Cambio - Excellence in Molecular Biology

Oligo Synthesis

Oligo Synthesis : CEPs

Prices quoted are for single packs only. For multiples of the same product please request a quote. Some of Glen's products are hazardous and may be subject to additional shipping charges. Full product information is available on Glen Research's website.

5'-Pyrene Cap Phosphoramidite

5'-Pyrene Cap Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1987-025'-Pyrene Cap Phosphoramidite 0.25g £396.00 Quantity Add to Order
10-1987-905'-Pyrene Cap Phosphoramidite 100µmoles £156.00 Quantity Add to Order

5'-Pyrene Cap Phosphoramidite

5'-Pyrene Cap Phosphoramidite

Glen Research

5'-Pyrene Cap Phosphoramidite

Structure

Catalog Number: 10-1987-xx

Description: 5'-Pyrene Cap Phosphoramidite

(N-(1-pyrenylmethyl)-pyrrolidin-3-oxy)-O-(2-cyanoethyl)-
(N,N-diisopropyl)-phosphoramidite
Formula: C30H36N3O2P M.W.: 501.60 F.W.: 363.35

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: 3 minute coupling time recommended
Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.
Storage: Freezer storage, -10 to -30°C, dry
Stability in Solution: 2-3 days

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 (Figures 1 and 2).

figure
fig
FIGURE 1: STACKING OF CAP ON TERMINAL BASE PAIR
FIGURE 2: STACKING OF Uaq CAP ON 3’ 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'-Pyrene Cap Phosphoramidite

5'-Pyrene Cap Phosphoramidite

Glen Research

MSDS

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

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

5'-Pyrene Cap Phosphoramidite

5'-Pyrene 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)
10-1987
350 26.2

11.8

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
10-1987-02 0.25grams .25grams 4.98 152.67 91.6 57.25 41.64 30.53 7.63
10-1987-90 100µmoles .05grams 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
10-1987-02 0.25grams .25grams 7.44 .07 142.4 89 64.73 8.9
10-1987-90 100µmoles .05grams 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
10-1987-02 0.25grams .25grams 7.44 .07 144 90 65.45

10-1987-90 100µmoles .05grams 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