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Full Catalog (page 4)
Product Number Product Name Molecular Formula Cas. No.

BA 0147

3'-Fluorescein CPG

N/A 

N/A 

Alternate Name(s):

3’-(6-FAM) CPG

BA 0149

3'-Dabsyl CPG

N/A 

N/A 

BA 0150

5-Hydroxymethyl-dU CEP

C42H51N4O10P 

148380-57-8 

Alternate Name(s):

5-Acetoxymethyl-dU CEP

BA 0155

Furano-dT CEP

C42H49N4O8P 

858132-37-3 

Description

Measurement of fluorescence due to nucleobase incorpration offers a desirable complement to the linked fluorophore approach. Once the CEP is incorporated, the Furano-dT is converted to pyrrolo-dC upon treatment of the oligonucleotide with ammonia. See our products BA 0170 and BA 0245 as well as Berry, et al. Tetrahedron Lett. 2004, 45 (11), 2457-2461, which has leading references for the use of Furano-dT CEP (BA 0155) in oligonucleotide synthesis.

Notes

Allows incorporation into DNA and conversion to a fluorescent deoxycytidine analog during the ammonia deblocking step.

BA 0157

ddT CEP

C19H31N4O5P 

None Assigned 

Alternate Name(s):

5-Me-ddU CEP

BA 0158

ddA CEP

C28H47N8O3P 

None Assigned 

BA 0160

ddC CEP

C27H47N6O4P 

None Assigned 

BA 0162

ddG CEP

C22H35N8O4P 

None Assigned 

BA 0163

Amino-modifier-C6-dC
CEP

C53H68F3N8O9P 

853955-92-7 

BA 0164

5-Hydroxy-dC CEP

C53H56N5O10P 

197579-70-7 

BA 0165

Amino-modifier-C6-dC
CPG

N/A 

N/A 

BA 0166

Amino-modifier-C6-dT
CPG

N/A 

N/A 

BA 0167

5-Ethynyl-dU CEP

C41H47N4O8P 

615288-66-9 

Description

Oligonucleotides with 5-ethynyl residues may also be used in transition metal-catalyzed coupling reactions. Two ethynyl-bearing oligonucleotides can be homo-coupled via a diyne linkage using copper catalysis. Further, the ethynyl groups may be used in copper-catalyzed couplings with arylacetylenes bearing anthraquinone, biotin, or fluorescein appendages.2 Palladium catalyzed cross-coupling of ethynyl-dU-bearing oligonucleotidies with 2-iodoanthraquinone provides anthraquinone-bearing nucleic acids useful in electrochemical applications of DNA.3

For more detail on the use of this product, download a Product Information Sheet here.

(1) Graham, D.; Parkinson, J. A.; Brown, T. J. Chem. Soc, Perkin Trans. 1 1998, 1131-1138.

(2) Minakawa, N.; Ono, Y.; Matsuda, A. J. Am. Chem. Soc. 2003, 125, 11545-11552.

(3) Gorodetsky, A. A.; Green, O.; Yavin, E.; Barton, J. K. Bioconjugate Chem. 2007, 18, 1434-1441.

Notes

Replacement of thymidine residues with 5-ethynyl-dU residues results in duplex stabilization. The degree of stabilization is less than that observed with propynyl-dU residues.1

(1) Graham, D.; Parkinson, J. A.; Brown, T. J. Chem. Soc, Perkin Trans. 1 1998, 1131-1138.

BA 0168

4-Triazolyl-dU CEP

C41H48N7O7P 

109389-31-3 

Notes

The convertible nucleoside 4-Triazolyl-dU CEP allows the formation of N4-alkyl-dC residues.

BA 0170

Pyrrolo-dC CEP

C42H50N5O7P 

644962-92-5 

Description

Pyrrolo-dC is a fluorescent analog of 2'-deoxycytidine (Berry, et. Al, Tetrahedron Lett. 2004, 45 (11), 2457-2461). This 2'-deoxycytidine analog is highly fluorescent, exhibiting an emission maximum at 473 nm when incorporated into a 19-mer oligodeoxyribonucleotide, where it base-pairs normally with dG. We also offer the phosphoramidite of pyrrolo-dC (BA 0170) as well as the 2'-O-TBS ribo version, pyrrolo-C CEP (BA 0245), and the 2'-O-Methyl riobo version (BA 0356). BA 0245 and BA 0170 are also available from Glen Research, our development partner for these products. Glen Research also offers the triphosphates of pyrrolo-C and -dC. We offer the two nucleosides (PYA 11090 and PYA 11092) as well as the simple fluorescent pyrrolocytosine heterocycle (i.e., pyrrolo-C aglycone (HC 9060). For photophysical studies on these fluorescent pyrrolopyrimidines, see: Thompson, K. C.; Miyake, N. J. Phys. Chem. B, 2005, 109, 6012-6019.

Notes

Pyrrolo-dC is a fluorescent analog of 2'-deoxycytidine (Berry, et. Al, Tetrahedron Lett. 2004, 45 (11), 2457-2461).

BA 0173

9-Deaza-dG CEP

C44H54N7O7P 

None Assigned 

Description

Learn more about this phosphoramidite and its use by downloading a Product Information Sheet for BA 0173.

Notes

May be used for incorporation into an oligonucleotide internally or at the 5'-terminus.

