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Full Catalog (page 7)
Product Number Product Name Molecular Formula Cas. No.

BA 0309

Anthraquinone-5-ethynyl-dU CEP

C55H53N4O10P 

None Assigned 

Description

Anthraquinones may be incorporated into oligonucleotides by a variety of methods using a host of different phosphoramidites. The anthraquinone moiety is useful for applications such as intercalation, duplex and triplex stabilization, photochemical immobilization, quenching of fluorescence, electrochemical detection, and charge transport through nucleic acids. Barton and co-workers1 have studied the importance of the tether in electronic coupling of the anthraquinone to the DNA. Connection of the anthraquinone moiety to the nucleobase of 2'-deoxyuridine via an ethynyl group provides an electronic coupling to the nucleobase pi-stack. Such nucleotides were made by incorporation of a 5-ethynyl-dU nucleotide using 5-Ethynyl-dU CEP (BA 0167) followed by a post-synthetic palladium-catalyzed Sonogashira coupling with 2-iodoanthraquinone.1 For the direct incorporation of an ethynyl-dU-linked anthraquinone into an oligonucleotide, Anthraquinone-5-ethynyl-dU CEP (BA 0309) may be used, avoiding post-synthetic palladium couplings.

Download a Product Information Sheet for BA 0309 here.

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

Notes

For the direct incorporation of an ethynyl-dU-linked anthraquinone into an oligonucleotide, providing an electronic coupling to the nucleobase pi-stack.

BA 0311

5-Aminoallyl-dU CEP

C44H51F3N5O9P 

144253-90-7 

Description

Early work on the introduction of a 5-aminoallyl-dU amino modifier into oligonucleotides involved the methyl phosphoramidite.1 5-Aminoallyl-dU CEP, employing a 2-cyanoethyl phosphoramidite, was reported later.2,3

Williams and co-workers3 studied the incorporation of 5-aminoallyl-dU residues into triplex-forming oligonucleotides (TFOs), where a single incorporation did not change the stability of the triplex vs. unmodified TFOs. Multiple incorporations led to a lower triplex stability. The pKa of the protonated form of the amino group of 5-aminoallyl-dU is expected to be 9.7 based on studies on the free nucleoside. Conformational studies on the nucleoside were also carried out.

For information on the use of this product, download a Product Information Sheet for BA 0311.

1. Cook, A. F.; Vuocolo, E.; Brakel, C. L. Nucleic Acids Res. 1988, 16, 4077-4095.

2. Lermer, L.; Yoann, R.; Ting, R.; Perrin, D. M. J. Am. Chem. Soc. 2002, 124, 9960-9961. See especially the Supporting Information.

3. Brazier, J. A.; Shibata, T.; Townsley, J.; Taylor, B. F.; Frary, E.; Williams, N. H.; Williams, D. M. Nucl. Acids Res. 2005, 33, 1362-1371.

Notes

Allows the introduction of a 5-aminoallyl-dU residue into oligonucleotides for the purpose of post-synthetic labeling by acylation. Further, triplex-forming oligonucleotides (TFOs) containing this residue form triplexes that are similar in stability to those bearing unmodified residues.

BA 0312

2'-Deoxypseudoguanosine CEP

C43H53N8O7P 

None Assigned 

Description

The transposition of atoms or groups in the purine nucleobase of G/dG provides isomers that have altered base-pairing capabilities.  We offer a family of guanosine isomers in nucleoside and phosphoramidite forms.  

Pseudo-dG CEP (BA 0312) may be used to incorporate Pseudo-dG nucleotides into DNA.  It is based on the nucleoside 2'-Deoxypseudoguanosine (Pseudo-dG, synthesized by Hosmane and co-workers1), which is also available (PRA 10103).

Pseudo-dG CEP and Pseudo-dG are part of a family that includes Guanosine (PR 3703), 2'-Deoxyguanosine (PR 3452), the isomeric nucleosides Isoguanosine (Iso-G, PR 3735), 2'-Deoxyisoguanosine (Iso-dG, PR 3465), 2'-Deoxypseudoisoguanosine (Pseudoiso-dG, PRA 10104), and the phosphoramidite Pseudoiso-dG CEP (BA 0314).

Learn more about these novel compounds and their use by downloading a Product Information sheet for our family of guanosine isomers.

1. Ujjinamatada, R. K.; Paulman, R. L.; Ptak, R. G.; Hosmane, R. S. Bioorg. Med. Chem. 2006, 14, 6359-6367.  See also: Ujjinamatada, R. K.; Phatak, P.; Burger, A. M.; Hosmane, R. S. J. Med. Chem. 2008, 51, 694-698.

Notes

2'-Deoxypseudoguanosine (Pseudo-dG) is related to dG by transposition of the nitrogen atom at position 3 and the C-NH2 group at position 2 of the nucleobase, providing a novel hydrogen bond donor/acceptor pattern.

