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Oligo Synthesis

Oligo Synthesis : CEPs

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5-Me-dC-CE Phosphoramidite

5-Me-dC-CE Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1060-025-Me-dC-CE Phosphoramidite 0.25g £100.00£92.00Offer until : 29-Feb-2020Offer Code : GLEN88% off all Glen Research products View Offer Quantity Add to Order
10-1060-905-Me-dC-CE Phosphoramidite 100µmoles £50.00£46.00Offer until : 29-Feb-2020Offer Code : GLEN88% off all Glen Research products View Offer Quantity Add to Order

5-Me-dC-CE Phosphoramidite

5-Me-dC-CE Phosphoramidite

Glen Research

5-Me-dC-CE Phosphoramidite

Structure

Catalog Number: 10-1060-xx

Description: 5-Me-dC-CE Phosphoramidite

5'-Dimethoxytrityl-N-benzoyl-5-methyl-2'-deoxyCytidine,3'-[(2-cyanoethyl)-
(N,N-diisopropyl)]-phosphoramidite
Formula: C47H54N5O8P M.W.: 847.9 F.W.: 303.21

Diluent: Anhydrous Acetonitrile
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.
Storage: Refrigerated storage, maximum of 2-8°C, dry
Stability in Solution: Similar to dA,C,G,T-CE Phosphoramidites

bases affecting duplex stability

C-5 methyl pyrimidine nucleosides are known to stabilize duplexes relative to the non-methylated bases. Therefore, enhanced binding can be achieved using 5-methyl-dC in place of dC, duplex melting temperature being increased by 1.3°. Improved stacking in this case is believed to be brought about by elimination of water molecules from the duplex. 2,6-Diaminopurine 2'-deoxyriboside (2-amino-dA) forms an additional hydrogen bond with Thymidine, thereby leading to duplex stabilization with a melting temperature increase of 3°. Our 2-amino-dA monomer exhibits fast and effective deprotection in ammonium hydroxide and it is stabilized to depurination during synthesis. Sequences with high GC content may contain mismatches and still hybridize because of the high stability of the G-C base pair. The N4-ethyl analogue of dC (N4-Et-dC) hybridizes specifically to natural dG but the stability of the base pair is reduced to about the level of an AT base pair.

AP-dC (G-clamp) enhances oligo hybridization since the AP-C....G base pair contains 4 hydrogen bonds, which makes the interaction much stronger than the regular C....G base pair with its 3 hydrogen bonds.

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5-Me-dC-CE Phosphoramidite

5-Me-dC-CE Phosphoramidite

Glen Research

MSDS

Glen Report 11.1: USING MODIFIED BASES TO OPTIMIZE HYBRIDIZATION

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5-Me-dC-CE Phosphoramidite

5-Me-dC-CE Phosphoramidite

Glen Research

  • 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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    5-Me-dC-CE Phosphoramidite

    5-Me-dC-CE Phosphoramidite

    Glen Research

    EXTINCTION DATA

    Item Nucleoside λMax-1 Emax-1 λMax-2 Emax-2 E260


    (nm) (ml/µmole) nm (ml/µmole) (ml/µmole)
    10-1060 5-Me-dC 277 9

    5.7

    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
    10-1060-02 0.25grams .25grams 2.95 85 51 31.88 23.18 17 4.25
    10-1060-90 100µmoles .085grams 1 20 12 7.5 5.45 4 1
    Expedite
    Cat.No. Pack
    Size
    Grams/
    Pack
    Dilution
    (mL)
    Molarity 50nm 0.2µm 1µm 15µm
    Approximate Number of Additions
    10-1060-02 0.25grams .25grams 4.4 .07 81.6 51 37.09 5.1
    10-1060-90 100µmoles .085grams 1.5 .07 23.6 14.75 10.73 1.48
    Beckman
    Cat.No. Pack
    Size
    Grams/
    Pack
    Dilution
    (mL)
    Molarity 30nm 200nm 1000nm

    Approximate Number of Additions
    10-1060-02 0.25grams .25grams 4.4 .07 83.2 52 37.82

    10-1060-90 100µmoles .085grams 1.5 .07 25.2 15.75 11.45

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