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2'-OMe-5-Me-C (Bz) CE-Phosphoramidite

2'-OMe-5-Me-C (Bz) CE-Phosphoramidite

Phosphoramidite for the incorporation of a 2'-O-methyl 5-Me-ribo-C nucleobase within an oligonucleotide
  • High performance product for use on commercial oliognucleotide synthesizers.
  • Quality ensured by full QC testing.
  • Available packaged options for all common synthesizer instruments, and in bulk.
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Product information

Oligonucleotides containing 2'-OMe-5-Me-U (2'-OMe-T), 2'-OMe-N-Ac-5-Me-C or 2'-OMe-I are particularly applicable to triplex and antisense studies using 2'-OMe-RNA. For example, the immune stimulatory activity of CpG containing oligonucleotides in which C or G was substituted with 2'-OMe ribonucleotides, 5-Me-dC, or 2'-OMe-5-Me-C has been studied alone and in combination with TLR agonists. (1)
When 2'-OMe residues are incorporated into triplex forming oligonucleotides (2) (TFOs), similar trends in nuclease resistance and triplex stability are seen as with duplexes.
Hence they have been used to develop TFOs for use as gene targeting reagents.(3) Triplex stability can be increased further with the incorporation of 2'-OMe-5-Me-U residues into the oligonucleotide (4) using 2'-OMe-5-Me-U. Interestingly, 2'-OMe-5-Me C can have the opposite effect and destabilise the triplex, yet is still more stable than a DNA and/or RNA triplex. Incorporation of both 2'-OMe-5-Me U and 2'-OMe-5-Me C enables fine tuning of the Tm of the resulting triplex.

Ref:

  1. Modifications incorporated in CpG motifs of oligodeoxynucleotides lead to antagonist activity of toll-like receptors 7 and 9, D. Yu, D. Wang, F.-G. Zhu, L. Bhagat, M. Dai, E. R. Kandimalla and S. Agrawal, J. Med. Chem., 52, 5108-5114, 2009.
  2. Pyrimidine motif triplexes containing polypurine RNA or DNA with oligo 2'-O-Methyl or DNA triplex forming oligonucleotides, M. Behan and P.S. Miller, Biochim. Biophys. Acta., 1492, 155-162, 2000.
  3. The development of bioactive triple helix-forming oligonucleotides, M.M. Seidman, N. Puri, A. Majumdar, B. Cuenoud, P.S. Miller and R. Alam, in volume 1058, Therapeutic Oligonucleotides: Transcriptional and Translational Strategies for Silencing Gene Expression, 119–127, November 2005, Wiley-Blackwell.
  4. Effects of 5-methyl substitution in 2'-O-methyl oligo(pyrimidine)nucleotides on triple-helix formation, M. Shimizu, T. Koizumi., H. Inoue and E. Ohstuka, Bioorg. Med. Chem. Letts., 4, 1029-1032, 1994.

Applicable Products

LK2098 2'-OMe-I-CE Phosphoramidite
LK2099 2'-OMe-5-Me-U-CE Phosphoramidite (2'-OMe-T)
LK2192 2'-OMe-N-Ac-5-Me-C-CE Phosphoramidite

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.

Item

Mol. Formula

Mol. Wt.

Unit Wt.

250mg

500mg

1g

LK2098 C41H49N6O8P 784.85 344.22 3.19 6.37 12.74
LK2099 C41H51N4O9P 774.85 334.23 3.23 6.45 12.91
LK2192 C43H54N5O9P 815.90 333.24 3.06 6.13 12.26

Coupling

ETT, BTT or DCI can be used as activators. A coupling time of 6min (360s) is recommended.

Oxidation

No changes are required from standard methods.

Cleavage & Deprotection

Standard oligonucleotide deprotection conditions can be applied when deprotecting an oligo containing these modifications. In general, AMA at 65ºC for 10min is used, employing dmf-G and Ac-C in the sequence.

Storage & Stability

Store in a freezer below -10°C. Diluted samples are freshly prepared and used within 24h.

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