Alternate Name(s):

Pseudo-dG CEP

BA 0313

2'-Deoxyxanthosine CEP

C56H61N8O12P 

292050-43-2 

Description

Xanthosine (X) and 2'-deoxyxanthosine (dX), the products of deamination of G and dG, have been incorporated into oligonucleotides,1-8 imparting a variety of properties to these nucleic acids. The pKa of the proton at N3 of dX is 5.5-5.7,2,8 therefore dX is present as a mono-anion to the extent of about 95% at neutral pH. dX residues have the same hydrogen-bond donor/acceptor pattern as thymidine, thus allowing base-pairing with dA.8 This leads to a distortion of the helix, since two purines are paired. Stronger base stacking interactions are apparent. Duplex stability variations as a function of the opposing base pair have been studied.4,8 dX is susceptible to depurination under acidic conditions, forming abasic sites.2,8 At pH 4, dX depurinates more quickly than dG by a factor of about 1000. At neutral pH, dX has about the same stability as dG. The recognition and excision of dX by base excision repair enzymes has been studied.2 dX has been considered to be a promiscuous or universal nucleoside.1,8 dX may expand the genetic code when paired to a pyrimidine-2,4-diamine C-nucleoside.6 Studies of polymerase-mediated incorporation of various nucleotides opposite dX have been carried out.2,4 The presence of dX residues may lead to triplexes, quartets, and other G-stranded structures.8

We now offer the phosphoramidite 2'-Deoxyxanthosine CEP (BA 0313), featuring 2-(4-nitrophenyl)ethyl (NPE) protecting groups at O2 and O6.1,2 Download a Product Information Sheet for BA 0313 for more information on the use of this monomer.

1. Jurczyk, S. C.; Horlacher, J.; Devined, K. G.; Benner, S. A.; Battersby, T. R. Helv. Chim. Acta 2000, 83, 1517-1524.

2. Weunschell, G. E.; O'Connor, T. R.; Termini, J. Biochemistry, 2003, 42, 3608-3616.

3. Tuschl, T.; Ng, M. M. P.; Pieken, W.; Benseler, F.; Eckstein, F. Biochemistry 1993, 32, 11658-11668.

4. Eritja, R.; Horowitz, D. M.; Walker, P. A.; Ziehler-Martin, J. P.; Boosalis, M. S.; Goodman, M. F.; Itakura, K.; Kaplan, B. E. Nucleic Acids Res. 1986, 14, 8135-8153.

5. Van Aerschot, A.; Mag, M.; Herdewijn, P.; Vanderhaeghe, H. Nucleosides Nucleotides Nucleic Acids 1989, 8, 159-178.

6. Lutz, M. J.; Held, H. A.; Hottiger, M.; Hubscher, U.; Benner, S. A. Nucleic Acids Res. 1996, 24, 1308-1313.

7. Groebke, K.; Hunziker, J.; Fraser, W.; Peng, L.; Diederichsen, U.; Zimmermann, K.; Holzner, A.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1998, 81, 375.

8. Seela, F.; Shaikh, K. I. Helv. Chim. Acta 2006, 89, 2794-2814.

Notes

2'-Deoxyxanthosine CEP (dX CEP) is useful for the installation of 2'-deoxyxanthosine (dX) nucleotides into oligonucleotides.

Alternate Name(s):

3'-O-[(Diisopropylamino)-(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2,6-di-O-[2-(4-nitrophenyl)ethyl]-2'-deoxyxanthosine

dX CEP

BA 0314

2'-Deoxypseudoisoguanosine CEP

C43H53N8O7P 

None Assigned 

Description

The transposition of atoms or groups in the purine nucleobase of G/dG provides isomers that have altered base-pairing capabilities.  We offer a family of guanosine isomers in nucleoside and phosphoramidite forms.

Pseudoiso-dG CEP (BA 0314) may be used to incorporate Pseudoiso-dG nucleotides into DNA. It is based on the nucleoside 2'-Deoxypseudoisoguanosine (Pseudoiso-dG, originally synthesized by Hosmane and co-workers1), which is also available (PRA 10104).

Pseudoiso-dG CEP and Pseudoiso-dG are part of a family that includes Guanosine (PR 3703), 2'-Deoxyguanosine (PR 3452), the isomeric nucleosides Isoguanosine (Iso-G, PR 3735), 2'-Deoxyisoguanosine (Iso-dG, PR 3465), 2'-Deoxypseudoguanosine (Pseudo-dG, PRA 10103), and the phosphoramidite Pseudo-dG CEP (BA 0312) .

Learn more about these novel compounds and their use by downloading a Product Information sheet for our family of guanosine isomers .

1. Ujjinamatada, R. K.; Paulman, R. L.; Ptak, R. G.; Hosmane, R. S. Bioorg. Med. Chem. 2006, 14, 6359-6367.  See also: Ujjinamatada, R. K.; Phatak, P.; Burger, A. M.; Hosmane, R. S. J. Med. Chem. 2008, 51, 694-698 and Berry, D. A.; Wotring, L. L.; Drach, J. C.; Townsend, L. B. Nucleosides Nucleotides 1994, 13, 2001-2011.