Alternate Name(s):

9-Deaza-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N2-(dimethylaminomethylidene)-2'-deoxyguanosine

BA 0174

5-Propargyloxy-dU CEP

C42H49N4O9P 

1311144-61-2 

Description

An attractive strategy for nucleic acid conjugation involves the Cu(I)-catalyzed click reaction between terminal alkynes and azides. While 5-Ethynyl-dU in oligonucleotides has been reported to undergo the click reaction,1 the short rigid nature of the alkyne group severely limits its application for this purpose. 5-Octadiynyl-dU CEP (BA 0308)1-4 is a much superior reagent for the installation of an alkyne-bearing nucleoside into an oligonucleotide when click reactions are contemplated. The terminal alkyne is more flexible and extends farther away from thr pyrimidine ring, thereby allowing more efficient ligation via click chemistry, even when multiple ligations to a single oligo are desired. 5-Propargyloxy-dU CEP (BA 0174) is an analogous reagent for the facilitation of oligo click ligations. The intermediate length of the alkyne appendage allows for efficient ligation.

For more information on this product and its use, download a Product Information Sheet for 5-Propargyloxy-dU CEP .

For a complete listing of our reagents for click chemistry, please see our Click-matesTM Collection page.

 We also offer the related nucleoside 5-(Propargyloxy)-2'-deoxyuridine (PY 7712) .

(1) Gierlich, J.; Burley, G. A.; Gramlich, P. M. E.; Hammond, D. M.; Carell, T. Org. Lett. 2006, 8, 3639-3642.

(2) Seela, F.; Sirivolu, V. R. Chem. Biodiversity 2006, 3, 509-514.

(3) Seela, F.; Sirivolu, V. R. Helv. Chim. Acta 2007, 90, 535-552.

(4) Hammond, D. M.; Manetto, A.; Gierlich, J.; Azov, V. A.; Gramlich, P. M. E.; Burley, G. A.; Maul, M.; Carell, T. Angew. Chem. Int. Ed. 2007, 46, 4184-4187.

The purchase of these products for use in applications relating to copper catalyzed azide-alkyne cycloaddition chemistry (“Click Chemistry”) includes a limited, nontransferable license to intellectual property owned by TSRI to use this product solely for internal non-commercial research activities and specifically excludes clinical, therapeutic, or diagnostic use in humans or animals. Information regarding a license for commercial use in Click Chemistry may be obtained directly from The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, or by contacting 858-784-8140 or click@scripps.edu.

Notes

 May be used for the installation of an alkyne into an oligonucleotide internally or at the 5'-terminus. Potentially useful for click conjugation with azide-bearing labeling agents.

BA 0175

8-Amino-dA CEP

C46H59N10O6P 

211676-21-0 

BA 0176

2-Fluoro-dI CEP

C48H53FN7O9P 

163668-79-9 

Description

The convertible nucleoside 2-Fluoro-dI CEP allows the formation of N2-alkyl-dG residues in DNA for structural studies. After incorporation of this unit into an oligoribonucleotide by standard phosphoramidite chemistry, treatment with ammonia, methylamine, or a higher alkylamine, including one bearing a tethered functional group, leads to displacement of fluoride ion with resultant installation of a 2-amino group, i.e., producing a deoxyguanosine or an N2-alkyl-dG residue.

Notes

The convertible nucleoside 2-Fluoro-dI CEP allows the formation of N2-alkyl-dG residues.

BA 0180

cis,syn-Thymidine dimer methyl
phosphoramidite

C49H63N5O15P2 

118187-67-0 

Description

BA 0180 is intended for construction of unique photolesion containing oligonucleosides for use in mutagenesis studies. (Taylor, J.-S.; Brockie, I.; and O’Day, C. J. Am. Chem. Soc. 1987, 109, 6735-6742; Taylor, J.-S.; Nadji, S.; and Wang, C.-I. J. Am. Chem. Soc. 1992, 114, 9266-9269; Smith, C.A.; and Taylor, J.-S. J. Biol. Chem. 1993, 268, 11143-11151).

BA 0184

Amino-modifier-C6-dA
CEP

C55H65F3N9O8P 

1301170-09-1 

BA 0187

Carbazole Alkyl CEP

C27H38N3O3P 

None Assigned 

Description

For more information, download a Product Information Sheet for BA 0187 here.

BA 0191

2'-O-Aminolinker-5-methyl U
CEP

C44H53F3N5O10P 

200423-98-9 

Description

For more information, download a Product Information Sheet for BA 0191 here.

BA 0194

8-Amino-dG CEP

C46H59N10O7P 

166092-91-7 

BA 0198

Thymidine glycol CEP

C52H79N4O10PSi2 

318497-58-4 

BA 0201

5-Methyl-2'-deoxyzebularine CEP

C40H49N4O7P 

125258-62-0 

Description

5-Methyl-2'-deoxyzebularine or m5K, is an intrinsically fluorescent nucleoside that, upon incorporation into oligonucleotides,1,2 allows the characterization of the assembly of RecA-ssDNA complexes that initiate DNA repair responses.2 Further, deletion of the C4 amino group of dC allows dissection of the roles of various hydrogen bonds, and the incorporation of 2-pyrimidinone residues into DNA allows the formation of abasic sites at selected positions after mild acid hydrolysis.3 See also a ribo version, Zebularine CEP (BA 0254).

1. Gildea, B.; McLaughlin, L. W. Nucleic Acids Res. 1989, 17(6), 2261-2281.
2. Singleton, S. F. et al., Organic Lett. 2001, 3, 3919-3922.
3. Iocono, J. A.; Gildea, B.; McLaughlin, L. W.,Tetrahedron Lett. 1990, 31, 175-178.

Notes

A fluorescent nucleoside useful for probing the characterisitcs of DNA repair complexes.


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