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Oligo Synthesis

Oligo Synthesis : CEPs

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5'-Trimethoxystilbene Cap Phosphoramidite

5'-Trimethoxystilbene Cap Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1986-025'-Trimethoxystilbene Cap Phosphoramidite 0.25g £400.00 Quantity Add to Order
10-1986-905'-Trimethoxystilbene Cap Phosphoramidite 100µmoles £156.00 Quantity Add to Order

5'-Trimethoxystilbene Cap Phosphoramidite

5'-Trimethoxystilbene Cap Phosphoramidite

Glen Research

Structure

Catalog Number: 10-1986-xx

Description: 5'-Trimethoxystilbene Cap Phosphoramidite

(3,4,5-trimethoxystilbene-4'-yl)-(3-carboxamidopropyl)-1-O-(2-cyanoethyl)-
(N,N-diisopropyl)-phosphoramidite
Formula: C30H42N3O6P M.W.: 571.65 F.W.: 433.39

Diluent: Anhydrous Acetonitrile
Add fresh diluent to product vial to recommended concentration and swirl vial occasionally over several minutes until product is completely dissolved. (Some oils may require between 5 and 10 minutes.) Use care to maintain anhydrous conditions. In case of transfer to alternate vial type, ensure recipient vial has been pre-dried. For more information, see http://www.glenres.com/Technical/TB_ABITransfer.pdf.
Coupling: No changes needed from standard method recommended by synthesizer.
Deprotection: No changes needed from standard methold recommended by synthesizer.
Storage: Freezer storage, -10 to -30°C, dry
Stability in Solution: 6 months

Melting point increases of over 10 °C per modification can be realized for short duplexes.1,2 The caps fit canonical Watson-Crick base pairs and do not stack well on mismatched base pairs. This leads to increased base pairing selectivity at the terminal and the penultimate position of oligonucleotides featuring the caps. Base pairing fidelity is usually low at the termini, where fraying occurs frequently in the absence of caps. The beneficial effects of the caps are also realized when longer target strands are bound, so there is no need for blunt ends for the duplexes formed.1,2 The caps, when attached to the 5’ terminus of an oligonucleotide, also facilitate purification as their lipophilicity leads to prolonged retention on reversed phase columns or cartridges. Finally, capping of termini may discourage the degradation of oligonucleotides by exonucleases.

3’-Uaq Cap CPG, a Uridine support modified with a 2’- anthraquinone residue, is the most effective oligonucleotide cap known to date.3,4 For short hybrid duplexes between DNA probes and RNA target strands, the increase in Tm is up to 18 °C and the modification is effective in increasing the Tm of DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. 3’-Uaq Cap also increases probe specificity by depressing the melting point of terminal mismatches.

Caps for Increased Duplex Stability and Base-Pairing Fidelity at Termini

New cap structures allow for the preparation of hybridization probes with increased affinity for complementary sequences. The monomers used to prepare capped oligonucleotides are phosphoramidites that can be readily introduced via automated DNA synthesis at the end of solid phase syntheses. The caps favor the formation of stable Watson-Crick duplexes by stacking on the terminal base pair.

Melting point increases of over 10 °C per modification can be realized for short duplexes.1,2 The caps fit canonical Watson-Crick base pairs and do not stack well on mismatched base pairs. This leads to increased base pairing selectivity at the terminal and the penultimate position of oligonucleotides featuring the caps. Base pairing fidelity is usually low at the termini, where fraying occurs frequently in the absence of caps. The beneficial effects of the caps are also realized when longer target strands are bound, so there is no need for blunt ends for the duplexes formed.1,2 The caps, when attached to the 5’ terminus of an oligonucleotide, also facilitate purification as their lipophilicity leads to prolonged retention on reversed phase columns or cartridges. Finally, capping of termini may discourage the degradation of oligonucleotides by exonucleases.

3’-Uaq Cap CPG, a Uridine support modified with a 2’- anthraquinone residue, is the most effective oligonucleotide cap known to date.3,4 For short hybrid duplexes between DNA probes and RNA target strands, the increase in Tm is up to 18 °C and the modification is effective in increasing the Tm of DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. 3’-Uaq Cap also increases probe specificity by depressing the melting point of terminal mismatches.