Notes

2'-Deoxypseudoisoguanosine (Pseudoiso-dG) is related to Iso-dG by transposition of the nitrogen atom at position 3 and the carbonyl group at position 2 of the nucleobase. It is also related to 2'-Deoxypseudoguanosine (Pseudo-dG) by transposition of the C-NH2 group at position 3 and the carbonyl group at position 6.  Pseudoiso-dG CEP may be useful for incorporation into nucleic acids, where it may provide a novel alternate base-pairing scheme.

Alternate Name(s):

Pseudoiso-dG CEP

BA 0315

Caged strand-breaker CEP

C45H49N4O9P 

1221188-51-7 

Description

The introduction of nicks in DNA may be accomplished using photolabile nucleotides or nucleotide surrogates, resulting in so-called "caged strand-breaks".1 Various non-nucleosidic monomers have been developed for this purpose.2-7 Caged Strand-Breaker CEP is the most advanced example of this strategy, allowing complete removal of the photolabile protecting group from both phosphorylated daughter strands and the avoidance of a second step involving base treatment.6

For information on the use of this product, download a Product Information Sheet for BA 0315.

1. Reviews: (a) Mayer, G.; Heckel, A. Angew. Chem. Int. Ed. 2006, 45, 4900-4921. (b) Young, D. D.; Deiters, A. Org. Biomol. Chem. 2007, 5, 999-1005. © Tang, X. Dmochowski, I. J. Mol. BioSyst. 2007, 3, 100-110.

2. Urdea, M. S.; Horn, T. US Patent 5,258,506, Nov. 2, 1993.

3. Ordoukhanian, P.; Taylor, J.-S. J. Am. Chem. Soc. 1995, 117, 9570-9571.

4. Zhang, K.; Taylor, J.-S. J. Am. Chem. Soc. 1999, 121, 11579-11580.

5. Ordoukhanian, P.; Taylor, J.-S. Bioconj. Chem. 2000, 11, 94-103.

6. Zhang, K.; Taylor, J.-S. Biochemistry 2001, 40, 153-159.

7. Dell'Aquila, C.; Imbach, J.-L.; Rayner, B. Tetrahedron Lett. 1997, 38, 5289-5292.

Notes

Once installed into an oligonucleotide, irradiation at 365 nm at neutral pH causes strand cleavage, leaving phosphate groups on both daughter strands. In contrast to other related monomers, a second step involving treatment with base is not required.

Alternate Name(s):

3-O-[(Diisopropylamino)-(2-cyanoethoxy)phosphino]-1-O-(4,4'-dimethoxytrityl)-1,3-di-(2-nitrophenyl)-1,3-propanediol

BA 0316

Alkynyl-modifier-C6-dT CEP

C48H58N5O9P 

None Assigned 

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. Alkynyl-modifier-C6-dT CEP (BA 0316) is an analogous reagent with a slightly longer alkyne appendage that we have introduced as an alternative for oligo click ligations.

For more information on this product and its use, download a Product Information Sheet for Alkynyl-Modifier-C6-dT CEP.

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

(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.

(5) Rozkiewicz, D. I.; Gierlich, J.; Burley, G. A.; Gutsmiedl, K.; Carell, T.; Ravoo, B. J.; Reinhoudt, D. N. ChemBioChem 2007, 8, 1997-2002.

This compound is sold under license from baseclick GmbH, and 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

This phosphoramidite features a well-established linker that places the alkyne at a sufficient distance from the oligonucleotide to allow efficient click conjugation.

Alternate Name(s):

3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-
5-[N-(hex-5-ynyl)-3-(E)-acrylamido]-2'-deoxyuridine

BA 0317

NPOM-Caged-dT CEP

C50H58N5O13P 

942218-71-5 

Description

Many strategies have surfaced for the caging of oligonucleotides using photochemically labile groups. Caging the nucleobase is particularly attractive.1,2 One of the most promising strategies for doing so involves the use of the 6-nitropiperonyloxymethyl (NPOM) group, installed at N1 of thymidine, as developed by Deiters and co-workers at North Carolina State University.3-5 Thus, NPOM-Caged-dT CEP (BA 0317) was incorporated it into oligonucleotides using standard automated DNA synthesis protocols, resins, and reagents.3,4 The bulky NPOM group was found to effectively block hydrogen-bond formation in duplexes, blocking DNAzyme activity, DNA/RNA hybridization, and allowing the control of PCR amplification. The caged thymidine is stable to a wide range of chemical and physiological conditions, but the NPOM caging group is removed within minutes by irradiation with 365 nm UV light, restoring normal biological function in all cases. This can be achieved using a standard fluorescent microscope, UV LED fiberoptic instruments, or even with a simple hand-held 25 watt UVA lamp. This wavelength is long enough to avoid damage to the oligonucleotides or cells.

