Alternate Name(s):

5-Acetoxymethyl-dU CEP

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

Alternate Name(s):

5-Me-ddU CEP

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

Notes

Notes

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

Description

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

This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research.

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

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-mates^TM Collection page.

 We also offer the related nucleosides 5-(Propargyloxy)-2'-deoxyuridine (PY 7712) and 5'-O-(Dimethoxytrityl)-5-(propargyloxy)-2'-deoxyuridine (PY 7714).

(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.

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.

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

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).

Description

This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research.

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).

Notes

Description

This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research.

Alternate Name(s):

2,6-Diaminopurine 2’-deoxyriboside, N⁶-methyl CEP

Description

This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research.