If you cannot find the answer to your problem below then please contact us or telephone 01954 210 200

5'-Trimethoxystilbene Cap Phosphoramidite

5'-Trimethoxystilbene Cap Phosphoramidite

Glen Research

5'-Trimethoxystilbene Cap Phosphoramidite

5'-Trimethoxystilbene Cap Phosphoramidite

Glen Research

(1) Dogan, Z.; Paulini, R.; Rojas Stütz, J. A.; Narayanan, S.; Richert, C. J. Am. Chem. Soc. 2004, 126, 4762-4763.

(2) Narayanan, S.; Gall, J.; Richert, C. Nucleic Acids Res. 2004, 32, 2901-2911.

(3) A. Patra, C. Richert, J. Amer. Chem. Soc., 2009, 131, 12671-12681.

(4) C. Ahlborn, K. Siegmund, C. Richert, J. Amer. Chem. Soc., 2007, 129, 15218-15232.

If you cannot find the answer to your problem below then please contact us or telephone 01954 210 200

5'-Trimethoxystilbene Cap Phosphoramidite

5'-Trimethoxystilbene Cap Phosphoramidite

Glen Research

5'-Trimethoxystilbene Cap Phosphoramidite

(3,4,5-trimethoxystilbene-4'-yl)-(3-carboxamidopropyl)-1-O-(2-cyanoethyl)-
(N,N-diisopropyl)-phosphoramidite
Formula: C30H42N3O6P M.W.: 571.65 F.W.: 433.39

Diluent: Anhydrous Acetonitrile
Add fresh diluent to product vial to recommended concentration and swirl vial occasionally over several minutes until product is completely dissolved. (Some oils may require between 5 and 10 minutes.) Use care to maintain anhydrous conditions. In case of transfer to alternate vial type, ensure recipient vial has been pre-dried. For more information, see http://www.glenres.com/Technical/TB_ABITransfer.pdf.
Coupling: No changes needed from standard method recommended by synthesizer.
Deprotection: No changes needed from standard methold recommended by synthesizer.
Storage: Freezer storage, -10 to -30°C, dry
Stability in Solution: 6 months
  Material Safety Data Sheet

EXTINCTION DATA

Item Nucleoside λMax-1 Emax-1 λMax-2 Emax-2 E260
    (nm) (ml/µmole) nm (ml/µmole) (ml/µmole)
10-1986   338 36.0   36.0 10.6

Literature Highlights

Glen Report 6.1: NEW LABELLING REAGENTS
Glen Report 18.1: Caps for Increased Duplex Stability and Base-Pairing Fidelity at Termini

DILUTION/COUPLING DATA

The table below shows pack size data and, for solutions, dilutions and approximate couplings based on normal priming procedures. Please link for more detailed usage information with the various synthesizers.

ABI 392/394
Cat.No. Pack
Size
Grams/
Pack
0.1M Dil.
(mL)
LV40 LV200 40nm 0.2µm 1µm 10µm
Approximate Number of Additions
10-1986-02 0.25grams .25grams 4.37 132.33 79.4 49.63 36.09 26.47 6.62
10-1986-90 100µmoles .057grams 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
10-1986-02 0.25grams .25grams 6.53 .067 124.2 77.63 56.45 7.76  
10-1986-90 100µmoles .057grams 1.5 .067 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
10-1986-02 0.25grams .25grams 6.53 .067 125.8 78.63 57.18    
10-1986-90 100µmoles .057grams 1.5 .067 25.2 15.75 11.45

If you cannot find the answer to your problem below then please contact us or telephone 01954 210 200

5'-Trimethoxystilbene Cap Phosphoramidite

5'-Trimethoxystilbene Cap Phosphoramidite

Glen Research

EXTINCTION DATA

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


(nm) (ml/µmole) nm (ml/µmole) (ml/µmole)
10-1986
338 36.0
36.0 10.6

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
10-1986-02 0.25grams .25grams 4.37 132.33 79.4 49.63 36.09 26.47 6.62
10-1986-90 100µmoles .057grams 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
10-1986-02 0.25grams .25grams 6.53 .07 124.2 77.63 56.45 7.76
10-1986-90 100µmoles .057grams 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
10-1986-02 0.25grams .25grams 6.53 .07 125.8 78.63 57.18

10-1986-90 100µmoles .057grams 1.5 .07 25.2 15.75 11.45

If you cannot find the answer to your problem below then please contact us or telephone 01954 210 200