Learn more about this phosphoramidite and its use in the control of oligonucleotide function by downloading a Product Information Sheet for BA 0317.

Also in our collection of photolabile tools for oligonucleotide research is the phosphoramidite Caged Strand-Breaker CEP (BA 0315), a monomer that allows the light-induced cleavage of oligonucleotides into two phosphate-terminated daughter strands.

1. Reviews: (a) Mayer, G.; Heckel, A. Angew. Chem. Int. Ed. 2006, 45, 4900-4921. (b) Young, D. D.; Deiters, A. Org. Biomol. Chem. 2007, 5, 999-1005. © Tang, X. Dmochowski, I. J. Mol. BioSyst. 2007, 3, 100-110.

2. Examples: (a) Ting, R.; Lermer, L.; Perrin, D. M. J. Am. Chem. Soc. 2004, 126, 12720-12721. (b) Heckel, A.; Meyer, G. J. Am. Chem. Soc. 2005, 127, 822-823. © Krock, L.; Heckel, A. Angew. Chem. Int. Ed. 2005, 44, 471-473. (d) Tang, X.; Dmochowski, I. J. Org. Lett. 2005, 7, 279-282. € Wenter, P.; Furtig, B.; Hainard, A.; Schwalbe, H.; Pitsch, S. Angew. Chem. Int. Ed. 2005, 44, 2600-2603. (f) Hobartner, C.; Silverman, S. K. Angew. Chem. Int. Ed. 2005, 44, 7305-7309.

3. Lusic, H.; Young, D. D.; Lively, M. O.; Deiters, A. Org. Lett. 2007, 9, 1903-1906.

4. Young, D. D.; Edwards, W. F.; Lusic, H.; Lively, M. O.; Deiters, A. Chem. Commun. 2008, 462-464.

5. Lusic, H.; Deiters, A., Synthesis 2006, 2147-2150.

Notes

Installs a thymidine residue bearing a bulky NPOM protecting group at N1, thus efficiently disrupting Watson-Crick base-pairing. Upon brief exposure to UV light of 365 nm, the "caged" oligonucleotide is uncaged, restoring base-pairing ability.

Alternate Name(s):

3'-O-[(Diisopropylamino)-(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N3-[[1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]methyl]thymidine

BA 0321

Cross-coupler-C6-dT CEP

C55H66BrN6O10P 

None Assigned 

Description

Cross-coupler-C6-dT CEP (BA 0321) allows the incorporation of a nucleotide containing an aryl bromide for post-synthetic modification via transition metal-mediated cross-coupling, e.g., using a Sonogashira coupling. A longer tether is employed in order to remove the sterically-demanding palladium chemistry further from the oligonucleotide. For more information, download a Product Information sheet.

Notes

May be used for the installation of a p-bromocarboxamide into an oligonucleotide internally or at the 5'-terminus. Potentially useful for the site-specific modification of an oligonucleotide via transition metal-mediated cross-coupling.

BA 0322

Cross-coupler CEP

C49H65BrN3O10P 

1159976-40-5 

Description

Cross-coupler CEP (BA 0322) allows the incorporation of a nucleotide containing an aryl bromide for post-synthetic modification via transition metal-mediated cross-coupling, e.g., using a Sonogashira coupling. A longer tether is employed in order to remove the sterically-demanding palladium chemistry further from the oligonucleotide. For more information, download Product Information.

Notes

May be used for the installation of a p-bromocarboxamide into an oligonucleotide internally or at the 5'-terminus. Potentially useful for the site-specific modification of an oligonucleotide via transition metal-mediated cross-coupling.

BA 0323

7-Deaza-G CEP

C50H68N7O8PSi 

None Assigned 

Description

G-Rich regions in nucleic acids often display disrupted Watson-Crick base-pairing due to the ability of dG and G residues to enter into non-Watson-Crick inter- and intramolecular hydrogen bonding. A solution to this problem is to replace the N7 nitrogen atom on the guanine nucleobase with a CH group, obviating the possibility of hydrogen bonding at that position. 1We have long offered 7-Deaza-dG CEP (BA 0008), and now also offer 7-Deaza-G CEP (BA 0323) for oligoribonucleotide synthesis.

For more information, download a Product Information sheet.

(1) Seela, F.; Driller, H. Nucleic Acids Res. 1989, 17(3), 901-910.

Notes

Installation of 7-Deaza-G residues in G-rich regions can disrupt unwanted hydrogen bonding.

