LK2017 and LK2529 standard oligonucleotide deprotection conditions can be applied when deprotecting an oligo containing these modifications, however LK2013, LK2016 and LK2529 are also compatible with AMA deprotection; typically 10min at 55oC.
LK2145 - Use AMA deprotection in conjunction with Ac-dC, rather than Bz-dC, or transamidation will occur. The supports are cleaved and deprotection carried out using the protocols required by the nucleobases.
LK2164 - Cleavage from support and primary deprotection is accomplished by treatment with ammonium hydroxide solution at room temperature for 24h.
After removing the solution1, the NPE groups are removed by treatment with 0.3M tetramethylguanidinium 2-nitrobenzaldoximate solution in water/dioxan (1:1) at 70°C for 48h. We find that this extended treatment is necessary to ensure complete removal of both of the NPE protecting groups.
It should be noted that this treatment generates a variety of low molecular weight by-products which are observed in the HPLC. Satisfactory results are obtained by de-salting the deprotection mixture into water using a NAP or G25 column before HPLC, from which the final oligonucleotide product can then be isolated.
Storage & Stability
Refrigerate dry compounds. Stability of phosphoramidites in solution is similar to standard dA, dC, dG and dT monomers.
- This is best achieved by removing the deprotection solution by G25 then freeze drying to remove the water. Heat cannot be used or the NPE groups would cleave.
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