5-Me-dC-CE Phosphoramidite

5'-Dimethoxytrityl-N-benzoyl-5-methyl-2'-deoxyCytidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
main product photo

Product Specifications

Formula:
C47H54N5O8P
M.W.:
847.9
F.W.:
303.21
CAS Number:
105931-57-5
To Retrieve a Catalog Number, Select a Pack Size and Format:
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Technical Documents

Epigenetics and DNA Methylation

Safety Data Sheet

Extinction Table: Extinction Coefficient and Fluorescence Data

Glen Report 11.11: Using Modified Bases to Optimize Hybridization

Glen Report 23.11: DNA Methylation Revisited

Glen Report 26.13: New Product - 5-Me-dC Now Compatible with AMA and UltraMild Deprotection

Glen Report 33-15: Technical Note - DNA and RNA Nucleoside Numbering System

Description

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°.  Ac-5-Me-dC-CE Phosphoramidite is fully compatible with AMA deprotection and none of the N4-Me transamination mutant is observed on deprotection.  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.  Note: we recommend the use of 0.5 M CSO in anhydrous acetonitrile (40-4632-xx) for best results with multiple additions of 2-amino-dA.

Details

Usage

  • Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
  • Deprotection: No changes needed from standard method recommended by synthesizer manufacturer. Note: Deprotection in AMA (50:50 Ammonium hydroxide/MethylAmine) may result in a 4-5% 5-Methyl-N4-methyl-dC side product at the modification site.
Specifications
Diluent Anhydrous Acetonitrile
Storage Refrigerated storage, maximum of 2-8°C, dry
Stability Similar to dA,C,G,T-CE Phosphoramidites

Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-1060-02 0.25 g .25grams 2.95 85 51 31.88 23.18 17 4.25
10-1060-90 100 µmol .085grams 1 20 12 7.5 5.45 4 1

Expedite

Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-1060-02 0.25 g .25grams 4.4 0.07 81.6 51 37.09 5.1
10-1060-90 100 µmol .085grams 1.5 0.07 23.6 14.75 10.73 1.48

References

Afaf H. El-Saghee and Tom Brown . Combined nucleobase and backbone modifications enhance DNA duplex stability and preserve biocompatibility

Ren, X., Linehan, M. M., Iwasaki, A., & Pyle, A. M. . RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling

Liu ZF, Ye QN, Yang J, Yang M, Pan DH, Dong MJ. . Preclinical evaluation of [68Ga]Ga-MALAT-1-antisense oligonucleotides for specific PET imaging of MALAT-1 expressing tumours

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