BA 0324

Cmoc-5'-amino-modifier-C6 CEP

C53H64Cl2N3O7P 

1246448-29-2 

Description

N-protecting groups for 5’-amino-modifiers be problematic in automated synthesis. DMT protection is frequently too labile for the amino group. MMT is usually preferred for its greater stability as an N-protecting group, however, it has two practical disadvantages: (1) It requires a custom deprotection protocol since NH-MMT is slightly more robust than O-DMT. (2) Automated synthesizers are designed to quantify DMT cleavage, not MMT cleavage. While the aforementioned Fmoc protected 5’-amino-modifiers offer one potential solution to these disadvantages, sometimes it is preferable to have acid-labile N-protection. BA 0324 has a novel N-protecting group that is based upon colorimetric-oxycarbonyl (Cmoc). In essence, the Cmoc group is an O-DMT that is tethered to an N-bis(4-chlorophenyl)-methoxycarbonyl protecting group. Both protecting groups are acid labile, but only the DMT cation generates a colorimetric signal because the tether quenches the bis(4-chlorophenyl)-methyl-carbocation in an intra-molecular fashion, affording a neutral tetrahydrofuran derivative. The acid lability of the Cmoc group allows the choice between on-column deprotection, and off column deprotection. Being more lipophilic than a traditional DMT group, the Cmoc protecting group does a superb job in facilitating SPE purification of full length oligos. If you like the DMT-on purification strategy, you will similarly like the Cmoc-on purification strategy.

For more information, download a Product Information Sheet for BA 0324 here.

Notes

Novel acid labile N-protected 5’-amino modifier.

BA 0329

(5'S)-8,5'-Cyclodeoxyadenosine
CEP

C47H50N7O7P 

211919-91-4 

Description

8,5’-Cyclodeoxyadenosine (cyclo-dA) is a naturally occurring free-radical-induced DNA lesion. This bulky lesion has been shown to be present in human cells.1 Cyclo-dA is a strong block to gene expression in both CHO and human cells but can be repaired via nucleoside excision repair mechanisms, but not by base excision repair mechanisms.2 Our (5'S)-8,5’-Cyclodeoxyadenosine CEP can be used for efficient incorporation of cyclo-dA into oligonucleotides.

For additional information, download a Product Information Sheet.

We also now offer the related THP protected cyclodeoxyguanosine analog. For information, see (5'S)-8,5'-Cyclodeoxyguanosine (THP) CEP (BA 0382).

References

(1) Dizdaroglu, M.; Dirksen, M.L.; Jiang, H.X.; Robbins, J.H. J. Biochem. 1987, 241, 929-932.

(2) Brooks, P.J.; Wise, D.S.; Berry, D.A.; Kosmoski, J.V.; Smerdon, M.J.; Somers, R.L.; Mackie, H.; Spoonde, A.Y.; Ackerman, E.J.; Coleman, K.; Tarone, R.E.; Robbins, J.H. J. Biol. Chem. 2000, 275 , 22355-22362.

 

Notes

This phosphoramidite is used for standard 3’ to 5’ oligonucleotide synthesis.

BA 0330

3'-Thiol-modifier-C6-S-S CPG (1000
Angstrom)

N/A 

None Assigned 

BA 0331

5'-Thio-dI CEP

C40H47N6O6PS 

None Assigned 

Description

For more information on the use of this product in oligonucleotide synthesis, download a Product Information Sheet here.

BA 0332

Thiol-modifier-oxa-C6-S-S CEP

C40H57N2O7PS2 

1159976-43-8 

BA 0334

Fluorescein III CEP

C69H80N3O14P 

1306615-53-1 

Description

For the installation of fluorescein at the 5'-terminus of an oligonucleotide, the phosphoramidite "6-FAM" (5'-Fluorescein CEP, BA 0054), which does not bear a DMT group, is a popular choice. However, the lack of a trityl group precludes multiple additions or assaying the coupling step. Fluorescein II CEP ("6-FAM II", BA 0253), which features the same tether length as 6-FAM, but includes a DMT group.1 We now offer Fluorescein III CEP ("6-FAM III",BA 0334) which also includes the DMT group, but with a 1,3-diol framework. This extended framework serves two functions. First, the one carbon extension disfavors cyclic phosphate formation when the DMT group is removed, thereby minimizing label loss. Second, the 1,3-diol framework maintains the natural 3-carbon atom internucleotide phosphate distance, which diminishes duplex destabilization.2 The DMT may also be used to facilitate cartridge purification with on-column detritylation, e.g. with Fluoro-Pak columns.

Download Product Information here.

1. 5'-Fluorescein II CEP incorporates 6-carboxyfluorescein. The 5-carboxyfluorescein isomer of this product (CA Reg. No. 144676-14-2) is also known. See: Theisen, P.; McCollum, C.; Upadhya, K.; Jacobson, K.; Vu, H.; Andrus, A. Tetrahedron Lett. 1992, 33, 5033-5036.

2. Nelson, P.S.; Kent, M.; Muthini, S. Nucleic Acids Res. 1992, 20 , 6253-6259.

Notes

Installs a 6-carboxyfluorescein internally or at the 5'-terminus of an oligonucleotide using a DMT-bearing phosphoramidite with a 1,3-diol framework.

