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Oligo Synthesis

Oligo Synthesis : CEPs

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5-Hydroxymethyl-dC-CE Phosphoramidite

5-Hydroxymethyl-dC-CE Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1062-025-Hydroxymethyl-dC-CE Phosphoramidite 0.25g £1,659.00 Quantity Add to Order
10-1062-905-Hydroxymethyl-dC-CE Phosphoramidite 100µmoles £609.00 Quantity Add to Order
10-1062-955-Hydroxymethyl-dC-CE Phosphoramidite 50µmoles £318.00 Quantity Add to Order

Description

5-Hydroxymethyl-dC-CE Phosphoramidite

Structure

Catalog Number: 10-1062-xx

Description: 5-Hydroxymethyl-dC-CE Phosphoramidite

5'-Dimethoxytrityl-N-benzoyl-5-cyanoethoxy-methyl-2'-deoxyCytidine,
3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Formula: C50H57N6O9P M.W.: 917.00 F.W.: 319.21

Diluent: Anhydrous Acetonitrile
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: 30% Ammonium Hydroxide for 17 hours at 75°C.
Storage: Refrigerated storage, maximum of 2-8°C, dry
Stability in Solution: 2-3 days

DNA Methylation

One of the fastest growing fields in biology and cancer research is epigenetics. While the underlying genetic code defines which proteins and gene products are synthesized, it is epigenetic control that defines when and where they are expressed. This dynamic control of gene expression is essential for X chromosome inactivation, embryogenesis, cellular differentiation and appears integral to memory formation and synaptic plasticity.

In 2009, two reports1,2 described the discovery of 5-hydroxymethyl-2’-deoxyCytidine (hmdC), a novel dC modification in Purkinje neurons and embryonic stem cells. Later, a third report found this modification to be strongly enriched in brain tissues associated with higher cognitive functions.3 This new dC modification is generated by the action of a-ketoglutarate dependent TET enzymes (ten eleven translocation), which oxidizes 5-Me-dC to hmdC. This finding stimulated discussion about active demethylation pathways that could occur, e.g., via base excision repair (BER), with the help of specialized DNA glycosylases. Alternatively, one could envision a process in which the hydroxymethyl group of hmdC is further oxidized to 5-formyl-dC (fdC) or 5-carboxy-dC (cdC) followed by elimination of either formic acid or carbon dioxide4,5.

Glen Research has supported this research since its inception by providing the building blocks for the synthesis of oligonucleotides containing all the new dC derivatives - hmdC, fdC and cdC. The first generation hmdC phosphoramidite was fairly very well accepted but requires fairly harsh deprotection conditions. Therefore, a second generation building block (5-Hydroxymethyl-dC II) developed by Carell and co-workers that is compatible with UltraMild deprotection has been introduced.6 A second generation fdC-phosphoramidite (5-Formyl-dC II), also developed by Carell and co-workers, has been introduced since it does not require the post synthesis elimination step of the first generation version.7

5-Formyl-dC and 5-carboxy-dC may find uses in research into DNA damage and repair processes.

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Protocols

MSDS

Glen Report 21.2

Glen Report 23.1

Glen Report 23.2

 

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References

  • S Kriaucionis and N Heintz, Science, 2009, 324, 929-30
  • D Globisch, et al., PLoS One, 2010, 5, e15367
  • S G Jin, X Wu, A X Li and G P Pfeifer, Nucleic Acides Res., 2011
  • K M Schmitz, et al., Mol Cell, 2009, 33, 344-53
  • S C Wu and Y Zhang, Nat Rev Mol Cell Biol, 11, 607-20
  • M Sumino, A Ohkubo, H Taguchi, K Seio and M Sekine, Bioorganic & Medicinal Chemistry Letters, 2008, 18, 274-277
  • N Karino, Y Ueno and A Matsuda, Nucleic Acids Res., 2001, 29, 2456-2463
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    Notes

    Applications & Benefits

    DILUTION/COUPLING DATA

    The table below shows pack size data and, for solutions, dilutions and approximate couplings based on normal priming procedures.

    ABI 392/394
    Cat.No. Pack
    Size
    Grams/
    Pack
    0.1M Dil.
    (mL)
    LV40 LV200 40nm 0.2µm 1µm 10µm
    Approximate Number of Additions
    10-1062-95 50µmoles .046grams .5 3.33 2 1.25 .91 .67 .17
    10-1062-90 100µmoles .092grams 1 20 12 7.5 5.45 4 1
    10-1062-02 0.25grams .25grams 2.73 77.67 46.6 29.13 21.18 15.53 3.88
    Expedite
    Cat.No. Pack
    Size
    Grams/
    Pack
    Dilution
    (mL)
    Molarity 50nm 0.2µm 1µm 15µm
    Approximate Number of Additions
    10-1062-95 50µmoles .046grams .75 .07 8.6 5.38 3.91 .54
    10-1062-90 100µmoles .092grams 1.5 .07 23.6 14.75 10.73 1.48
    10-1062-02 0.25grams .25grams 4.07 .07 75 46.88 34.09 4.69
    Beckman
    Cat.No. Pack
    Size
    Grams/
    Pack
    Dilution
    (mL)
    Molarity 30nm 200nm 1000nm

    Approximate Number of Additions
    10-1062-95 50µmoles .046grams .75 .07 10.2 6.38 4.64

    10-1062-90 100µmoles .092grams 1.5 .07 25.2 15.75 11.45

    10-1062-02 0.25grams .25grams 4.07 .07 76.6 47.88 34.82

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