Alternate Name(s):

6-FAM III

BA 0335

Fmoc-amino-modifier III CEP

C53H64N3O8P 

1306615-50-8 

Description

The (fluorenylmethyl)carbamoyl (Fmoc) group has been shown to be useful as such an amine protecting group for amine modification of oligonucleotides.1 It is removed during cleavage/deprotection with ammonium hydroxide. Our new Fmoc-amino Modifier III (BA 0335) contains a 1,3,5-triol framework which serves two functions. First, extended framework disfavors cyclic phosphate formation when the DMT group is removed, thereby minimizing loss of the amine modification. Second, the 1,3,5-triol framework maintains the natural 3-carbon atom internucleotide phosphate distance. 1

We also offer a version of such an Fmoc-protected amino-modifier for installation of an amino group at the 3'-terminus, i.e., 3'-Fmoc-amino-modifier CPG, in both higher- and lower-loaded versions, namely BA 0299 (500 Å CPG) and BA 0307 (1000 Å CPG). It features a 7-atom spacer between the amino group and the O-DMT group.

For more information, download a Product Information Sheet for BA 0335 here..

1. Nelson, P. S.; Kent, M.; Muthini, S. Nucl. Acids Res. 1992, 20, 6253-6259.

Notes

For installation of an Fmoc protected amino group internally or at the 5’-end of an oligonucleotide.

BA 0337

N2-Benzyl-dG
CEP

C47H54N7O7P 

209785-74-0 

Description

Guanine bases in DNA are susceptible to N-alkylation by various carcinogens, leading to miscoding and mutagenicity. Choi and Guengerich have prepared a series of N2-alkyl-2'-deoxyguanosine phosphoramidites where the alkyl group ranges in size from methyl to anthracenylmethyl for studies on the effect of the size of these groups on the catalytic efficiency and fidelity of various DNA polymerases.1 We offer the N2-methyl- (BA 0249), N2-ethyl- (BA 0076), and N2-isobutyl-dG (BA 0250) phosphoramidites1 as well as two additional bulkier choices, the N2-neopentyl version (BA 0200), and the N2-benzyl version (BA 0337) . Researchers may find this "steric tool box" useful for probing the steric requirements at N2 of dG in various applications.

Use: Add 2 parts of anhydrous dichloromethane to dissolve the phosphoramidite, followed by 1 part of anhydrous acetonitrile. Couple as recommended by instrument manufacturer. See Product Information.

(1) Choi, J.-Y.; Guengerich, F. P. J. Biol. Chem. 2004, 279 , 19217-19229.

Notes

Useful for probing the steric requirements at N2 of dG in various applications.

Alternate Name(s):

N2-Benzyl-deoxyguanosine CEP

BA 0338

N-Benzoyl-5-((2-cyanoethoxy)
methyl)-2'-deoxycytidine CEP

C50H57N6O9P 

188411-06-5 

BA 0339

8-OxoG clamp CEP

C55H61N6O11P 

1134373-47-9 

Description

The Sasaki labs have identified a variation of Matteucci’s cytosine analog “G-Clamp”1 that is specific for 8-oxoG. This fluorescent phenoxazine analog 8-oxoG Clamp CEP (BA 0339) appears to be highly specific for pairing with 8-oxoG.2 When incorporated into an oligonucleotide, the duplex stabilization was lowered only slightly, and 8-oxoG was selectively detected by fluorescence quenching the 8-oxoG Clamp.3

For more information, download a Product Information Sheet for BA 0339 here..

1. Lin, K.-Y.; Jones, R.J.; Matteucci, M. J. Am. Chem. Soc., 1995, 117, 3873-3874.

2. Nakagawa, O.; Ono, S.; Li, Z.; Tsujimoto, A.; Sasaki, S. Angew. Chem. Int. Ed., 2007, 46, 4500-4503.

3. Nasr, T.; Li, Z.; Nakagawa, O.; Taniguchi, Y.; Ono, S.; Sasaki, S. Bioorg. & Med. Chem. Lett. 2009, 19, 727-730.

Notes

Fluorescent molecule for the selective recognition of 8-oxoG

Alternate Name(s):

8-Oxo-dG Clamp CEP

BA 0342

5-(3-Aminophenyl)-2'-dU CEP

C48H57N6O8P 

None assigned 

Description

Electrochemical detection is a less expensive alternative to common optical methods in DNA biosensors and chips. Hocek and coworkers1 have shown that when aminophenyl (BA 0342) and nitrophenyl (BA 0355) substituted 2’-deoxyribonucleosides are incorporated into oligonucleotides, they exhibit excellent electrochemical label properties. Both types of markers in the same oligonucleotide can be easily detected and differentiated since the aminophenyl tag is irreversibly oxidized, and the nitophenyl tag is irreversibly reduced.

For more information on this product and its use, download a Product Information Sheet here.

References

1. Cahova, H.; Havran, L.; Brazdilova, P.; Pivonkova, H.; Pohl, R.; Fojta, M.; Hocek, M. Angew. Chem. Int. Ed. 2008, 47, 2059-2062.

Notes

Simple organic 2’-deoxyribonucleoside derivatives for use as electroactive DNA markers.

BA 0343

dNaM CEP

C46H53N2O7P 

1117893-10-3 

Description

The dNaM (BA 0343) and d5SICS (BA 0344) matched pair appears to be a very interesting novel base pair, achieving pair recognition through hydrophobic interactions that rivals the A-T and G-C pairing in the natural genetic alphabet.1-7 In addition, they have been shown to be well-replicated by DNA polymerases under steady-state conditions, regardless of sequence. The fidelity and efficiency of dNaM and d5SICS replication approach those of natural synthesis. Both dNaM and d5SICS are also efficiently transcribed by T7 RNA polymerase in either direction. In 2009, the Romesberg and Marx groups reported data that showed KlenTaq polymerase induces the dNaM-d5SICS unnatural base pair to adopt a natural Watson-Crick like strucutre.8 More recently, an additional coupling partner for dNaM has been identified which gives higher amplification efficiency and fidelity under standard PCR conditions.9 For more information, download a Product Information Sheet for BA 0343 here.

1. Seo, Y.J.; Matsuda, S.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 5046-7.

2. Seo, Y.J.; Hwang, G.T.; Ordoukhanian, P.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 3246-52.

3. Seo, Y.J.; Romesberg, F.E. ChemBioChem, 2009, 10, 2394-2400.

4. Hwang, G.T.; Hari, Y.; Romesberg, F.E. Nucleic Acids Res., 2009, 37, 4757-63.

5. Hari, Y.; Hwang, G.T.; Leconte, A.M.; Joubert, N.; Hocek, M.; Romesberg, F.E. ChemBioChem, 2008, 9, 2796-9.

6. Hwang, G.T.; Romesberg, F.E. J. Am. Chem. Soc., 2008, 130, 14872-82.

7. a)Leconte, A.M.; Hwang, G.T.; Matsuda, S.; Capek, P.; Hari, Y.; Romesberg, F.E J. Am. Chem. Soc., 2008, 130, 2336-43. b) Lavergne, T.; Lamichhane, R.; Malyshev, D. A.; Li, Z.; Li, L.; Sperling, E.; Williamson, J.R.; Miller, D.P.; Romesberg, F.E. ACS Chem Biol. 2016, 11 1347-1353. c) Betz, K.; Malyshev, D.A.; Lavergne, T.; Welte, W.; Diederichs, K.; Romesberg, F.E.; Marx, A. J. Am. Chem. Soc. 2013 135 18637-18643.

8. Betz, K.; Malyshev, D.A.; Lavergne, T.; Welte, W.; Diederichs, K.; Dwyer, T.J.; Ordoukhanian, P.; Romesberg, F.E.; Marx, A. Nat. Chem. Biol. 2012, 8, 612-614.

9. Li, L.; Degardin, M.; Lavergne, T.; Malyshev, D.A.; Dhami, K.; Ordoukhanian, P.; Romsberg, F.E. J. Am. Chem. Soc. 2014, 136, 826-829.

Notes

Half of a novel base pair that achieves pair recognition through hydrophobic interactions.

Alternate Name(s):

3-(3-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyribofuranosyl)-2-methoxy naphthalene

BA 0344

d5SICS CEP

C45H52N3O6PS 

1010689-04-9 

Description

The dNaM (BA 0343) and d5SICS (BA 0344)matched pair appears to be a very interesting novel base pair, achieving pair recognition through hydrophobic interactions that rivals the A-T and G-C pairing in the natural genetic alphabet.1-7 In addition, they have been shown to be well-replicated by DNA polymerases under steady-state conditions, regardless of sequence. The fidelity and efficiency of dNaM and d5SICS replication approach those of natural synthesis. Both dNaM and d5SICS are also efficiently transcribed by T7 RNA polymerase in either direction. In 2009, the Romesberg and Marx groups reported data that showed KlenTaq polymerase induces the dNaM-d5SICS unnatural base pair to adopt a natural Watson-Crick like strucutre.8 For more information, download a Product Information Sheet for BA 0344 here.

1. Seo, Y.J.; Matsuda, S.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 5046-7.

2. Seo, Y.J.; Hwang, G.T.; Ordoukhanian, P.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 3246-52.

3. Seo, Y.J.; Romesberg, F.E. ChemBioChem, 2009, 10, 2394-2400.

4. Hwang, G.T.; Hari, Y.; Romesberg, F.E. Nucleic Acids Res., 2009, 37, 4757-63.

5. Hari, Y.; Hwang, G.T.; Leconte, A.M.; Joubert, N.; Hocek, M.; Romesberg, F.E. ChemBioChem, 2008, 9, 2796-9.

6. Hwang, G.T.; Romesberg, F.E. J. Am. Chem. Soc., 2008, 130, 14872-82.

7. Leconte, A.M.; Hwang, G.T.; Matsuda, S.; Capek, P.; Hari, Y.; Romesberg, F.E J. Am. Chem. Soc., 2008, 130, 2336-43.

8. Betz, K.; Malyshev, D.A.; Lavergne, T.; Welte, W.; Diederichs, K.; Dwyer, T.J.; Ordoukhanian, P.; Romesberg, F.E.; Marx, A. Nat. Chem. Biol. 2012, 8, 612-614.

Notes

Half of a novel base pair that achieves pair recognition through hydrophobic interactions.

Alternate Name(s):

3-(3-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyribofuranosyl)-6-methylisoquinoline-1(2H)-thione

BA 0345

Carbazole dT CEP

C62H72N7O10P 

None Assigned 

Description

Template-directed DNA ligation has multiple potential biotechnological applications.1-4 The research of Fujimoto, Saito and coworkers have illustrated the utility of 5-vinyldeoxyuridine5a and a carbazole-tethered 5-carboxyvinyldeoxyuridine5b for photo induced non-enzymatic chemical DNA ligation. This carbazole-tethered analog (BA 0345) gives a photo ligation system where ligation and splitting (at 366 nm) can be repeated without damage to the normal DNA. Data suggests that the carbazole group intercalates in the duplex formed when photo ligation takes place in the presence of template DNA. This intercalation prevents photo induced splitting when in the duplex form, allowing control of the ligation/splitting based on the presence or absence of the template DNA strand. Our Carbazole dT CEP (BA 0345) provides an efficient way to form carbazole-tethered vinyl dU containing oligonucleotides.

For more information, download a Product Information Sheet for BA 0345 here.

References

1. (a) Silverman, A.P.; Kool. E.T. Chem. Rev., 2006, 106, 3775-3789. (b) Gartner, Z.J.; Kanan, M.W.; Liu, D.R. J. Am. Chem. Soc. 2002, 124, 10304-10306.

2. (a) Gothelf, K.V.; Brown, R.S. Chem. Eur. J. 2005, 11, 1062-1069. (b) Shih, W.M.; Quispe, Erben, C.M.; Berry, R.M.; Schmidt, C.F.; Turberfield, A.J. Science 2005, 310, 1661-1665.

3. (a) Su, X.; Smith, L.M. Nucleic Acids Res. 2004, 32, 3115-3123. (b) Fujimoto, K.; Matsuda, S.; Takahashi, N.; Saito, I. J. Am. Chem. Soc. 2000, 122, 5646-5647. (b) Weizmann, Y.; Elnathan, R.; Lioubashevski, O.; Willner, I. J. Am. Chem. Soc. 2005, 127, 12666-12672.

4. (a) Shin, J.-S.; Pierce, N.A.; Nano Lett., 2004, 4, 905-909. (b) Le, J.D.; Pinto, Y.; Seeman, N.C.; Musier-Forsyth, K.; Taton, T.A.; Kiehl, R.A Nano Lett., 2004, 4, 2343-2347.

5. (a) Fujimoto, K.; Yoshino, H.; Ami, T. Yoshimura, Y.; Saito, I. Org. Lett., 2008, 10(3), 397-400. (b) Fujimoto, K.; Matsuda, S.; Takahashi, N.; Saito, I. J. Am. Chem. Soc. 2000, 122, 5646-5647.

Notes

For use as a light-controlled, reversible DNA photoligation tool.

Alternate Name(s):

5'-O-(4,4'-Dimethoxytrityl)-3'-O-[2-cyanoethoxy-(N,N-diisopropylamino)-phosphino]-5-(,em>E)-(2-(6-(2-carbazol-9-yl-acetylamiono)-hexylamino)-carbonylvinyl)-2'-deoxyuridine

BA 0346

5-(2-Furyl)-dU CEP

C43H49N4O9P 

863713-51-3 

Description

BA 0346 is a phosphoramidite of a small, fluorescent nucleoside that is an isosteric mimic of thymidine.1,2 This probe has been shown to pair with adenine to form a stable duplex. DNA probes constructed to contain BA 0346 at a selected sequence position show a significant emission enhancement when hybridization results in an opposing abasic residue as compared to an opposing adenine residue.1 This property makes BA 0346 useful for the preparation of probes that are designed to detect sequence-specific depurination and depyrimidination.

For more information, download a Product Information Sheet for BA 0346 here.

1) Greco, N.J.; Tor, Y. J. Am. Chem. Soc. 2005, 127, 10784-10785.

2) Greco, N.J.; Tor, Y. Nature Protocols, 2007, 2, 305-316.

Notes

Small, fluorescent natural base mimic that can signal the presence of abasic sites in hybridized DNA oligonucleotides.

Alternate Name(s):

5-Furan-2-yl dU CEP



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